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	TranscriptID	Exon	ChromChange	AAChange	COSMIC_Codon	COSMIC_Gene	Drug_Target
PRR14	78994	broad.mit.edu	36	16	30571863	30571864	+	Frame_Shift_Ins	INS	-	C	C	novel		TCGA-AG-4001-01	TCGA-AG-4001-01							Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_024031	exon5	c.442_443insC	p.A148fs	.	.	.
AP2A1	160	broad.mit.edu	36	19	54996458	54996459	+	Splice_Site	INS	-	C	C	novel		TCGA-AG-4001-01	TCGA-AG-4001-01							Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	.	.	.	.	.	.	.
DGKI	9162	broad.mit.edu	36	7	137025274	137025274	+	Missense_Mutation	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_004717	exon2	c.G416A	p.R139Q	.	.	.
ADCY1	107	broad.mit.edu	36	7	45719954	45719954	+	Missense_Mutation	SNP	C	G	G	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_021116	exon20	c.C3195G	p.I1065M	.	.	.
C7orf57	136288	broad.mit.edu	36	7	48056066	48056066	+	Missense_Mutation	SNP	A	G	G	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	A	A					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_001100159	exon6	c.A572G	p.N191S	.	.	.
FBXL18	80028	broad.mit.edu	36	7	5506661	5506661	+	Missense_Mutation	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_024963	exon3	c.C1765T	p.R589W	.	.	.
KRIT1	889	broad.mit.edu	36	7	91689255	91689255	+	Nonsense_Mutation	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_194455	exon14	c.G1460A	p.W487X	.	.	.
MYL9	10398	broad.mit.edu	36	20	34610908	34610908	+	Missense_Mutation	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_006097	exon4	c.G361A	p.D121N	.	.	.
TSHZ2	128553	broad.mit.edu	36	20	51304248	51304248	+	Missense_Mutation	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_173485	exon2	c.G844A	p.D282N	.	.	.
FOXA1	3169	broad.mit.edu	36	14	37131383	37131383	+	Silent	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_004496	exon2	c.G357A	p.Q119Q	.	.	.
CLEC14A	161198	broad.mit.edu	36	14	37794040	37794040	+	Silent	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_175060	exon1	c.C939T	p.P313P	.	.	.
PRKCH	5583	broad.mit.edu	36	14	61065645	61065645	+	Silent	SNP	G	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_006255	exon11	c.G1533T	p.T511T	.	.	.
CABIN1	23523	broad.mit.edu	36	22	22796813	22796813	+	Silent	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_001199281	exon17	c.C2295T	p.N765N	.	.	.
SLC1A6	6511	broad.mit.edu	36	19	14924790	14924790	+	Silent	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_005071	exon8	c.C1449T	p.V483V	.	.	.
ZNF507	22847	broad.mit.edu	36	19	37543275	37543275	+	Silent	SNP	A	G	G	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	A	A					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_001136156	exon5	c.A2271G	p.Q757Q	.	.	.
ZNF382	84911	broad.mit.edu	36	19	41809639	41809639	+	Missense_Mutation	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_032825	exon5	c.C1000T	p.R334C	.	.	.
PSG2	5670	broad.mit.edu	36	19	48271376	48271376	+	Missense_Mutation	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_031246	exon3	c.C679T	p.R227C	.	.	.
PSG4	5672	broad.mit.edu	36	19	48390414	48390414	+	Silent	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_002780	exon5	c.G1161A	p.K387K	.	.	.
NLRP4	147945	broad.mit.edu	36	19	61061256	61061256	+	Missense_Mutation	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_134444	exon3	c.G685A	p.V229I	.	.	.
ZNF586	54807	broad.mit.edu	36	19	62982114	62982114	+	Missense_Mutation	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_017652	exon3	c.G347A	p.R116H	.	.	.
ZNF560	147741	broad.mit.edu	36	19	9441372	9441372	+	Missense_Mutation	SNP	T	G	G	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_152476	exon8	c.A463C	p.K155Q	.	.	.
SYBU	55638	broad.mit.edu	36	8	110657374	110657374	+	Missense_Mutation	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_001099746	exon6	c.G572A	p.R191Q	.	.	.
TRPS1	7227	broad.mit.edu	36	8	116495517	116495517	+	Nonsense_Mutation	SNP	G	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_014112	exon7	c.C3795A	p.C1265X	.	.	.
NDUFB9	4715	broad.mit.edu	36	8	125631280	125631280	+	Missense_Mutation	SNP	A	G	G	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	A	A					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_005005	exon4	c.A506G	p.Y169C	.	.	.
ADAM32	203102	broad.mit.edu	36	8	39198336	39198336	+	De_novo_Start_InFrame	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_145004	exon13	c.C1284T	p.D428D	.	.	.
ZFHX4	79776	broad.mit.edu	36	8	77782650	77782650	+	Missense_Mutation	SNP	C	G	G	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_024721	exon3	c.C2905G	p.Q969E	.	.	.
AMPD2	271	broad.mit.edu	36	1	109965174	109965175	+	Missense_Mutation	DNP	CA	TG	TG	novel		TCGA-AG-4001-01	TCGA-AG-4001-01							Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_004037	exon1	c.16_17TG	.	.	.	.
BCL9	607	broad.mit.edu	36	1	145557861	145557861	+	Missense_Mutation	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_004326	exon8	c.G1276A	p.V426M	.	.	.
OR10K2	391107	broad.mit.edu	36	1	156657003	156657003	+	Missense_Mutation	SNP	G	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_001004476	exon1	c.C278A	p.S93Y	.	.	.
SPTA1	6708	broad.mit.edu	36	1	156892987	156892987	+	Silent	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_003126	exon20	c.C2889T	p.N963N	.	.	.
PIK3C2B	5287	broad.mit.edu	36	1	202679242	202679242	+	Missense_Mutation	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_002646	exon20	c.C2974T	p.R992C	.	.	.
CNTN2	6900	broad.mit.edu	36	1	203297145	203297145	+	Missense_Mutation	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C	C	T	C	T	Unknown	Valid	Germline	Phase_I	Unspecified	454			Illumina	NM_005076	exon8	c.C947T	p.T316I	.	.	.
PPP2R5A	5525	broad.mit.edu	36	1	210569149	210569149	+	Silent	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_001199756	exon2	c.G60A	p.Q20Q	.	.	.
OR2G6	391211	broad.mit.edu	36	1	246751784	246751784	+	Missense_Mutation	SNP	T	C	C	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	T	T					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_001013355	exon1	c.T214C	p.C72R	.	.	.
CLIC4	25932	broad.mit.edu	36	1	25039892	25039892	+	Silent	SNP	A	G	G	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	A	A					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_013943	exon6	c.A639G	p.E213E	.	.	.
SLC44A5	204962	broad.mit.edu	36	1	75481193	75481193	+	Missense_Mutation	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_152697	exon8	c.G437A	p.R146H	.	.	.
C11orf87	399947	broad.mit.edu	36	11	108799890	108799890	+	Silent	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_207645	exon2	c.C321T	p.S107S	.	.	.
OR10G4	390264	broad.mit.edu	36	11	123392173	123392173	+	Missense_Mutation	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_001004462	exon1	c.C682T	p.R228C	.	.	.
ATHL1	80162	broad.mit.edu	36	11	284589	284589	+	Missense_Mutation	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_025092	exon14	c.G2054A	p.R685Q	.	.	.
CREB3L1	90993	broad.mit.edu	36	11	46278091	46278091	+	Silent	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_052854	exon2	c.G132A	p.T44T	.	.	.
OR5D18	219438	broad.mit.edu	36	11	55344124	55344124	+	Missense_Mutation	SNP	G	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_001001952	exon1	c.G443T	p.G148V	.	.	.
AMOTL1	154810	broad.mit.edu	36	11	94232420	94232420	+	Missense_Mutation	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_130847	exon9	c.G2027A	p.R676Q	.	.	.
MAP3K4	4216	broad.mit.edu	36	6	161375396	161375396	+	Nonsense_Mutation	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_006724	exon2	c.C268T	p.R90X	.	.	.
HIST1H2BH	8345	broad.mit.edu	36	6	26360197	26360197	+	Missense_Mutation	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_003524	exon1	c.G340A	p.E114K	.	.	.
BAT2	7916	broad.mit.edu	36	6	31708003	31708003	+	Silent	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_004638	exon16	c.C3574T	p.L1192L	.	.	.
DAAM2	23500	broad.mit.edu	36	6	39977606	39977606	+	Missense_Mutation	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_015345	exon25	c.C3019T	p.R1007W	.	.	.
PKHD1	5314	broad.mit.edu	36	6	51876484	51876484	+	Missense_Mutation	SNP	T	C	C	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_170724	exon43	c.A6866G	p.D2289G	.	.	.
IBTK	25998	broad.mit.edu	36	6	82948425	82948425	+	Silent	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_015525	exon26	c.G3615A	p.R1205R	.	.	.
SLC35B3	51000	broad.mit.edu	36	6	8375340	8375340	+	Missense_Mutation	SNP	G	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_001142541	exon3	c.C53A	p.T18N	.	.	.
NCOR1	9611	broad.mit.edu	36	17	15945662	15945662	+	Nonsense_Mutation	SNP	T	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	T	T					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_001190440	exon19	c.A2365T	p.K789X	.	.	.
BCAS3	54828	broad.mit.edu	36	17	56379391	56379391	+	Missense_Mutation	SNP	G	C	C	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_001099432	exon14	c.G1117C	p.G373R	.	.	.
CACNG5	27091	broad.mit.edu	36	17	62311351	62311351	+	Silent	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_014404	exon4	c.G681A	p.P227P	.	.	.
TP53	7157	broad.mit.edu	36	17	7520046	7520047	+	Frame_Shift_Del	DEL	CA	-	-	novel		TCGA-AG-4001-01	TCGA-AG-4001-01			CA	-	CA	CA	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_001126114	exon4	c.365_366del	p.122_122del	.	.	.
MYH11	4629	broad.mit.edu	36	16	15839506	15839506	+	Silent	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_001040114	exon2	c.C105T	p.L35L	.	.	.
SRRM2	23524	broad.mit.edu	36	16	2756325	2756325	+	Missense_Mutation	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_016333	exon11	c.G5795A	p.R1932H	.	.	.
MMP2	4313	broad.mit.edu	36	16	54076809	54076809	+	Silent	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_004530	exon4	c.C627T	p.D209D	.	.	.
CNGB1	1258	broad.mit.edu	36	16	56510580	56510580	+	Silent	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_001297	exon20	c.C1881T	p.C627C	.	.	.
GRIN2A	2903	broad.mit.edu	36	16	9939361	9939361	+	Silent	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_001134408	exon3	c.C963T	p.Y321Y	.	.	.
MYH15	22989	broad.mit.edu	36	3	109730800	109730800	+	Missense_Mutation	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_014981	exon1	c.G3A	p.M1I	.	.	.
IQCB1	9657	broad.mit.edu	36	3	122971991	122971991	+	Missense_Mutation	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_001023570	exon15	c.C1688T	p.P563L	.	.	.
ALDH1L1	10840	broad.mit.edu	36	3	127355067	127355067	+	Silent	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_012190	exon7	c.C768T	p.P256P	.	.	.
MLF1	4291	broad.mit.edu	36	3	159800534	159800534	+	Missense_Mutation	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_001195434	exon7	c.G416A	p.S139N	.	.	.
IFT80	57560	broad.mit.edu	36	3	161479686	161479686	+	Missense_Mutation	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_001190242	exon15	c.C1414T	p.R472C	.	.	.
ZCWPW2	152098	broad.mit.edu	36	3	28429697	28429697	+	Missense_Mutation	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_001040432	exon2	c.C134T	p.S45L	.	.	.
CLASP2	23122	broad.mit.edu	36	3	33700934	33700934	+	Silent	SNP	A	G	G	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	A	A					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_015097	exon6	c.T565C	p.L189L	.	.	.
KIF9	64147	broad.mit.edu	36	3	47257505	47257505	+	Missense_Mutation	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_182902	exon17	c.G1714A	p.D572N	.	.	.
CNTN3	5067	broad.mit.edu	36	3	74556736	74556736	+	Missense_Mutation	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_020872	exon4	c.G404A	p.R135H	.	.	.
NELL2	4753	broad.mit.edu	36	12	43555391	43555391	+	Missense_Mutation	SNP	C	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_001145108	exon2	c.G68T	p.G23V	.	.	.
CACNB3	784	broad.mit.edu	36	12	47506485	47506485	+	Missense_Mutation	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_000725	exon10	c.G811A	p.A271T	.	.	.
CLEC4C	170482	broad.mit.edu	36	12	7785308	7785308	+	Missense_Mutation	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_203503	exon3	c.G118A	p.V40I	.	.	.
ARID2	196528	broad.mit.edu	36	12	44519397	44519397	+	Frame_Shift_Del	DEL	T	-	-	novel		TCGA-AG-4001-01	TCGA-AG-4001-01			T	-	T	T	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_152641	exon11	c.1349delT	p.V450fs	.	.	.
ATP10A	57194	broad.mit.edu	36	15	23577290	23577290	+	Missense_Mutation	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_024490	exon2	c.G623A	p.R208Q	.	.	.
OCA2	4948	broad.mit.edu	36	15	25903908	25903908	+	Missense_Mutation	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_000275	exon13	c.C1261T	p.R421W	.	.	.
CTDSPL2	51496	broad.mit.edu	36	15	42598663	42598663	+	Missense_Mutation	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_016396	exon11	c.C1117T	p.R373W	.	.	.
FBN1	2200	broad.mit.edu	36	15	46575002	46575002	+	Missense_Mutation	SNP	C	G	G	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_000138	exon21	c.G2495C	p.C832S	.	.	.
DENND4A	10260	broad.mit.edu	36	15	63751245	63751245	+	Nonsense_Mutation	SNP	G	C	C	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_001144823	exon25	c.C4400G	p.S1467X	.	.	.
SNX33	257364	broad.mit.edu	36	15	73736538	73736538	+	Missense_Mutation	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_153271	exon2	c.G1652A	p.R551H	.	.	.
SH3GL3	6457	broad.mit.edu	36	15	82028410	82028410	+	Missense_Mutation	SNP	G	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_003027	exon4	c.G313T	p.G105W	.	.	.
SPATA8	145946	broad.mit.edu	36	15	95128415	95128415	+	Missense_Mutation	SNP	A	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_173499	exon2	c.A118T	p.M40L	.	.	.
FAT4	79633	broad.mit.edu	36	4	126593098	126593098	+	Missense_Mutation	SNP	T	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_024582	exon9	c.T11477A	p.V3826E	.	.	.
NR3C2	4306	broad.mit.edu	36	4	149576931	149576931	+	Missense_Mutation	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_001166104	exon2	c.C532T	p.R178C	.	.	.
GLRB	2743	broad.mit.edu	36	4	158311267	158311267	+	Silent	SNP	A	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	A	A					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_001166060	exon10	c.A1431T	p.A477A	.	.	.
FSTL5	56884	broad.mit.edu	36	4	162595652	162595652	+	Missense_Mutation	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_020116	exon15	c.G1795A	p.D599N	.	.	.
SPATA4	132851	broad.mit.edu	36	4	177346264	177346264	+	Missense_Mutation	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_144644	exon5	c.C805T	p.P269S	.	.	.
TMPRSS11F	389208	broad.mit.edu	36	4	68617065	68617065	+	Silent	SNP	G	C	C	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_207407	exon7	c.C621G	p.V207V	.	.	.
AFM	173	broad.mit.edu	36	4	74576587	74576587	+	Missense_Mutation	SNP	A	C	C	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	A	A					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_001133	exon8	c.A978C	p.L326F	.	.	.
THOC2	57187	broad.mit.edu	36	X	122593364	122593364	+	Silent	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_001081550	exon22	c.G2337A	p.Q779Q	.	.	.
STAG2	10735	broad.mit.edu	36	X	123006882	123006882	+	Missense_Mutation	SNP	A	G	G	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	A	A					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_001042750	exon8	c.A650G	p.H217R	.	.	.
ZNF280C	55609	broad.mit.edu	36	X	129222096	129222096	+	Silent	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_017666	exon2	c.C9T	p.D3D	.	.	.
FHL1	2273	broad.mit.edu	36	X	135116263	135116263	+	Silent	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_001159702	exon3	c.G6A	p.A2A	.	.	.
OPN1LW	5956	broad.mit.edu	36	X	153073306	153073306	+	Silent	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_020061	exon4	c.C642T	p.P214P	.	.	.
MAOB	4129	broad.mit.edu	36	X	43511704	43511704	+	Missense_Mutation	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_000898	exon15	c.G1516A	p.A506T	.	.	.
SYN1	6853	broad.mit.edu	36	X	47321802	47321802	+	Missense_Mutation	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_133499	exon6	c.G817A	p.A273T	.	.	.
WDR13	64743	broad.mit.edu	36	X	48342730	48342730	+	Missense_Mutation	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_001166426	exon2	c.C52T	p.R18C	.	.	.
HSD17B10	3028	broad.mit.edu	36	X	53477501	53477501	+	Nonsense_Mutation	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_001037811	exon2	c.C85T	p.R29X	.	.	.
ZC4H2	55906	broad.mit.edu	36	X	64055687	64055687	+	Missense_Mutation	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_001178032	exon4	c.G452A	p.R151Q	.	.	.
MED12	9968	broad.mit.edu	36	X	70259328	70259328	+	Missense_Mutation	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_005120	exon10	c.G1364A	p.R455Q	.	.	.
TAF1	6872	broad.mit.edu	36	X	70511859	70511859	+	Missense_Mutation	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_138923	exon4	c.G530A	p.G177D	.	.	.
SLC16A2	6567	broad.mit.edu	36	X	73662395	73662395	+	Missense_Mutation	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_006517	exon4	c.G1334A	p.R445H	.	.	.
PCDH19	57526	broad.mit.edu	36	X	99549316	99549316	+	Silent	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_001105243	exon1	c.C936T	p.Y312Y	.	.	.
PCDP1	200373	broad.mit.edu	36	2	120113892	120113892	+	Silent	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_001029996	exon22	c.C1341T	p.D447D	.	.	.
LRP1B	53353	broad.mit.edu	36	2	141529297	141529297	+	Silent	SNP	G	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_018557	exon10	c.C1410A	p.V470V	.	.	.
XIRP2	129446	broad.mit.edu	36	2	167808482	167808482	+	Silent	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_001199144	exon7	c.G1668A	p.P556P	.	.	.
ABCB11	8647	broad.mit.edu	36	2	169560194	169560194	+	Missense_Mutation	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_003742	exon7	c.G522A	p.M174I	.	.	.
TTN	7273	broad.mit.edu	36	2	179104524	179104524	+	Missense_Mutation	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_003319	exon186	c.G77868A	p.A25956A	.	.	.
ZNF804A	91752	broad.mit.edu	36	2	185509052	185509052	+	Silent	SNP	C	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_194250	exon4	c.C684A	p.S228S	.	.	.
SP110	3431	broad.mit.edu	36	2	230759033	230759033	+	Silent	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_004510	exon11	c.C1200T	p.D400D	.	.	.
MEMO1	51072	broad.mit.edu	36	2	31947001	31947001	+	Missense_Mutation	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_015955	exon9	c.C827T	p.S276L	.	.	.
TTC15	51112	broad.mit.edu	36	2	3384663	3384663	+	Nonsense_Mutation	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_016030	exon3	c.C1156T	p.Q386X	.	.	.
MSH6	2956	broad.mit.edu	36	2	47881561	47881561	+	Missense_Mutation	SNP	C	G	G	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_000179	exon4	c.C2935G	p.L979V	.	.	.
CCT4	10575	broad.mit.edu	36	2	61953194	61953194	+	Missense_Mutation	SNP	T	C	C	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	T	T					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_006430	exon11	c.A1159G	p.T387A	.	.	.
DYSF	8291	broad.mit.edu	36	2	71648921	71648921	+	Missense_Mutation	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_001130982	exon27	c.C2851T	p.R951C	.	.	.
SNRNP200	23020	broad.mit.edu	36	2	96308082	96308082	+	Silent	SNP	G	A	A	rs72937669	by-1000genomes	TCGA-AG-4001-01	TCGA-AG-4001-01	G	G					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_014014	exon38	c.C5418T	p.D1806D	.	.	.
AFF3	3899	broad.mit.edu	36	2	99576600	99576600	+	Missense_Mutation	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_001025108	exon14	c.C2030T	p.T677M	.	.	.
SETX	23064	broad.mit.edu	36	9	134193156	134193156	+	Missense_Mutation	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_015046	exon10	c.C3650T	p.T1217M	.	.	.
NFIB	4781	broad.mit.edu	36	9	14110603	14110603	+	Missense_Mutation	SNP	G	C	C	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_001190738	exon8	c.C1159G	p.P387A	.	.	.
TRPM3	80036	broad.mit.edu	36	9	72341969	72341969	+	Missense_Mutation	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_001007471	exon25	c.C3844T	p.R1282C	.	.	.
ANXA1	301	broad.mit.edu	36	9	74965099	74965099	+	Missense_Mutation	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_000700	exon5	c.G371A	p.R124H	.	.	.
CRYL1	51084	broad.mit.edu	36	13	19876863	19876863	+	Missense_Mutation	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_015974	exon7	c.G757A	p.D253N	.	.	.
SACS	26278	broad.mit.edu	36	13	22810013	22810013	+	Missense_Mutation	SNP	C	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_014363	exon10	c.G6002T	p.R2001I	.	.	.
SUCLA2	8803	broad.mit.edu	36	13	47421667	47421667	+	Missense_Mutation	SNP	C	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_003850	exon9	c.G1180T	p.A394S	.	.	.
METTL10	399818	broad.mit.edu	36	10	126443958	126443958	+	Silent	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	NM_212554	exon5	c.C609T	p.F203F	.	.	.
APC	324	broad.mit.edu	36	5	112201816	112201816	+	Nonsense_Mutation	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_001127511	exon14	c.C2572T	p.R858X	APC,large_intestine,NS,Substitution - Nonsense,0	.	.
PCDHA13	56136	broad.mit.edu	36	5	140244214	140244214	+	Missense_Mutation	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_031865	exon1	c.C2177T	p.P726L	.	.	.
PCDHB6	56130	broad.mit.edu	36	5	140512127	140512127	+	Missense_Mutation	SNP	C	T	T	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_018939	exon1	c.C2105T	p.S702L	.	.	.
SPEF2	79925	broad.mit.edu	36	5	35677322	35677322	+	Missense_Mutation	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Unspecified	454			Illumina	NM_024867	exon3	c.G194A	p.R65H	.	.	.
FAM74A3	728495	broad.mit.edu	36	9	40706047	40706047	+	Missense_Mutation	SNP	G	A	A	novel		TCGA-AG-4001-01	TCGA-AG-4001-01	G	G					Unknown	Unknown	Somatic	Phase_I	Unspecified				Illumina	.	.	.	.	.	.	.