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hw1.txt
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Lei Wei
1.30.25
DUE: Feb 5th, 2025, 12 Noon
GGG 210B Lab HW1
Answer the following homework questions in this file:
- which variants are present in which samples?
- which variants are shared between two or more samples?
Name variants by location and give both the reference and sample alleles as in the VCF file.
Two SNPs are sShared between SRR2584403_1 and SRR2584404_1 --
----ecoli 1329520 . T G 225.417 .
----ecoli 4141016 . C A 228.407 .
Compared to reference genome,
- SRR2584857_1 has 5 variants (4 SNPs and one Indel):
----ecoli 920514 . T C 225.417 .
----ecoli 3931002 . A C 225.417 .
----ecoli 4141441 . C T 225.417 .
----ecoli 4202391 . T G 228.366 .
----ecoli 4530767 . CACCCTAACCCT CACCCTAACCCTAACCCT 219.016 .
- SRR2584403_1 has 2 variants: (2 SNPs)
----ecoli 1329520 . T G 225.417 .
----ecoli 4141016 . C A 228.411 .
- SRR2584404_1 has 4 variants: (3 SNPs + one INDEL)
----ecoli 238917 . G T 225.417 .
----ecoli 806308 . ATT AT 228.21 .
----ecoli 1329520 . T G 225.417 .
----ecoli 4141016 . C A 228.407 .
- SRR2584405_1 has 42 variants:
----ecoli 15382 . C T 222.227 .
----ecoli 154497 . T G 6.592 .
----ecoli 254101 . T G 20.4306 .
----ecoli 649522 . C T 225.417 .
----ecoli 692265 . C T 32.7182 .
----ecoli 692268 . A G 29.7603 .
----ecoli 708118 . T C 225.417 .
----ecoli 1176010 . T G 16.6655 .
----ecoli 1503866 . A C 15.018 .
----ecoli 1680445 . A T 222.348 .
----ecoli 1680446 . A T 222.348 .
----ecoli 1733754 . A T 225.421 .
----ecoli 1996109 . A T 22.4238 .
----ecoli 2000253 . A T 20.4058 .
----ecoli 2020126 . C G 46.5562 .
----ecoli 2103887 . ACAGCCAGCCAGCCAGCCAGCCAGCCAGCCAG ACAGCCAGCCAGCCAGCCAGCCAGCCAGCCAGCCAG 225.773 .
----ecoli 2296329 . A C 24.409 .
----ecoli 2330469 . A T 117.729 .
----ecoli 2330472 . A T 112.609 .
----ecoli 2416966 . C T 6.69011 .
----ecoli 2671373 . T G 10.8815 .
----ecoli 2671376 . C A 12.0361 .
----ecoli 2682710 . G C 8.05859 .
----ecoli 2682764 . C T 67.9216 .
----ecoli 3090762 . C A 23.3315 .
----ecoli 3090763 . T G 26.309 .
----ecoli 3268057 . T C 5.19833 .
----ecoli 3351282 . C T 37.7022 .
----ecoli 3509753 . T C 10.0064 .
----ecoli 3568506 . T G 3.29159 .
----ecoli 3762120 . C A 225.417 .
----ecoli 4029556 . G T 66.2544 .
----ecoli 4029559 . A C 100.617 .
----ecoli 4192865 . G A 52.2799 .
----ecoli 4497049 . T G 4.12806 .
----ecoli 4503866 . T C 19.2253 .
----ecoli 4504217 . G A 114.964 .
----ecoli 4504253 . G A 29.0436 .
----ecoli 4505396 . T C 87.5131 .
----ecoli 4505407 . G A 34.1722 .
----ecoli 4506070 . A T 21.2129 .
----ecoli 4593578 . C T 39.3189 .
******************************************************************************
Terminal Output:
******************************************************************************
(mapping) lwei1123@cpu-3-57:~/2025-ggg-201b-hw1-lwei-2203$ grep -v ^# outputs/SRR2584857_1.x.ecoli-rel606.vcf
ecoli 920514 . T C 225.417 . DP=71;VDB=0.914208;SGB=-0.693147;MQSBZ=-0.760117;MQ0F=0;AC=2;AN=2;DP4=0,0,26,45;MQ=59GT:PL:AD 1/1:255,214,0:0,71
ecoli 3931002 . A C 225.417 . DP=41;VDB=0.11962;SGB=-0.693145;MQSBZ=0;MQ0F=0;AC=2;AN=2;DP4=0,0,22,19;MQ=60 GT:PL:AD 1/1:255,123,0:0,41
ecoli 4141441 . C T 225.417 . DP=36;VDB=0.937813;SGB=-0.693139;MQSBZ=0;MQ0F=0;AC=2;AN=2;DP4=0,0,17,19;MQ=60 GT:PL:AD 1/1:255,108,0:0,36
ecoli 4202391 . T G 228.366 . DP=53;VDB=0.0318119;SGB=-0.693147;RPBZ=-1.69975;MQBZ=-0.247306;MQSBZ=-0.772136;BQBZ=1.62703;SCBZ=0;MQ0F=0;AC=2;AN=2;DP4=1,0,27,24;MQ=58 GT:PL:AD 1/1:255,131,0:1,51
ecoli 4530767 . CACCCTAACCCT CACCCTAACCCTAACCCT 219.016 . INDEL;IDV=35;IMF=0.636364;DP=55;VDB=0.00042381;SGB=-0.693136;RPBZ=-2.77437;MQBZ=1.32288;MQSBZ=-0.894427;BQBZ=-2.43136;SCBZ=-3.29556;MQ0F=0;AC=1;AN=2;DP4=7,12,17,18;MQ=59 GT:PL:AD 0/1:255,0,22:19,35
(mapping) lwei1123@cpu-3-57:~/2025-ggg-201b-hw1-lwei-2203$ grep -v ^# outputs/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
(mapping) lwei1123@cpu-3-57:~/2025-ggg-201b-hw1-lwei-2203$ grep -v ^# outputs/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=58GT: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
(mapping) lwei1123@cpu-3-57:~/2025-ggg-201b-hw1-lwei-2203$ grep -v ^# outputs/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=59GT: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