Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_File	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	COSMIC_Codon	COSMIC_Gene	Transcript_Id	Exon	ChromChange	AAChange	Genome_Plus_Minus_10_Bp	Drug_Target	TTotCov	TVarCov	NTotCov	NVarCov	dbSNPPopFreq	COSMIC_Gene_Freq	COSMIC_Site_Freq	TVarRat	NVarRat	dbSNP_Strength	dbSNP_AF	dbSNP_PopFreq	Confidence	Algorithm
RERE	473	hgsc.bcm.edu	hg19	1	8422784	8422784	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	RERE	NM_012102	exon17	c.A1861G	p.S621G	CATTGCTGGAGGT	.	201.0	70.0	233.0	0.0	.	129	.	.	.	none	.	.	PASS	Atlas-SNP
SPEN	23013	hgsc.bcm.edu	hg19	1	16260463	16260463	+	Silent	SNP	T	T	G	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	SPEN	NM_015001	exon11	c.T7728G	p.V2576V	GCCAGTTGACTCT	.	25.0	10.0	42.0	0.0	.	374	.	.	.	none	.	.	PASS	Atlas-SNP
AKR7A3	22977	hgsc.bcm.edu	hg19	1	19611546	19611546	+	Silent	SNP	A	A	G	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	AKR7A3	NM_012067	exon4	c.T570C	p.F190F	CAGTCCAAAGTGC	.	296.0	116.0	338.0	0.0	.	30	.	.	.	none	.	.	PASS	Atlas-SNP
ZMYM1	79830	hgsc.bcm.edu	hg19	1	35569920	35569920	+	Silent	SNP	G	G	C	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	ZMYM1	NM_024772	exon5	c.G444C	p.V148V	GGATGTGATTAGT	.	78.0	31.0	96.0	0.0	.	86	.	.	.	none	.	.	PASS	Atlas-SNP
FAM46C	54855	hgsc.bcm.edu	hg19	1	118165851	118165851	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	FAM46C	NM_017709	exon2	c.C361G	p.P121A	TTCCTGCCAGAGG	.	146.0	64.0	173.0	0.0	.	25	.	.	.	none	.	.	PASS	Atlas-SNP
ZC3H11A	9877	hgsc.bcm.edu	hg19	1	203819761	203819761	+	Silent	SNP	C	C	T	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	ZC3H11A	NM_014827	exon18	c.C2058T	p.L686L	GCCACTCAGCTCC	.	142.0	62.0	184.0	0.0	.	71	.	.	.	none	.	.	PASS	Atlas-SNP
PLXNA2	5362	hgsc.bcm.edu	hg19	1	208213052	208213052	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	PLXNA2	NM_025179	exon24	c.G4414A	p.G1472S	TGGGGCCCTTCTC	.	111.0	31.0	140.0	0.0	.	178	.	.	.	none	.	.	PASS	Atlas-SNP
CAPN2	824	hgsc.bcm.edu	hg19	1	223900487	223900487	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	CAPN2	NM_001748	exon1	c.C145A	p.P49T	CAGGACCCGTCCT	.	71.0	30.0	132.0	0.0	.	69	.	.	.	none	.	.	PASS	Atlas-SNP
ASXL2	55252	hgsc.bcm.edu	hg19	2	25972919	25972919	+	Silent	SNP	C	C	T	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	ASXL2	NM_018263	exon11	c.G1506A	p.E502E	GTTCTTCTCAGAT	.	57.0	29.0	44.0	0.0	.	217	.	.	.	none	.	.	PASS	Atlas-SNP
HADHA	3030	hgsc.bcm.edu	hg19	2	26427053	26427053	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	HADHA	NM_000182	exon12	c.T1098G	p.I366M	ACCAAGAATAGCC	.	131.0	36.0	125.0	0.0	.	87	.	.	.	none	.	.	PASS	Atlas-SNP
TET3	200424	hgsc.bcm.edu	hg19	2	74320721	74320721	+	Silent	SNP	G	G	T	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	TET3	NM_144993	exon7	c.G2790T	p.G930G	CGCGGGGGTCACG	.	152.0	46.0	159.0	0.0	.	101	.	.	.	none	.	.	PASS	Atlas-SNP
MAP4K4	9448	hgsc.bcm.edu	hg19	2	102493592	102493592	+	Silent	SNP	C	C	G	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	MAP4K4	NM_145686	exon25	c.C3036G	p.V1012V	GAATGTCTTGGTG	.	420.0	124.0	311.0	0.0	.	111	.	.	.	none	.	.	PASS	Atlas-SNP
CCDC74B	91409	hgsc.bcm.edu	hg19	2	130899739	130899739	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	CCDC74B	NM_207310	exon3	c.A511C	p.S171R	GGAAGCTTGACGT	.	433.0	205.0	383.0	1.0	.	27	.	.	.	none	.	.	PASS	Atlas-SNP
C2orf69	205327	hgsc.bcm.edu	hg19	2	200790075	200790075	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	C2orf69	NM_153689	exon2	c.T624A	p.N208K	TTTGAATGTTTGG	.	46.0	12.0	54.0	0.0	.	17	.	.	.	none	.	.	PASS	Atlas-SNP
ORC2	4999	hgsc.bcm.edu	hg19	2	201778083	201778083	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	ORC2	NM_006190	exon17	c.A1582T	p.S528C	GATCACTATTGAC	.	76.0	42.0	86.0	0.0	.	48	.	.	.	none	.	.	PASS	Atlas-SNP
FN1	2335	hgsc.bcm.edu	hg19	2	216271073	216271073	+	Silent	SNP	C	C	T	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	FN1	NM_212476	exon19	c.G2874A	p.R958R	GGTGTTCCTGCTG	.	144.0	24.0	137.0	0.0	.	521	.	.	.	none	.	.	PASS	Atlas-SNP
OSBPL10	114884	hgsc.bcm.edu	hg19	3	31705657	31705657	+	Missense_Mutation	SNP	G	G	A	rs375455808		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	OSBPL10	NM_017784	exon11	c.C2164T	p.R722W	GGTGCCGCTTCTG	.	183.0	58.0	133.0	0.0	.	160	.	.	.	weak	.	.	PASS	Atlas-SNP
PRKCD	5580	hgsc.bcm.edu	hg19	3	53220041	53220041	+	Nonsense_Mutation	SNP	A	A	T	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	PRKCD	NM_212539	exon11	c.A1084T	p.K362X	TTCGGGAAGGTGA	.	450.0	235.0	371.0	0.0	.	124	.	.	.	none	.	.	PASS	Atlas-SNP
FAM208A	23272	hgsc.bcm.edu	hg19	3	56667344	56667344	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	FAM208A	NM_001112736	exon18	c.G3475C	p.V1159L	TTTCTACTTCAGT	.	282.0	153.0	255.0	1.0	.	113	.	.	.	none	.	.	PASS	Atlas-SNP
FRMD4B	23150	hgsc.bcm.edu	hg19	3	69247894	69247894	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	FRMD4B_ENST00000398540,NS,carcinoma,0,2	FRMD4B	NM_015123	exon12	c.A908G	p.Y303C	CGGAAATATAAGT	.	98.0	57.0	80.0	1.0	.	90	.	.	.	none	.	.	PASS	Atlas-SNP
CEP97	79598	hgsc.bcm.edu	hg19	3	101450739	101450739	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	CEP97	NM_024548	exon5	c.T503C	p.L168P	CTTACCTACCCAG	.	72.0	15.0	77.0	0.0	.	122	.	.	.	none	.	.	PASS	Atlas-SNP
ITGB5	3693	hgsc.bcm.edu	hg19	3	124536482	124536482	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	ITGB5	NM_002213	exon8	c.A1114T	p.I372F	CATTAATAATCAG	.	60.0	33.0	61.0	0.0	.	66	.	.	.	none	.	.	PASS	Atlas-SNP
IFT122	55764	hgsc.bcm.edu	hg19	3	129200472	129200472	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	IFT122	NM_052985	exon15	c.G1741C	p.A581P	AAGCTGGCCGTGG	.	1002.0	371.0	829.0	2.0	.	117	.	.	.	none	.	.	PASS	Atlas-SNP
DZIP1L	199221	hgsc.bcm.edu	hg19	3	137790541	137790541	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	DZIP1L	NM_001170538	exon13	c.C1559T	p.A520V	TCCTTCGCTCTGC	.	112.0	65.0	104.0	0.0	.	88	.	.	.	none	.	.	PASS	Atlas-SNP
KNG1	3827	hgsc.bcm.edu	hg19	3	186445075	186445075	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	KNG1	NM_000893	exon5	c.A614C	p.N205T	AAACGAATTGTTC	.	77.0	27.0	101.0	0.0	.	129	.	.	.	none	.	.	PASS	Atlas-SNP
TIGD4	201798	hgsc.bcm.edu	hg19	4	153690653	153690653	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	TIGD4	NM_145720	exon2	c.C1504G	p.L502V	TTTCAAGGTCTGC	.	51.0	13.0	68.0	0.0	.	53	.	.	.	none	.	.	PASS	Atlas-SNP
CARD6	84674	hgsc.bcm.edu	hg19	5	40852818	40852818	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	CARD6	NM_032587	exon3	c.T1384C	p.Y462H	CTAGGATACTGTA	.	145.0	64.0	115.0	0.0	.	141	.	.	.	none	.	.	PASS	Atlas-SNP
MSH3	4437	hgsc.bcm.edu	hg19	5	80037368	80037368	+	Splice_Site	SNP	G	G	C	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	MSH3	NM_002439	exon11	c.1653+1G>C	.	AATCAGGTCAGGC	.	103.0	34.0	166.0	0.0	.	129	.	.	.	none	.	.	PASS	Atlas-SNP
PAM	5066	hgsc.bcm.edu	hg19	5	102203044	102203044	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	PAM	NM_138822	exon2	c.G157A	p.D53N	CCTATTGATTCAT	.	80.0	22.0	108.0	0.0	.	180	.	.	.	none	.	.	PASS	Atlas-SNP
SYCP2L	221711	hgsc.bcm.edu	hg19	6	10931696	10931696	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	SYCP2L	NM_001040274	exon20	c.A1657G	p.S553G	CCCAGTAGTGGCA	.	104.0	37.0	99.0	0.0	.	101	.	.	.	none	.	.	PASS	Atlas-SNP
GPLD1	2822	hgsc.bcm.edu	hg19	6	24450018	24450018	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	GPLD1	NM_001503	exon15	c.A1445G	p.K482R	CTTACTTTGTAGG	.	69.0	32.0	90.0	0.0	.	91	.	.	.	none	.	.	PASS	Atlas-SNP
NOTCH4	4855	hgsc.bcm.edu	hg19	6	32169043	32169043	+	Silent	SNP	C	C	T	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	NOTCH4	NM_004557	exon22	c.G3990A	p.R1330R	ATCCTTCCTTACC	.	142.0	53.0	229.0	0.0	.	201	.	.	.	none	.	.	PASS	Atlas-SNP
C6orf106	64771	hgsc.bcm.edu	hg19	6	34664262	34664262	+	Missense_Mutation	SNP	T	T	C	rs369638409		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	C6orf106	NM_024294	exon1	c.A119G	p.N40S	GCAGGATTGAGCT	.	50.0	7.0	38.0	0.0	.	29	.	.	.	weak	.	.	PASS	Atlas-SNP
DST	667	hgsc.bcm.edu	hg19	6	56501422	56501422	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	DST	NM_001723	exon9	c.G1382A	p.W461X	CAGCTCCACTGCG	.	40.0	23.0	55.0	0.0	.	1427	.	.	.	none	.	.	PASS	Atlas-SNP
KIAA1009	22832	hgsc.bcm.edu	hg19	6	84872967	84872967	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	KIAA1009	NM_014895	exon19	c.A2408C	p.E803A	ATGTCTTCCAATA	.	31.0	11.0	57.0	0.0	.	119	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF292	23036	hgsc.bcm.edu	hg19	6	87943085	87943085	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	ZNF292	NM_015021	exon5	c.T581A	p.M194K	TGGATATGAGAAT	.	85.0	24.0	88.0	0.0	.	479	.	.	.	none	.	.	PASS	Atlas-SNP
PNRC1	10957	hgsc.bcm.edu	hg19	6	89793801	89793801	+	Silent	SNP	T	T	C	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	PNRC1	NM_006813	exon2	c.T870C	p.P290P	TTCTCCTAGTGTT	.	105.0	43.0	124.0	0.0	.	17	.	.	.	none	.	.	PASS	Atlas-SNP
MCM9	254394	hgsc.bcm.edu	hg19	6	119245294	119245294	+	Splice_Site	SNP	T	T	C	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	MCM9	NM_017696	exon3	c.305-2A>G	.	CAAACCTGATGGA	.	54.0	21.0	49.0	0.0	.	73	.	.	.	none	.	.	PASS	Atlas-SNP
FGFR1OP	11116	hgsc.bcm.edu	hg19	6	167435950	167435950	+	Silent	SNP	C	C	A	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	FGFR1OP	NM_007045	exon8	c.C633A	p.P211P	AGAACCCAAGAGC	.	38.0	11.0	61.0	0.0	.	24	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF727	442319	hgsc.bcm.edu	hg19	7	63537955	63537955	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	ZNF727	NM_001159522	exon4	c.A528T	p.E176D	ATGTGAAGAATGT	.	122.0	67.0	87.0	0.0	.	35	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF727	442319	hgsc.bcm.edu	hg19	7	63538777	63538777	+	Silent	SNP	G	G	A	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	ZNF727,NS,carcinoma,0,1	ZNF727	NM_001159522	exon4	c.G1350A	p.K450K	AGAGAAGCCCTAC	.	120.0	5.0	89.0	0.0	.	35	.	.	.	none	.	.	PASS	Atlas-SNP
WBSCR27	155368	hgsc.bcm.edu	hg19	7	73249148	73249148	+	Silent	SNP	A	A	C	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	WBSCR27	NM_152559	exon6	c.T663G	p.S221S	TGGCAGAGATGCC	.	117.0	42.0	100.0	0.0	.	21	.	.	.	none	.	.	PASS	Atlas-SNP
ACER2	340485	hgsc.bcm.edu	hg19	9	19435060	19435060	+	Silent	SNP	C	C	T	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	ACER2	NM_001010887	exon4	c.C481T	p.L161L	ACTGCACTGCTCA	.	212.0	50.0	243.0	0.0	.	24	.	.	.	none	.	.	PASS	Atlas-SNP
GPR21	2844	hgsc.bcm.edu	hg19	9	125797664	125797664	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	GPR21	NM_005294	exon2	c.G819T	p.L273F	CTTCTTGTTGGAA	.	129.0	49.0	136.0	0.0	.	29	.	.	.	none	.	.	PASS	Atlas-SNP
SPTAN1	6709	hgsc.bcm.edu	hg19	9	131386741	131386741	+	Silent	SNP	G	G	A	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	SPTAN1	NM_001130438	exon46	c.G5967A	p.K1989K	CTGGAAGGCGGAC	.	159.0	68.0	165.0	0.0	.	266	.	.	.	none	.	.	PASS	Atlas-SNP
KIF5B	3799	hgsc.bcm.edu	hg19	10	32320043	32320043	+	Silent	SNP	A	A	G	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	KIF5B	NM_004521	exon14	c.T1539C	p.T513T	TTCCTTAGTTTTG	.	37.0	10.0	48.0	0.0	.	81	.	.	.	none	.	.	PASS	Atlas-SNP
CYP26A1	1592	hgsc.bcm.edu	hg19	10	94834101	94834101	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	CYP26A1	NM_000783	exon2	c.G226A	p.G76S	AAATACGGCTTCA	.	51.0	17.0	70.0	0.0	.	59	.	.	.	none	.	.	PASS	Atlas-SNP
LGI1	9211	hgsc.bcm.edu	hg19	10	95549895	95549895	+	Silent	SNP	T	T	C	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	LGI1	NM_005097	exon5	c.T471C	p.D157D	AAAAGATATTTTC	.	10.0	5.0	5.0	0.0	.	69	.	.	.	none	.	.	PASS	Atlas-SNP
SEMA4G	57715	hgsc.bcm.edu	hg19	10	102738660	102738660	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	SEMA4G	NM_001203244	exon7	c.G698A	p.G233D	CAGTGGGTGATGA	.	288.0	106.0	370.0	0.0	.	55	.	.	.	none	.	.	PASS	Atlas-SNP
NAALAD2	10003	hgsc.bcm.edu	hg19	11	89896525	89896525	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	NAALAD2	NM_005467	exon10	c.G1123A	p.A375T	TTTGGAGCTATTG	.	59.0	19.0	80.0	0.0	.	113	.	.	.	none	.	.	PASS	Atlas-SNP
GPRC5D	55507	hgsc.bcm.edu	hg19	12	13102558	13102558	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	GPRC5D	NM_018654	exon1	c.T761A	p.L254Q	AGCAGCAGGAAAA	.	245.0	129.0	194.0	0.0	.	23	.	.	.	none	.	.	PASS	Atlas-SNP
SP7	121340	hgsc.bcm.edu	hg19	12	53722359	53722359	+	Silent	SNP	C	C	T	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	SP7	NM_152860	exon2	c.G867A	p.R289R	CTTCTTCCGCAGC	.	43.0	17.0	54.0	0.0	.	30	.	.	.	none	.	.	PASS	Atlas-SNP
DNAJC14	85406	hgsc.bcm.edu	hg19	12	56216194	56216194	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	DNAJC14	NM_032364	exon6	c.T1861C	p.F621L	AACCAAATGAGAT	.	120.0	62.0	104.0	0.0	.	52	.	.	.	none	.	.	PASS	Atlas-SNP
DPY19L2	283417	hgsc.bcm.edu	hg19	12	63991615	63991615	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	DPY19L2	NM_173812	exon14	c.C1435T	p.P479S	ATTCGGGAGCACA	.	129.0	29.0	132.0	0.0	.	97	.	.	.	none	.	.	PASS	Atlas-SNP
TMPO	7112	hgsc.bcm.edu	hg19	12	98925573	98925573	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	TMPO	NM_003276	exon3	c.G522C	p.Q174H	AAGGCAGAATGGA	.	160.0	36.0	135.0	0.0	.	111	.	.	.	none	.	.	PASS	Atlas-SNP
IPO4	79711	hgsc.bcm.edu	hg19	14	24654679	24654679	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	IPO4	NM_024658	exon13	c.T1264A	p.S422T	TTTCTGAGAACTG	.	141.0	60.0	133.0	0.0	.	74	.	.	.	none	.	.	PASS	Atlas-SNP
NIN	51199	hgsc.bcm.edu	hg19	14	51223359	51223359	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	NIN	NM_020921	exon18	c.G4389C	p.E1463D	AGTCAGCTCCTGT	.	81.0	27.0	125.0	0.0	.	475	.	.	.	none	.	.	PASS	Atlas-SNP
CHGA	1113	hgsc.bcm.edu	hg19	14	93397675	93397675	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	CHGA	NM_001275	exon6	c.A436G	p.T146A	GAAGCCACAGACG	.	118.0	43.0	147.0	0.0	.	32	.	.	.	none	.	.	PASS	Atlas-SNP
GCNT3	9245	hgsc.bcm.edu	hg19	15	59911000	59911000	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	GCNT3	NM_004751	exon3	c.T563C	p.I188T	TCTTCATAGCCAG	.	72.0	31.0	76.0	0.0	.	42	.	.	.	none	.	.	PASS	Atlas-SNP
UACA	55075	hgsc.bcm.edu	hg19	15	70991969	70991969	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	UACA	NM_018003	exon2	c.C109T	p.R37X	TCAATCGGTCATC	.	58.0	20.0	61.0	0.0	.	235	.	.	.	none	.	.	PASS	Atlas-SNP
ST8SIA2	8128	hgsc.bcm.edu	hg19	15	92973323	92973323	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	ST8SIA2	NM_006011	exon2	c.T143C	p.L48S	ACAGCTTACATAG	.	82.0	30.0	74.0	0.0	.	41	.	.	.	none	.	.	PASS	Atlas-SNP
SRCAP	10847	hgsc.bcm.edu	hg19	16	30733555	30733555	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	SRCAP	NM_006662	exon22	c.G3654C	p.L1218F	GACTTTGACTGGT	.	267.0	72.0	233.0	0.0	.	298	.	.	.	none	.	.	PASS	Atlas-SNP
ITGAX	3687	hgsc.bcm.edu	hg19	16	31371302	31371302	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	ITGAX,NS,carcinoma,0,1	ITGAX	NM_000887	exon7	c.G623A	p.R208H	TCAGGCGCAGCTC	.	71.0	43.0	57.0	0.0	.	198	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF319	57567	hgsc.bcm.edu	hg19	16	58031774	58031774	+	Silent	SNP	G	G	A	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	ZNF319	NM_020807	exon2	c.C396T	p.F132F	ACAGACGAAGGGC	.	98.0	46.0	69.0	0.0	.	42	.	.	.	none	.	.	PASS	Atlas-SNP
AP1G1	164	hgsc.bcm.edu	hg19	16	71772895	71772895	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	AP1G1	NM_001030007	exon22	c.A2227T	p.S743C	CTGTGCTGTTGGA	.	348.0	94.0	252.0	0.0	.	83	.	.	.	none	.	.	PASS	Atlas-SNP
ACACA	31	hgsc.bcm.edu	hg19	17	35615281	35615281	+	Silent	SNP	A	A	T	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	ACACA	NM_198834	exon13	c.T1515A	p.I505I	TAGAGGAATCCCC	.	108.0	61.0	104.0	0.0	.	395	.	.	.	none	.	.	PASS	Atlas-SNP
KRT23	25984	hgsc.bcm.edu	hg19	17	39092459	39092459	+	Splice_Site	SNP	C	C	G	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	KRT23	NM_015515	exon3	c.396+1G>C	.	ATCTTACCTGCTC	.	63.0	32.0	45.0	0.0	.	59	.	.	.	none	.	.	PASS	Atlas-SNP
PSMD12	5718	hgsc.bcm.edu	hg19	17	65362549	65362549	+	Silent	SNP	G	G	C	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	PSMD12	NM_174871	exon1	c.C87G	p.P29P	ACACTCGGGTAGG	.	34.0	14.0	31.0	0.0	.	32	.	.	.	none	.	.	PASS	Atlas-SNP
TRIM47	91107	hgsc.bcm.edu	hg19	17	73872839	73872839	+	Missense_Mutation	SNP	G	G	A	rs377764139	alternate_allele	TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	TRIM47	NM_033452	exon2	c.C731T	p.A244V	ATGCCAGCACCCA	.	167.0	106.0	133.0	0.0	.	40	.	.	.	alt	.	.	PASS	Atlas-SNP
MADCAM1	8174	hgsc.bcm.edu	hg19	19	504882	504882	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	MADCAM1	NM_130760	exon5	c.C1066A	p.P356T	CACCCACCAGCTT	.	66.0	22.0	158.0	0.0	.	29	.	.	.	none	.	.	PASS	Atlas-SNP
MADCAM1	8174	hgsc.bcm.edu	hg19	19	504883	504883	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	MADCAM1	NM_130760	exon5	c.C1067T	p.P356L	ACCCACCAGCTTC	.	66.0	22.0	159.0	0.0	.	29	.	.	.	none	.	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	hg19	19	4511773	4511773	+	Silent	SNP	G	G	A	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	PLIN4	NM_001080400	exon3	c.C2157T	p.V719V	ACTGCAGACGGTG	.	234.0	37.0	293.0	0.0	.	191	.	.	.	none	.	.	PASS	Atlas-SNP
PLIN3	10226	hgsc.bcm.edu	hg19	19	4839279	4839279	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	PLIN3	NM_005817	exon8	c.G1230C	p.Q410H	TGTGTTCTGGGCC	.	80.0	7.0	122.0	0.0	.	36	.	.	.	none	.	.	PASS	Atlas-SNP
PLIN3	10226	hgsc.bcm.edu	hg19	19	4839466	4839466	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	PLIN3	NM_005817	exon8	c.T1043G	p.I348S	CCCTGAATGCTGG	.	89.0	27.0	135.0	0.0	.	36	.	.	.	none	.	.	PASS	Atlas-SNP
DCAF15	90379	hgsc.bcm.edu	hg19	19	14070072	14070072	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	DCAF15	NM_138353	exon7	c.G1000A	p.A334T	AAAGAGGCCAAGG	.	12.0	6.0	14.0	0.0	.	30	.	.	.	none	.	.	PASS	Atlas-SNP
NAPA	8775	hgsc.bcm.edu	hg19	19	47996229	47996229	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	NAPA	NM_003827	exon7	c.A550G	p.I184V	CGTAGATGTCAAT	.	186.0	74.0	146.0	0.0	.	34	.	.	.	none	.	.	PASS	Atlas-SNP
MZF1	7593	hgsc.bcm.edu	hg19	19	59082640	59082640	+	Silent	SNP	G	G	A	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	MZF1	NM_198055	exon2	c.C117T	p.G39G	TTCAGGGCCTGGG	.	50.0	16.0	91.0	0.0	.	37	.	.	.	none	.	.	PASS	Atlas-SNP
PLCB1	23236	hgsc.bcm.edu	hg19	20	8608961	8608961	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	PLCB1	NM_015192	exon4	c.C267G	p.N89K	TGAACTTTTGGAT	.	116.0	34.0	102.0	0.0	.	394	.	.	.	none	.	.	PASS	Atlas-SNP
ASIP	434	hgsc.bcm.edu	hg19	20	32856797	32856797	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	ASIP	NM_001672	exon3	c.A223G	p.K75E	ACGCAGAAGGAGG	.	67.0	33.0	89.0	0.0	.	6	.	.	.	none	.	.	PASS	Atlas-SNP
ARVCF	421	hgsc.bcm.edu	hg19	22	19967432	19967432	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	ARVCF	NM_001670	exon6	c.C1230A	p.D410E	CGGGTGGTCCAGC	.	8.0	4.0	9.0	0.0	.	54	.	.	.	none	.	.	PASS	Atlas-SNP
LARGE	9215	hgsc.bcm.edu	hg19	22	33679190	33679190	+	Silent	SNP	G	G	A	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	LARGE	NM_004737	exon14	c.C1875T	p.F625F	TCACCTGAATGTG	.	187.0	61.0	224.0	0.0	.	98	.	.	.	none	.	.	PASS	Atlas-SNP
AKAP17A	8227	hgsc.bcm.edu	hg19	X	1714403	1714403	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	AKAP17A	NM_005088	exon3	c.G889A	p.E297K	GCGGAGGAGAGGC	.	89.0	73.0	152.0	1.0	.	46	.	.	.	none	.	.	PASS	Atlas-SNP
BCOR	54880	hgsc.bcm.edu	hg19	X	39923132	39923132	+	Silent	SNP	G	G	T	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	BCOR	NM_001123385	exon8	c.C3576A	p.T1192T	CAGGTTGGTCAGC	.	56.0	4.0	88.0	0.0	.	351	.	.	.	none	.	.	PASS	Atlas-SNP
MFN2	9927	hgsc.bcm.edu	hg19	1	12052666	12052667	+	Frame_Shift_Del	DEL	AC	AC	-	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	MFN2	NM_014874	exon4	c.229_230del	p.77_77del	.	.	347.0	129.0	472.0	0.0	.	83	.	0.371758	0	none	.	.	PASS	Atlas-Indel,Pindel
DENND4A	10260	hgsc.bcm.edu	hg19	15	65956990	65956991	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	DENND4A	NM_001144823	exon31	c.5427_5428insA	p.S1809fs	.	.	53.0	15.0	84.0	0.0	.	217	.	0.283019	0	none	.	.	PASS	Atlas-Indel,Pindel
PRPF8	10594	hgsc.bcm.edu	hg19	17	1585300	1585301	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	PRPF8	NM_006445	exon5	c.467_468insA	p.R156fs	.	.	123.0	10.0	110.0	0.0	.	169	.	0.0813008	0	none	.	.	PASS	Atlas-INDEL
PAM	5066	hgsc.bcm.edu	hg19	5	102203042	102203042	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	PAM	NM_138821	exon2	c.154delA	p.I52fs	.	.	79.0	21.0	104.0	0.0	.	180	.	0.265823	0	none	.	.	PASS	Atlas-INDEL
GALNT6	11226	hgsc.bcm.edu	hg19	12	51751976	51751982	+	Frame_Shift_Del	DEL	ACCAGGA	ACCAGGA	-	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	ACCAGGA	ACCAGGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	GALNT6	NM_007210	exon9	c.1433_1439del	p.478_480del	.	.	242.0	33.0	194.0	0.0	.	63	.	0.136364	0	none	.	.	PASS	Atlas-Indel,Pindel
TRNT1	51095	hgsc.bcm.edu	hg19	3	3182301	3182309	+	In_Frame_Del	DEL	CAGAGATCT	CAGAGATCT	-	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	CAGAGATCT	CAGAGATCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	TRNT1	NM_182916	exon4	c.449_457del	p.150_153del	.	.	104.0	24.0	151.0	0.0	.	34	.	0.230769	0	none	.	.	PASS	Atlas-Indel,Pindel
RNF34	80196	hgsc.bcm.edu	hg19	12	121855373	121855374	+	Frame_Shift_Del	DEL	AG	AG	-	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	RNF34	NM_194271	exon4	c.294_295del	p.98_99del	.	.	82.0	44.0	68.0	0.0	.	54	.	0.536585	0	none	.	.	PASS	Atlas-Indel,Pindel
GATA1	2623	hgsc.bcm.edu	hg19	X	48650855	48650855	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	GATA1	NM_002049	exon4	c.723delC	p.L241fs	.	.	132.0	99.0	148.0	0.0	.	342	.	0.75	0	none	.	.	PASS	Atlas-Indel,Pindel
BRMS1L	84312	hgsc.bcm.edu	hg19	14	36300676	36300676	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	BRMS1L	NM_032352	exon2	c.202delC	p.L68fs	.	.	203.0	80.0	242.0	0.0	.	26	.	0.394089	0	none	.	.	PASS	Atlas-Indel,Pindel
PRRG3	79057	hgsc.bcm.edu	hg19	X	150869380	150869380	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	PRRG3	NM_024082	exon4	c.570delT	p.P190fs	.	.	154.0	102.0	149.0	0.0	.	74	.	0.662338	0	none	.	.	PASS	Atlas-Indel,Pindel
NUAK2	81788	hgsc.bcm.edu	hg19	1	205272646	205272646	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	NUAK2	NM_030952	exon7	c.1820delT	p.L607fs	.	.	85.0	32.0	106.0	0.0	.	107	.	0.376471	0	none	.	.	PASS	Atlas-Indel,Pindel
TECR	9524	hgsc.bcm.edu	hg19	19	14674655	14674657	+	In_Frame_Del	DEL	CGT	CGT	-	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	CGT	CGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	TECR	NM_138501	exon5	c.206_208del	p.69_70del	.	.	87.0	35.0	116.0	0.0	.	22	.	0.402299	0	none	.	.	PASS	Atlas-Indel,Pindel
RNF168	165918	hgsc.bcm.edu	hg19	3	196214285	196214286	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	RNF168	NM_152617	exon3	c.543_544insA	p.K181fs	.	.	180.0	89.0	155.0	0.0	.	49	.	0.494444	0	none	.	.	PASS	Atlas-Indel,Pindel
C2CD3	26005	hgsc.bcm.edu	hg19	11	73748552	73748561	+	Frame_Shift_Del	DEL	AGGTTACTGG	AGGTTACTGG	-	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	AGGTTACTGG	AGGTTACTGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	C2CD3	NM_015531	exon30	c.5844_5853del	p.1948_1951del	.	.	98.0	29.0	141.0	0.0	.	288	.	0.295918	0	none	.	.	PASS	Atlas-Indel,Pindel
GDAP1	54332	hgsc.bcm.edu	hg19	8	75274164	75274164	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	GDAP1	NM_018972	exon4	c.529delG	p.E177fs	.	.	31.0	16.0	31.0	0.0	.	36	.	0.516129	0	none	.	.	PASS	Atlas-Indel,Pindel
CLK1	1195	hgsc.bcm.edu	hg19	2	201721517	201721517	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	CLK1	NM_001162407	exon9	c.1072delT	p.L358X	.	.	164.0	98.0	153.0	0.0	.	103	.	0.597561	0	none	.	.	PASS	Atlas-Indel,Pindel
ZNF836	162962	hgsc.bcm.edu	hg19	19	52658860	52658860	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	ZNF836	NM_001102657	exon5	c.2077delC	p.P693fs	.	.	36.0	20.0	55.0	0.0	.	158	.	0.555556	0	none	.	.	PASS	Atlas-INDEL
SACS	26278	hgsc.bcm.edu	hg19	13	23906370	23906371	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	SACS	NM_014363	exon10	c.11645_11646insT	p.S3882fs	.	.	46.0	14.0	58.0	0.0	.	871	.	0.304348	0	none	.	.	PASS	Atlas-Indel,Pindel
KRT2	3849	hgsc.bcm.edu	hg19	12	53045635	53045636	+	In_Frame_Ins	INS	-	-	TCCAAAGCCGCTGCCGCC	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	KRT2	NM_000423	exon1	c.292_293insGGCGGCAGCGGCTTTGGA	p.G98delinsGGSGFGG	.	.	225.0	20.0	209.0	0.0	.	94	.	0.0888889	0	none	.	.	PASS	Atlas-INDEL
MFAP3L	9848	hgsc.bcm.edu	hg19	4	170913188	170913189	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	MFAP3L	NM_021647	exon3	c.571_572insT	p.R191_T192delinsX	.	.	162.0	52.0	186.0	0.0	.	59	.	0.320988	0	none	.	.	PASS	Atlas-Indel,Pindel
PDZRN4	29951	hgsc.bcm.edu	hg19	12	41966603	41966603	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	PDZRN4	NM_001164595	exon10	c.2021delG	p.R674fs	.	.	212.0	64.0	155.0	0.0	.	346	.	0.301887	0	none	.	.	PASS	Atlas-Indel,Pindel
SALL4	57167	hgsc.bcm.edu	hg19	20	50401006	50401006	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	SALL4	NM_020436	exon4	c.2961delC	p.I987fs	.	.	211.0	66.0	193.0	0.0	.	168	.	0.313	.	none	.	.	PASS	Pindel
PAM	5066	hgsc.bcm.edu	hg19	5	102203043	102203044	+	Frame_Shift_Del	DEL	TG	TG	-	novel		TCGA-HE-A5NI-01A-11D-A26P-10	TCGA-HE-A5NI-10A-01D-A26P-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	40a609bb-2c8f-4146-83c4-e7b0d1b23619	a08286b5-7084-40d6-bbfe-9601634344bc	.	PAM	NM_138821	exon2	c.155_156del	p.52_52del	.	.	80.0	17.0	107.0	0.0	.	180	.	0.213	.	none	.	.	PASS	Pindel