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hw1.txt
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question 1: which variants are present in which samples?
grep -v ^# SRR2584403_1.x.ecoli-rel606.vcf
ecoli 1329520 . T G 225.417 . DP=38;VDB=0.516133;SGB=-0.693143;MQSBZ=-1.51072;MQ0F=0;AC=2;AN=2;DP4=0,0,20,18;MQ=59 GT:PL:AD 1/1:255,114,0:0,38
ecoli 4141016 . C A 228.411 . DP=44;VDB=0.713245;SGB=-0.693146;RPBZ=1.69378;MQBZ=-0.270301;MQSBZ=-0.84038;BQBZ=1.62628;SCBZ=0;MQ0F=0;AC=2;AN=2;DP4=0,1,25,18;MQ=58 GT:PL:AD 1/1:255,116,0:1,43
grep -v ^# SRR2584404_1.x.ecoli-rel606.vcf
ecoli 238917 . G T 225.417 . DP=29;VDB=0.876741;SGB=-0.693054;MQSBZ=0.0515662;MQ0F=0;AC=2;AN=2;DP4=0,0,13,15;MQ=58 GT:PL:AD 1/1:255,84,0:0,28
ecoli 806308 . ATT AT 228.21 . INDEL;IDV=20;IMF=0.869565;DP=23;VDB=0.370777;SGB=-0.692067;RPBZ=-2.73997;MQBZ=-0.560032;MQSBZ=-0.168415;BQBZ=-1.67789;SCBZ=0;MQ0F=0;AC=2;AN=2;DP4=1,2,11,9;MQ=58 GT:PL:AD 1/1:255,29,0:3,20
ecoli 1329520 . T G 225.417 . DP=18;VDB=0.146336;SGB=-0.691153;MQSBZ=0;MQ0F=0;AC=2;AN=2;DP4=0,0,12,6;MQ=60 GT:PL:AD 1/1:255,54,0:0,18
ecoli 4141016 . C A 228.407 . DP=30;VDB=0.615347;SGB=-0.693079;RPBZ=1.67711;MQBZ=-0.391106;MQSBZ=0.473482;BQBZ=1.60122;SCBZ=0;MQ0F=0;AC=2;AN=2;DP4=0,1,19,10;MQ=57 GT:PL:AD 1/1:255,76,0:1,29
grep -v ^# SRR2584405_1.x.ecoli-rel606.vcf
ecoli 15382 . C T 222.227 . DP=98;VDB=1.27393e-33;SGB=-0.693147;RPBZ=-6.63826;MQBZ=-8.40598;MQSBZ=6.09726;BQBZ=0.211317;SCBZ=2.2818;MQ0F=0;AC=1;AN=2;DP4=6,30,46,16;MQ=42 GT:PL:AD 0/1:255,0,247:36,62
ecoli 154497 . T G 6.592 . DP=55;VDB=0.00512227;SGB=-0.692562;RPBZ=2.07156;MQBZ=-4.31459;MQSBZ=5.03012;BQBZ=-4.94013;SCBZ=-0.545895;MQ0F=0;AC=1;AN=2;DP4=2,31,22,0;MQ=54 GT:PL:AD 0/1:40,0,173:33,22
ecoli 254101 . T G 20.4306 . DP=23;VDB=0.0920818;SGB=-0.676189;RPBZ=0.339257;MQBZ=-1.30378;MQSBZ=-0.488364;BQBZ=-0.285851;SCBZ=-0.991863;MQ0F=0;AC=1;AN=2;DP4=0,12,8,3;MQ=53 GT:PL:AD 0/1:53,0,60:12,11
ecoli 649522 . C T 225.417 . DP=72;VDB=0.039647;SGB=-0.693147;MQSBZ=0;MQ0F=0;AC=2;AN=2;DP4=0,0,35,37;MQ=60 GT:PL:AD 1/1:255,217,0:0,72
ecoli 692265 . C T 32.7182 . DP=40;VDB=0.998923;SGB=-0.616816;RPBZ=0.967243;MQBZ=0.420084;MQSBZ=1.29099;BQBZ=1.17368;SCBZ=0.197748;MQ0F=0;AC=1;AN=2;DP4=13,21,2,4;MQ=58 GT:PL:AD 0/1:68,0,255:34,6
ecoli 692268 . A G 29.7603 . DP=40;VDB=0.998923;SGB=-0.616816;RPBZ=0.967562;MQBZ=0.420084;MQSBZ=1.29099;BQBZ=0.957372;SCBZ=0.197748;MQ0F=0;AC=1;AN=2;DP4=13,21,2,4;MQ=58 GT:PL:AD 0/1:65,0,255:34,6
ecoli 708118 . T C 225.417 . DP=61;VDB=0.00175637;SGB=-0.693147;MQSBZ=-0.270704;MQ0F=0;AC=2;AN=2;DP4=0,0,34,27;MQ=57 GT:PL:AD 1/1:255,184,0:0,61
ecoli 1176010 . T G 16.6655 . DP=55;VDB=0.376181;SGB=-0.693021;RPBZ=-0.732797;MQBZ=-2.67939;MQSBZ=2.90557;BQBZ=-3.45783;SCBZ=0.559196;MQ0F=0;AC=1;AN=2;DP4=8,20,27,0;MQ=52 GT:PL:AD 0/1:50,0,181:28,27
ecoli 1503866 . A C 15.018 . DP=83;VDB=0.0860584;SGB=-0.693079;RPBZ=0.587787;MQBZ=-2.0015;MQSBZ=-2.28777;BQBZ=-5.73978;SCBZ=3.72103;MQ0F=0;AC=1;AN=2;DP4=47,7,0,29;MQ=58 GT:PL:AD 0/1:50,0,255:54,29
ecoli 1680445 . A T 222.348 . DP=86;VDB=1;SGB=-0.693141;RPBZ=-1.97766;MQBZ=0.868966;MQSBZ=-1.17851;BQBZ=1.56622;SCBZ=-1.54344;MQ0F=0;AC=1;AN=2;DP4=24,25,26,11;MQ=59 GT:PL:AD 0/1:255,0,255:49,37
ecoli 1680446 . A T 222.348 . DP=86;VDB=1;SGB=-0.693141;RPBZ=-1.93812;MQBZ=0.868966;MQSBZ=-1.17851;BQBZ=1.82724;SCBZ=-1.54344;MQ0F=0;AC=1;AN=2;DP4=24,25,26,11;MQ=59 GT:PL:AD 0/1:255,0,255:49,37
ecoli 1733754 . A T 225.421 . DP=40;VDB=0.521259;SGB=-0.693145;MQSBZ=0;MQ0F=0;AC=2;AN=2;DP4=0,0,23,17;MQ=60 GT:PL:AD 1/1:255,117,0:0,39
ecoli 1996109 . A T 22.4238 . DP=82;VDB=0.66732;SGB=-0.680642;RPBZ=2.41538;MQBZ=-0.234762;MQSBZ=-0.324739;BQBZ=0.717407;SCBZ=0.138758;MQ0F=0.0121951;AC=1;AN=2;DP4=47,23,3,9;MQ=53 GT:PL:AD 0/1:58,0,255:70,12
ecoli 2000253 . A T 20.4058 . DP=64;VDB=0.852145;SGB=-0.662043;RPBZ=-2.35811;MQBZ=0.828534;MQSBZ=0.741887;BQBZ=1.03545;SCBZ=-0.273142;MQ0F=0.03125;AC=1;AN=2;DP4=30,25,6,3;MQ=57 GT:PL:AD 0/1:56,0,255:55,9
ecoli 2020126 . C G 46.5562 . DP=62;VDB=0.99982;SGB=-0.662043;RPBZ=-1.50994;MQBZ=0;MQSBZ=0;BQBZ=1.46551;SCBZ=1.92057;MQ0F=0;AC=1;AN=2;DP4=34,19,5,4;MQ=60 GT:PL:AD 0/1:82,0,255:53,9
ecoli 2103887 . ACAGCCAGCCAGCCAGCCAGCCAGCCAGCCAG ACAGCCAGCCAGCCAGCCAGCCAGCCAGCCAGCCAG 225.773 . INDEL;IDV=24;IMF=0.685714;DP=35;VDB=2.76335e-05;SGB=-0.692831;RPBZ=-3.62517;MQBZ=0;MQSBZ=0;BQBZ=-1.59432;SCBZ=-1.489;MQ0F=0;AC=2;AN=2;DP4=7,3,9,15;MQ=60 GT:PL:AD 1/1:255,0,3:10,24
ecoli 2296329 . A C 24.409 . DP=51;VDB=0.270952;SGB=-0.692976;RPBZ=0.660076;MQBZ=-2.2821;MQSBZ=-2.10929;BQBZ=-5.12719;SCBZ=1.13448;MQ0F=0;AC=1;AN=2;DP4=23,2,0,26;MQ=57 GT:PL:AD 0/1:58,0,195:25,25
ecoli 2330469 . A T 117.729 . DP=58;VDB=1;SGB=-0.680642;RPBZ=-0.894082;MQBZ=0.900217;MQSBZ=-0.689213;BQBZ=0.698571;SCBZ=-0.542792;MQ0F=0;AC=1;AN=2;DP4=23,23,7,5;MQ=59 GT:PL:AD 0/1:152,0,255:46,12
ecoli 2330472 . A T 112.609 . DP=62;VDB=1;SGB=-0.683931;RPBZ=-0.874248;MQBZ=0.906807;MQSBZ=-0.739824;BQBZ=0.20992;SCBZ=-0.72729;MQ0F=0;AC=1;AN=2;DP4=26,23,7,6;MQ=59 GT:PL:AD 0/1:147,0,255:49,13
ecoli 2416966 . C T 6.69011 . DP=38;VDB=0.0246506;SGB=-0.689466;RPBZ=0.843729;MQBZ=-1.35962;MQSBZ=-2.19498;BQBZ=-4.46722;SCBZ=2.30568;MQ0F=0;AC=1;AN=2;DP4=20,2,0,16;MQ=57 GT:PL:AD 0/1:40,0,177:22,16
ecoli 2671373 . T G 10.8815 . DP=65;VDB=0.190636;SGB=-0.662043;RPBZ=3.54286;MQBZ=0.400892;MQSBZ=-0.765092;BQBZ=1.71773;SCBZ=-1.11182;MQ0F=0;AC=1;AN=2;DP4=23,33,1,8;MQ=59 GT:PL:AD 0/1:46,0,255:56,9
ecoli 2671376 . C A 12.0361 . DP=65;VDB=0.190636;SGB=-0.662043;RPBZ=3.38984;MQBZ=0.400892;MQSBZ=-0.765092;BQBZ=1.99791;SCBZ=-1.19815;MQ0F=0;AC=1;AN=2;DP4=23,33,1,8;MQ=59 GT:PL:AD 0/1:47,0,255:56,9
ecoli 2682710 . G C 8.05859 . DP=105;VDB=0.00302672;SGB=-0.693079;RPBZ=-5.61943;MQBZ=-0.288951;MQSBZ=-0.846861;BQBZ=0.626238;SCBZ=-0.480425;MQ0F=0.0761905;AC=1;AN=2;DP4=42,34,25,4;MQ=23 GT:PL:AD 0/1:41,0,240:76,29
ecoli 2682764 . C T 67.9216 . DP=103;VDB=0.261759;SGB=-0.693132;RPBZ=2.76548;MQBZ=1.55818;MQSBZ=-1.26712;BQBZ=-0.918256;SCBZ=2.38156;MQ0F=0.174757;AC=1;AN=2;DP4=41,28,22,12;MQ=15 GT:PL:AD 0/1:101,0,143:69,34
ecoli 3090762 . C A 23.3315 . DP=57;VDB=0.991495;SGB=-0.651104;RPBZ=-2.30026;MQBZ=0.576508;MQSBZ=-1.35357;BQBZ=0.271239;SCBZ=-0.712388;MQ0F=0;AC=1;AN=2;DP4=21,28,6,2;MQ=59 GT:PL:AD 0/1:59,0,255:49,8
ecoli 3090763 . T G 26.309 . DP=58;VDB=0.991495;SGB=-0.651104;RPBZ=-2.19005;MQBZ=0.570626;MQSBZ=-1.33135;BQBZ=0.739817;SCBZ=-0.70501;MQ0F=0;AC=1;AN=2;DP4=21,29,6,2;MQ=59 GT:PL:AD 0/1:62,0,255:50,8
ecoli 3268057 . T C 5.19833 . DP=48;VDB=0.724522;SGB=-0.616816;RPBZ=2.34065;MQBZ=0.540301;MQSBZ=1.2607;BQBZ=3.07099;SCBZ=3.80421;MQ0F=0;AC=1;AN=2;DP4=26,16,1,5;MQ=57 GT:PL:AD 0/1:39,0,255:42,6
ecoli 3351282 . C T 37.7022 . DP=41;VDB=0.000235966;SGB=-0.651104;RPBZ=3.82195;MQBZ=-2.46011;MQSBZ=0.214312;BQBZ=0.800423;SCBZ=4.91969;MQ0F=0;AC=1;AN=2;DP4=12,21,3,5;MQ=53 GT:PL:AD 0/1:73,0,255:33,8
ecoli 3509753 . T C 10.0064 . DP=20;VDB=0.00018837;SGB=-0.651104;RPBZ=-3.36465;MQBZ=1.49071;MQSBZ=-0.366988;BQBZ=-2.34291;SCBZ=0.332106;MQ0F=0;AC=1;AN=2;DP4=9,3,0,8;MQ=53 GT:PL:AD 0/1:43,0,155:12,8
ecoli 3568506 . T G 3.29159 . DP=72;VDB=0.0542204;SGB=-0.693136;RPBZ=1.49557;MQBZ=-1.96715;MQSBZ=2.90095;BQBZ=-6.17398;SCBZ=0.855357;MQ0F=0;AC=1;AN=2;DP4=6,30,35,0;MQ=53 GT:PL:AD 0/1:35,0,236:36,35
ecoli 3762120 . C A 225.417 . DP=53;VDB=0.818137;SGB=-0.693147;MQSBZ=-0.909718;MQ0F=0;AC=2;AN=2;DP4=0,0,24,29;MQ=59 GT:PL:AD 1/1:255,160,0:0,53
ecoli 4029556 . G T 66.2544 . DP=66;VDB=1;SGB=-0.688148;RPBZ=0.796389;MQBZ=-0.674976;MQSBZ=0.193216;BQBZ=-1.68315;SCBZ=0.535148;MQ0F=0;AC=1;AN=2;DP4=25,26,6,9;MQ=58 GT:PL:AD 0/1:101,0,255:51,15
ecoli 4029559 . A C 100.617 . DP=63;VDB=1;SGB=-0.688148;RPBZ=1.09832;MQBZ=-1.29805;MQSBZ=-0.785373;BQBZ=-2.0796;SCBZ=0.399176;MQ0F=0;AC=1;AN=2;DP4=22,26,6,9;MQ=58 GT:PL:AD 0/1:135,0,255:48,15
ecoli 4192865 . G A 52.2799 . DP=39;VDB=8.97585e-05;SGB=-0.636426;RPBZ=-4.11045;MQBZ=0.467707;MQSBZ=0.748331;BQBZ=0.746695;SCBZ=5.26425;MQ0F=0.025641;AC=1;AN=2;DP4=19,13,6,1;MQ=58 GT:PL:AD 0/1:87,0,255:32,7
ecoli 4497049 . T G 4.12806 . DP=29;VDB=0.126368;SGB=-0.683931;RPBZ=-0.345916;MQBZ=-0.586431;MQSBZ=-1.04293;BQBZ=-1.1031;SCBZ=0.30551;MQ0F=0;AC=1;AN=2;DP4=6,9,10,3;MQ=52 GT:PL:AD 0/1:35,0,134:15,13
ecoli 4503866 . T C 19.2253 . DP=239;VDB=0.0269394;SGB=-0.693147;RPBZ=-5.59945;MQBZ=-5.35258;MQSBZ=0.0551777;BQBZ=4.83861;SCBZ=-0.609823;MQ0F=0;AC=1;AN=2;DP4=94,96,39,9;MQ=56 GT:PL:AD 0/1:54,0,255:190,48
ecoli 4504217 . G A 114.964 . DP=248;VDB=0.713416;SGB=-0.693147;RPBZ=-5.64424;MQBZ=-5.24278;MQSBZ=-0.160063;BQBZ=2.41166;SCBZ=3.05912;MQ0F=0;AC=1;AN=2;DP4=77,113,23,35;MQ=57 GT:PL:AD 0/1:149,0,255:190,58
ecoli 4504253 . G A 29.0436 . DP=225;VDB=1;SGB=-0.693145;RPBZ=1.93487;MQBZ=-4.90667;MQSBZ=0.394414;BQBZ=-0.462616;SCBZ=3.22813;MQ0F=0;AC=1;AN=2;DP4=69,114,20,21;MQ=57 GT:PL:AD 0/1:64,0,255:183,41
ecoli 4505396 . T C 87.5131 . DP=119;VDB=0.12252;SGB=-0.692831;RPBZ=2.80551;MQBZ=0.729493;MQSBZ=0.105546;BQBZ=-0.40458;SCBZ=2.63348;MQ0F=0.235294;AC=1;AN=2;DP4=51,44,10,14;MQ=44 GT:PL:AD 0/1:122,0,255:95,24
ecoli 4505407 . G A 34.1722 . DP=117;VDB=0.509928;SGB=-0.692067;RPBZ=2.82456;MQBZ=0.631362;MQSBZ=-0.102815;BQBZ=2.05496;SCBZ=3.12065;MQ0F=0.333333;AC=1;AN=2;DP4=47,50,10,10;MQ=38 GT:PL:AD 0/1:69,0,245:97,20
ecoli 4506070 . A T 21.2129 . DP=135;VDB=1.81827e-09;SGB=-0.692976;RPBZ=-6.88041;MQBZ=3.78966;MQSBZ=-3.67614;BQBZ=0.193852;SCBZ=-0.368429;MQ0F=0.274074;AC=1;AN=2;DP4=52,57,22,4;MQ=41 GT:PL:AD 0/1:55,0,249:109,24
ecoli 4593578 . C T 39.3189 . DP=61;VDB=0.174327;SGB=-0.693141;RPBZ=3.22686;MQBZ=-3.30282;MQSBZ=3.30282;BQBZ=-6.06424;SCBZ=2.55725;MQ0F=0;AC=1;AN=2;DP4=0,23,37,0;MQ=53 GT:PL:AD 0/1:72,0,154:23,37
question 2: which variants are shared between two or more samples?
Variants shared between SRR2584403 and SRR2584404:
ecoli 1329520 . ref:T sample:G
ecoli 4141016 . ref:C sample:A
Variants shared between SRR2584403 and SRR2584405: none
Variants shared between SRR2584404 and SRR2584405: none
Variants shared between SRR2584403 and SRR2584404 and SRR2584405: none