Sample Resequencing Stats
Note: The mutation counts shown below represent unfiltered mutation sets.
| ALE, Flask, Isolate |
Predicted Mutations |
Mean Coverage |
Total Reads |
Percent Mapped |
Mapped Reads |
Average Read Length |
|
A5 F21 I0 R2
|
316 |
65.6 |
5147759 |
97.4% |
5013917 |
60.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,036,407 |
A→G |
40.6% |
E72E (GAA→GAG) |
hyaD → |
protein involved in processing of HyaA and HyaB proteins |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,036,407 | 0 | A | G | 40.6%
| 12.8
/ 36.7
| 32 | E72E (GAA→GAG) | hyaD | protein involved in processing of HyaA and HyaB proteins |
| Reads supporting (aligned to +/- strand): ref base A (8/11); new base G (6/7); total (14/18) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.43e-01 |
GAACTTGCTGGGGTATGTCGAAAGCGCCAGCCATCTGTTGATTCTCGATGCCATTGACTACGGGCTGGAACCTGGAACGCTGCGAACCTATGCCGGAGAACGCATTCCGGCTTATCTCAGCGCGAAGAAAATGAGCC > W3110S.gb/1036338‑1036474
|
gAACTTGCTGGGGTATGTCGAAAGCGCCAGCCATCTGTTGATTCTCGATGCCATTGACTACGGGctggaac > 1:97824/1‑71 (MQ=255)
aaCTTGCTGGGGTATGTCGAAAGCGCCAGCCATCTGTTGATTCTCGATGCCATTGACTACGGGctggagcc < 1:3039944/71‑1 (MQ=255)
aaCTTGCTGGGGTATGTCGAAAGCGCCAGCCATCTGTTGATTCTCGATGCCATTGACTACGGGctggaacc > 1:3694235/1‑71 (MQ=255)
aaCTTGCTGGGGTATGTCGAAAGCGCCAGCCATCTGTTGATTCTCGATGCCATTGACTACGGGctggaacc < 1:4560755/71‑1 (MQ=255)
cTGGGGTATGTCGAAAGCGCCAGCCATCTGTTGATTCTCGATGCCATTGACTACGGGctggagcctggaac < 1:852338/71‑1 (MQ=255)
aTGTCGAAAGCGCCAGCCATCTGTTGATTCTCGATGCCATTGACTACGGGCTGGAACCTGGAACGCTGCg > 1:2491422/1‑70 (MQ=255)
cGAAAGCGCCAGCCATCTGTTGATTCTCGATGCCATTGACTACGGGctggagcc < 1:4683304/54‑1 (MQ=255)
aaaGCGCCAGCCATCTGTTGATTCTCGATGCCATTGACTACGGGCTGGAGCCTGGAACGCTGCGAACCTAt < 1:2614044/71‑1 (MQ=255)
cagccaTCTGTTGATTCTCGATGCCATTGACTACGGGCTGGAACCTGGAACGCTGCGAACCTATGCCGgag < 1:3640306/71‑1 (MQ=255)
cagccaTCTGTTGATTCTCGATGCCATTGACTACGGGCTGGAACCTGGAACGCTGCGAACCTATGCCGgag < 1:5079889/71‑1 (MQ=255)
gccaTCTGTTGATTCTCGATGCCATTGACTACGGGCTGGAACCTGGAACGCTGCGAACCTATGCCGgag < 1:981788/69‑1 (MQ=255)
ttGATTCTCGATGCCATTGACTACGGGCTGGAGCCTGGAACGCTGCGAACCTATGCCGGAGAACGCa < 1:1765559/67‑1 (MQ=255)
ttCTCGATGCCATTGACTACGGGCTGGAGCCTGGAACGCTGCGAACCTATGc < 1:1024935/52‑1 (MQ=255)
ttCTCGATGCCATTGACTACGGGCTGGAAGCTGGAACGCTGCGAACCTATGCCGGAGAACGCATTCCgg < 1:4055398/69‑1 (MQ=255)
tctcGATGCCATTGACTACGGGCTGGAACCTGGAACGCTGCGAACCTATGCCg > 1:1522244/1‑53 (MQ=255)
ctcGATGCCATTGACTACGGGCTGGAGCCTGGAACGCTGCGAACCTATGCCg > 1:3629340/1‑52 (MQ=255)
tagATGCCATTGACTACGGGCTGGAACCTGGAACGCTGCGAACCTATGCCGGAGAACGCAt < 1:3722072/59‑1 (MQ=255)
gATGCCATTGACTACGGGCTGGAACCTGGAACGCTGCGAACCTATGCCGGAGAACGCATTCCGGCTTAtct < 1:4086507/71‑1 (MQ=255)
gATGCCATTGACTACGGGCTGGAACCTGGAACGCTGCGAACCTATGCCGGAGAACGCATTCCGGCTTAt < 1:1531334/69‑1 (MQ=255)
ttGACTACGGGCTGGAGCCTGGAACGCTGCGAACCTATGCCGGAGAACGCATTCCGGCTTAt < 1:4780932/62‑1 (MQ=255)
ttGACTACGGGCTGGAGCCTGGAACGCTGCGAACCTATGCCGGAGAACGCATTCCGGCTTAt < 1:3949182/62‑1 (MQ=255)
ttGACTACGGGCTGGAGCCTGGAACGCTGCGAACCTATGCCGGAGAACGCATTCCGGCTTAt < 1:1747181/62‑1 (MQ=255)
ttGACTACGGGCTGGAGCCTGGAACGCTGCGAACCTATGCCGGAGAACGCATTCCGGCTTATCTCAgcgc > 1:2216212/1‑70 (MQ=255)
ttGACTACGGGCTGGAACCTGGAACGCTGCGAACCTATGCCGGAGAACGCATTCCGGCtt < 1:4361740/60‑1 (MQ=255)
ttGACTACGGGCTGGAACCCGGAACGCTGCGAACCTATGCCGGAGAACGCATTCCGGCtt < 1:2319108/60‑1 (MQ=255)
gACTACGGGCTGGAGCCTGGAACGCTGCGAACCTATGCCGGAGAACGCATTCCGGCTTAtct > 1:3470183/1‑62 (MQ=255)
gACTACGGGCTGGAGCCTGGAACGCTGCGAACCTATGCCGGAGAACGCATTCCGGCTTAtct > 1:2971995/1‑62 (MQ=255)
gACTACGGGCTGGAACCTGGAACGCTGCGAACCTa > 1:3579495/1‑35 (MQ=255)
gACTACGGGCTGGAACCTGGAACGCTGCGAACCTAt > 1:2935113/1‑36 (MQ=255)
gACTACGGGCTGGAACCTGGAACGCTGCGAACCTAt > 1:1084614/1‑36 (MQ=255)
gACTACGGGCTGGAACCTGGAACGCTGCGAACCTATGCCGGAGAACGCATTCCGGCTTATCTCAGcgcg > 1:4912019/1‑69 (MQ=255)
cGGGCTGGAGCCTGGAACGCTGCGAACCTATGCCGGAGaa > 1:4144501/1‑40 (MQ=255)
cGGGCTGGAGCCTGGAACGCTGCGAACCTATGCCGGAGaa > 1:122974/1‑40 (MQ=255)
cGGGCTGGAGCCTGGAACGCTGCGAACCTATGCCGGAGAACGCATTCCGGCTTATCTCAGCGCGAAGaaa < 1:147975/70‑1 (MQ=255)
cGGGCTGGAACCTGGAACGCTGCGAACCTATGCCGGAGAACGCATTCCGGCTTATCTCAGCGCGAAGaaaa > 1:3552566/1‑71 (MQ=255)
cGGGCTGGAACCTGGAACGCTGCGAACCTATGCCGGAGAACGCATTCCGGCTTATCTCAGCGCGAAGaaaa > 1:3148237/1‑71 (MQ=255)
cGGGCTGGAACCTGGAACGCTGCGAACCTATGCCGGAGAACGCATTCCGGCTTATCTCAGCGCGAAGaaa < 1:3957175/70‑1 (MQ=255)
cGGGCTGGAACCTGGAACGCTGCGAACCTATGCCGGAGAACGCATTCCGGCTTATCTCAGCGCGAAGaaa < 1:92747/70‑1 (MQ=255)
ctggagcctggaacGCTGCGAACCTATGCCGGAGAACGCATTCCGGCTTATCTCAGCGCGAAGAAAATGAg < 1:2117719/71‑1 (MQ=255)
ggaacctggaacGCTGCGAACCTATGCCGGAGAACGCATTCCGGCTTATCTCAGCGCGAAGAAAATGAGcc > 1:2609225/1‑71 (MQ=255)
|
GAACTTGCTGGGGTATGTCGAAAGCGCCAGCCATCTGTTGATTCTCGATGCCATTGACTACGGGCTGGAACCTGGAACGCTGCGAACCTATGCCGGAGAACGCATTCCGGCTTATCTCAGCGCGAAGAAAATGAGCC > W3110S.gb/1036338‑1036474
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
