#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR
1	17125019	.	TCCTTGC	T	.	PASS	IC=0;IHP=14;NT=ref;QSI=34;QSI_NT=34;RC=1;RU=CCTTGC;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1;EFF=INTERGENIC(MODIFIER||||||||||1)	DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50	79:79:79,102:0,0:1,1:71.94:6.14:0.00	157:157:142,184:4,5:12,12:146.46:14.62:0.00
1	120587279	rs146325911	TTAAAA	T	.	PASS	IC=0;IHP=7;NT=ref;QSI=38;QSI_NT=38;RC=1;RU=TAAAA;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1;EFF=INTRON(MODIFIER||||2471|NOTCH2|protein_coding|CODING|ENST00000256646|1|1);RSPOS=120587280;dbSNPBuildID=134;SSR=0;SAO=0;VP=05000008000500000c000200;GENEINFO=NOTCH2:4853;WGT=1;VC=DIV;INT;ASP;KGPilot123;KGPROD	DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50	88:88:89,91:0,0:2,2:88.16:0.60:0.00	234:234:219,225:10,11:18,20:235.09:2.02:0.00
1	121138123	.	G	GCCTCGGCTTGTTGC	.	PASS	IC=1;IHP=8;NT=ref;QSI=48;QSI_NT=48;RC=0;RU=CCTCGGCTTGTTGC;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1;EFF=DOWNSTREAM(MODIFIER|||||AL358175.1|processed_transcript|NON_CODING|ENST00000429055||1),INTRON(MODIFIER|||||AL358175.1|processed_transcript|NON_CODING|ENST00000437515|2|1),UPSTREAM(MODIFIER|||||AL592494.5|processed_transcript|NON_CODING|ENST00000417218||1)	DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50	110:110:95,203:0,0:14,5:105.72:31.25:0.00	199:199:122,314:4,7:76,105:204.44:52.34:0.00
2	87587199	.	GATGAA	G	.	PASS	IC=0;IHP=3;NT=ref;QSI=44;QSI_NT=44;RC=1;RU=ATGAA;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1;EFF=INTERGENIC(MODIFIER||||||||||1),UPSTREAM(MODIFIER|||||AC068279.4|pseudogene|NON_CODING|ENST00000453126||1)	DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50	94:94:99,125:0,0:2,4:95.16:1.40:0.00	246:246:234,347:7,7:16,23:240.91:6.76:0.00
2	87591482	.	GATGAA	G	.	PASS	IC=1;IHP=3;NT=ref;QSI=33;QSI_NT=33;RC=2;RU=ATGAA;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1;EFF=INTERGENIC(MODIFIER||||||||||1),UPSTREAM(MODIFIER|||||AC068279.1|pseudogene|NON_CODING|ENST00000393756||1)	DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50	73:73:73,74:0,0:4,4:73.54:2.19:0.00	242:242:211,219:14,16:27,30:230.85:10.02:0.00
2	87651512	.	C	CAGCCA	.	PASS	IC=2;IHP=2;NT=ref;QSI=30;QSI_NT=30;RC=1;RU=AGCCA;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1;EFF=INTERGENIC(MODIFIER||||||||||1)	DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50	69:69:62,73:0,0:10,9:68.32:6.70:0.00	128:128:105,119:3,4:22,26:126.98:12.09:0.00
2	89870289	.	A	AAATTG	.	PASS	IC=1;IHP=2;NT=ref;QSI=34;QSI_NT=34;RC=0;RU=AATTG;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1;EFF=INTERGENIC(MODIFIER||||||||||1)	DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50	82:82:75,100:0,0:7,3:113.25:15.57:0.00	198:198:155,220:5,11:33,26:284.45:49.59:0.00
2	121199275	.	T	TCTCTC	.	PASS	IC=1;IHP=11;NT=ref;QSI=31;QSI_NT=31;RC=0;RU=CTCTC;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1;EFF=INTERGENIC(MODIFIER||||||||||1)	DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50	21:21:13,17:0,0:13,13:25.11:1.19:0.00	56:56:19,24:12,12:36,39:68.02:3.58:0.00
4	49538376	rs111924683	TTTTACCTGTATTATTGATTATAATAAAC	T	.	PASS	IC=0;IHP=6;NT=ref;QSI=33;QSI_NT=33;RC=1;RU=TTTACCTGTATTATTGATTATAATAAAC;SGT=ref->het;SOMATIC;TQSI=2;TQSI_NT=2;EFF=INTERGENIC(MODIFIER||||||||||1);RSPOS=49538377;dbSNPBuildID=132;SSR=0;SAO=0;VP=050100000005000102000200;WGT=1;VC=DIV;SLO;ASP;GNO;OTHERKG	DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50	97:97:101,132:0,0:2,0:96.33:1.37:0.00	218:218:229,312:5,5:12,12:215.42:4.04:0.00
6	131431998	.	C	CT	.	PASS	IC=3;IHP=4;NT=ref;QSI=33;QSI_NT=33;RC=2;RU=T;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1;EFF=INTERGENIC(MODIFIER||||||||||1)	DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50	29:29:27,27:0,0:2,2:31.15:0.01:0.00	65:65:35,35:15,16:14,14:71.62:1.02:0.00
7	102391987	.	G	GCTGTGGTAGAAGACCCCTTA	.	PASS	IC=2;IHP=2;NT=ref;QSI=32;QSI_NT=32;RC=1;RU=CTGTGGTAGAAGACCCCTTA;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1;EFF=INTRON(MODIFIER||||193|FAM185A|protein_coding|CODING|ENST00000418198|1|1),INTRON(MODIFIER||||275|FAM185A|protein_coding|CODING|ENST00000409231|1|1),INTRON(MODIFIER||||392|FAM185A|protein_coding|CODING|ENST00000413034|1|1),INTRON(MODIFIER|||||FAM185A|nonsense_mediated_decay|CODING|ENST00000420217|1|1),INTRON(MODIFIER|||||FAM185A|nonsense_mediated_decay|CODING|ENST00000442873|1|1),INTRON(MODIFIER|||||FAM185A|processed_transcript|CODING|ENST00000481697|1|1),INTRON(MODIFIER|||||FAM185A|processed_transcript|CODING|ENST00000487807|1|1),INTRON(MODIFIER|||||FAM185A|processed_transcript|CODING|ENST00000496790|1|1),UPSTREAM(MODIFIER|||||RP11-577H5.1|processed_pseudogene|NON_CODING|ENST00000434317||1)	DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50	24:24:18,18:0,0:6,6:24.07:0.01:0.00	71:71:34,34:23,23:16,16:80.55:0.44:0.00
9	74298469	rs147197801	C	CAAACTT	.	PASS	IC=1;IHP=2;NT=ref;QSI=32;QSI_NT=32;RC=0;RU=AAACTT;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1;EFF=DOWNSTREAM(MODIFIER||||1320|TMEM2|protein_coding|CODING|ENST00000377066||1),DOWNSTREAM(MODIFIER||||376|TMEM2|protein_coding|CODING|ENST00000396272||1),DOWNSTREAM(MODIFIER|||||TMEM2|nonsense_mediated_decay|CODING|ENST00000542935||1),DOWNSTREAM(MODIFIER|||||TMEM2|retained_intron|CODING|ENST00000538669||1),EXON(MODIFIER|||||TMEM2|retained_intron|CODING|ENST00000377057|5|1),UTR_3_PRIME(MODIFIER||||1383|TMEM2|protein_coding|CODING|ENST00000377044|24|1);RSPOS=74298469;dbSNPBuildID=134;SSR=0;SAO=0;VP=050000800215000002000200;GENEINFO=TMEM2:23670;WGT=1;VC=DIV;REF;U3;OTH;ASP;OTHERKG	DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50	32:32:31,31:0,0:1,1:32.98:0.74:0.00	71:71:51,51:12,12:8,8:72.77:2.86:0.00
12	7349870	.	TATATA	T	.	PASS	IC=0;IHP=3;NT=ref;QSI=35;QSI_NT=35;RC=1;RU=ATATA;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1;EFF=INTRON(MODIFIER||||114|PEX5|protein_coding|CODING|ENST00000536883|4|1),INTRON(MODIFIER||||117|PEX5|protein_coding|CODING|ENST00000543974|5|1),INTRON(MODIFIER||||127|PEX5|protein_coding|CODING|ENST00000545845|3|1),INTRON(MODIFIER||||167|PEX5|protein_coding|CODING|ENST00000537873|4|1),INTRON(MODIFIER||||247|PEX5|protein_coding|CODING|ENST00000542539|5|1),INTRON(MODIFIER||||271|PEX5|protein_coding|CODING|ENST00000545574|4|1),INTRON(MODIFIER||||409|PEX5|protein_coding|CODING|ENST00000396637|5|1),INTRON(MODIFIER||||602|PEX5|protein_coding|CODING|ENST00000266563|5|1),INTRON(MODIFIER||||631|PEX5|protein_coding|CODING|ENST00000266564|4|1),INTRON(MODIFIER||||639|PEX5|protein_coding|CODING|ENST00000420616|5|1),INTRON(MODIFIER||||639|PEX5|protein_coding|CODING|ENST00000455147|6|1),INTRON(MODIFIER||||654|PEX5|protein_coding|CODING|ENST00000434354|5|1),INTRON(MODIFIER||||660|PEX5|protein_coding|CODING|ENST00000412720|5|1),INTRON(MODIFIER|||||PEX5|processed_transcript|CODING|ENST00000545220|4|1),INTRON(MODIFIER|||||PEX5|retained_intron|CODING|ENST00000539304|1|1)	DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50	77:77:81,121:0,0:1,1:62.23:4.50:0.00	241:241:234,326:7,9:19,25:197.39:13.53:0.00
12	108741563	.	AT	A	.	PASS	IC=3;IHP=5;NT=ref;QSI=34;QSI_NT=34;RC=4;RU=T;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1;EFF=INTERGENIC(MODIFIER||||||||||1)	DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50	42:42:38,48:0,0:4,1:38.47:3.75:0.00	159:159:123,160:27,32:9,5:147.31:12.97:0.00
15	64224362	.	T	TAA	.	PASS	IC=2;IHP=4;NT=ref;QSI=30;QSI_NT=30;RC=0;RU=A;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1;EFF=INTRON(MODIFIER||||370|DAPK2|protein_coding|CODING|ENST00000261891|4|1),INTRON(MODIFIER||||370|DAPK2|protein_coding|CODING|ENST00000457488|5|1),INTRON(MODIFIER||||488|DAPK2|protein_coding|CODING|ENST00000558069|5|1),INTRON(MODIFIER|||||DAPK2|nonsense_mediated_decay|CODING|ENST00000559007|4|1),INTRON(MODIFIER|||||DAPK2|processed_transcript|CODING|ENST00000558482|5|1),INTRON(MODIFIER|||||RP11-111E14.1|antisense|NON_CODING|ENST00000558050|2|1)	DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50	20:20:18,18:0,0:3,3:24.79:2.82:0.00	69:69:27,28:27,27:17,17:79.75:10.75:0.00
15	102499142	.	G	GGTTGACCA	.	PASS	IC=1;IHP=2;NT=ref;QSI=41;QSI_NT=41;RC=0;RU=GTTGACCA;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1;EFF=DOWNSTREAM(MODIFIER|||||AC140725.4|lincRNA|NON_CODING|ENST00000559045||1),DOWNSTREAM(MODIFIER|||||AC140725.4|lincRNA|NON_CODING|ENST00000561145||1),DOWNSTREAM(MODIFIER|||||FAM138E|lincRNA|NON_CODING|ENST00000507796||1),DOWNSTREAM(MODIFIER|||||FAM138E|lincRNA|NON_CODING|ENST00000559252||1),DOWNSTREAM(MODIFIER|||||MIR1302-2|miRNA|NON_CODING|ENST00000408734||1),INTERGENIC(MODIFIER||||||||||1),UPSTREAM(MODIFIER|||||WASH3P|processed_transcript|NON_CODING|ENST00000354296||1),UPSTREAM(MODIFIER|||||WASH3P|processed_transcript|NON_CODING|ENST00000558686||1),UPSTREAM(MODIFIER|||||WASH3P|processed_transcript|NON_CODING|ENST00000559163||1),UPSTREAM(MODIFIER|||||WASH3P|processed_transcript|NON_CODING|ENST00000559884||1),UPSTREAM(MODIFIER|||||WASH3P|unprocessed_pseudogene|NON_CODING|ENST00000338304||1),UPSTREAM(MODIFIER|||||WASH3P|unprocessed_pseudogene|NON_CODING|ENST00000398121||1)	DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50	109:109:87,97:0,0:19,23:98.38:1.39:0.00	241:241:158,179:5,5:72,86:216.48:0.98:0.00
20	29600571	.	GCTCTCATT	G	.	PASS	IC=0;IHP=2;NT=ref;QSI=42;QSI_NT=42;RC=1;RU=CTCTCATT;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1;EFF=INTERGENIC(MODIFIER||||||||||1),UPSTREAM(MODIFIER|||||RP4-610C12.1|antisense|NON_CODING|ENST00000432067||1)	DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50	104:104:97,121:0,0:10,4:100.28:11.71:0.00	282:282:253,318:8,9:43,22:274.52:28.61:0.00
21	9671216	.	T	TATTTA	.	PASS	IC=1;IHP=12;NT=ref;QSI=54;QSI_NT=54;RC=0;RU=ATTTA;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1;EFF=INTERGENIC(MODIFIER||||||||||1)	DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50	117:117:116,122:0,0:0,0:115.03:0.83:0.00	247:247:223,243:8,9:16,17:251.3:1.64:0.00
21	10855703	.	C	CACTCG	.	PASS	IC=1;IHP=2;NT=ref;QSI=37;QSI_NT=37;RC=0;RU=ACTCG;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1;EFF=INTERGENIC(MODIFIER||||||||||1)	DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50	86:86:80,153:0,0:4,3:84.23:5.83:0.00	241:241:195,400:5,6:41,24:231.64:26.17:0.00
21	11187491	rs140494737	CTTATA	C	.	PASS	IC=0;IHP=3;NT=ref;QSI=45;QSI_NT=45;RC=1;RU=TTATA;SGT=ref->het;SOMATIC;TQSI=2;TQSI_NT=2;EFF=INTERGENIC(MODIFIER||||||||||1);RSPOS=11187492;dbSNPBuildID=134;SSR=0;SAO=0;VP=05000000000500000c000200;WGT=1;VC=DIV;ASP;KGPilot123;KGPROD	DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50	16:16:235,403:1,1:1,0:90.52:1.43:0.00	41:41:31,46:3,3:772,1390:303.08:3.60:0.00