-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathhw1.txt
51 lines (33 loc) · 3.04 KB
/
hw1.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
Brief overview of what I did
- Modified the first line in the snakemake to run all 4 samples
SRR2584403_1.fastq.gz
SRR2584404_1.fastq.gz
SRR2584405_1.fastq.gz
SRR2584857_1.fastq.gz
- Changed the ploidy to 1 because E. Coli is the organism
- Ran the snakemake file - it ran
Questions
Which variants are present in which samples?
SRR2584403_1
ecoli 1329520 . T G 225.417 . DP=38;VDB=0.516133;SGB=-0.693143;MQSBZ=-1.51072;MQ0F=0;AC=1;AN=1;DP4=0,0,20,18;MQ=59 GT:PL:AD 1:255,0:0,38
ecoli 4141016 . C A 228.419 . 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=1;AN=1;DP4=0,1,25,18;MQ=58 GT:PL:AD 1:255,0:1,43
SRR2584404_1
ecoli 238917 . G T 225.417 . DP=29;VDB=0.876741;SGB=-0.693054;MQSBZ=0.0515662;MQ0F=0;AC=1;AN=1;DP4=0,0,13,15;MQ=58 GT:PL:AD 1:255,0:0,28
ecoli 806308 . ATT AT 228.317 . 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=1;AN=1;DP4=1,2,11,9;MQ=58 GT:PL:AD 1:255,0:3,20
ecoli 1329520 . T G 225.417 . DP=18;VDB=0.146336;SGB=-0.691153;MQSBZ=0;MQ0F=0;AC=1;AN=1;DP4=0,0,12,6;MQ=60 GT:PL:AD 1:255,0:0,18
ecoli 4141016 . C A 228.417 . 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=1;AN=1;DP4=0,1,19,10;MQ=57 GT:PL:AD 1:255,0:1,29
SRR2584405_1
ecoli 649522 . C T 225.417 . DP=72;VDB=0.039647;SGB=-0.693147;MQSBZ=0;MQ0F=0;AC=1;AN=1;DP4=0,0,35,37;MQ=60 GT:PL:AD 1:255,0:0,72
ecoli 708118 . T C 225.417 . DP=61;VDB=0.00175637;SGB=-0.693147;MQSBZ=-0.270704;MQ0F=0;AC=1;AN=1;DP4=0,0,34,27;MQ=57 GT:PL:AD 1:255,0:0,61
ecoli 1733754 . A T 225.421 . DP=40;VDB=0.521259;SGB=-0.693145;MQSBZ=0;MQ0F=0;AC=1;AN=1;DP4=0,0,23,17;MQ=60 GT:PL:AD 1:255,0:0,39
ecoli 2103887 . ACAGCCAGCCAGCCAGCCAGCCAGCCAGCCAG ACAGCCAGCCAGCCAGCCAGCCAGCCAGCCAGCCAG 225.21 . 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=1;AN=1;DP4=7,3,9,15;MQ=60 GT:PL:AD 1:255,3:10,24
ecoli 3762120 . C A 225.417 . DP=53;VDB=0.818137;SGB=-0.693147;MQSBZ=-0.909718;MQ0F=0;AC=1;AN=1;DP4=0,0,24,29;MQ=59 GT:PL:AD 1:255,0:0,53
SRR2584857_1
ecoli 920514 . T C 225.417 . DP=71;VDB=0.914208;SGB=-0.693147;MQSBZ=-0.760117;MQ0F=0;AC=1;AN=1;DP4=0,0,26,45;MQ=59 GT:PL:AD 1:255,0:0,71
ecoli 3931002 . A C 225.417 . DP=41;VDB=0.11962;SGB=-0.693145;MQSBZ=0;MQ0F=0;AC=1;AN=1;DP4=0,0,22,19;MQ=60 GT:PL:AD 1:255,0:0,41
ecoli 4141441 . C T 225.417 . DP=36;VDB=0.937813;SGB=-0.693139;MQSBZ=0;MQ0F=0;AC=1;AN=1;DP4=0,0,17,19;MQ=60 GT:PL:AD 1:255,0:0,36
ecoli 4202391 . T G 228.397 . 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=1;AN=1;DP4=1,0,27,24;MQ=58 GT:PL:AD 1:255,0:1,51
ecoli 4530767 . CACCCTAACCCT CACCCTAACCCTAACCCT 206.148 . 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=1;DP4=7,12,17,18;MQ=59 GT:PL:AD 1:255,22:19,35
Which variants are shared between two or more samples?
ecoli 1329520
ecoli 4141016