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 R1
|
148 |
22.8 |
1772010 |
97.0% |
1718849 |
61.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,532,412 |
T→C |
40.0% |
M236T (ATG→ACG) |
cpxA → |
sensory histidine kinase in two‑component regulatory system with CpxR |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,532,412 | 0 | T | C | 40.0%
| 4.5
/ 13.0
| 15 | M236T (ATG→ACG) | cpxA | sensory histidine kinase in two‑component regulatory system with CpxR |
| Reads supporting (aligned to +/- strand): ref base T (6/3); new base C (3/3); total (9/6) |
| Fisher's exact test for biased strand distribution p-value = 6.22e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TCCTTGCCGCAGGTGCCAGTTTTAACCAGATGGTCACCGCGCTGGAGCGCATGATGACCTCTCAGCAGCGTCTGCTTTCTGATATCTCTCACGAGCTGCGCACCCCGCTGACGCGTCTGCAACTG > W3110S.gb/3532358‑3532482
|
tCCTTGCCGCAGGTGCCAGTTTTAACCAGATGGTCACCGCGCTGGAGCGCATGATGACCTCTCAGCAGCGt > 1:1639641/1‑71 (MQ=255)
ccTTGCCGCAGGTGCCAGTTTTAACCAGATGGTCACCGCGCTGGAGCGCatgat > 1:1208448/1‑54 (MQ=255)
cTTGCCGCAGGTGCCAGTTTTAACCAGATGGTCACCGCGCTGGAGCGCATGATGACCTCTCAGCAGCGTCt < 1:1376507/71‑1 (MQ=255)
cTTGCCGCAGGTGCCAGTTTTAACCAGATGGTCACCGCGCTGGAGCGCATGACGACCTCTCagcagc < 1:168053/67‑1 (MQ=255)
cTTGCCGCAGGTGCCAGTTTTAACCAGATGGTCACCGCGCTGGAGCGCATGACGACCTCTCagcagc < 1:1733258/67‑1 (MQ=255)
gCCGCAGGTGCCAGTTTTAACCAGATGGTCACCGCGCTGGAGCGCATGATGACCTCTCAGCAGCGTCTGCt > 1:519316/1‑71 (MQ=255)
gCCGCAGGTGCCAGTTTTAACCAGATGGTCACCGCGCTGGAGCGCATGACGACCTCTCAGCAGCGTCTGCt > 1:55780/1‑71 (MQ=255)
cAGGTGCCAGTTTTAACCAGATTGTCACCGCGCTGGAGCGCATGACGACCTCTCAGCAGCGTCTGCTTTCt < 1:954194/71‑1 (MQ=255)
aGTTTTAACCAGATGGTCACCGCGCTGGAGCGCATGATGTCCTCTCAGCAGCGTCTGCTTTCTGATAtctc > 1:1289214/1‑71 (MQ=255)
tttAACCAGATGGTCACCGCGCTGGAGCGCATGATGACCtctc > 1:1459029/1‑43 (MQ=255)
tttAACCAGATGGTCACCGCGCTGGAGCGCATGACTACCtctc > 1:174769/1‑43 (MQ=38)
ttAACCAGATGGTCACCGCGCTGGAGCGCATGACGACCTCTCAGCAGCGTCTGCt > 1:1215962/1‑55 (MQ=255)
gATGGTCACCGCGCTGGAGCGCATGATGACCTCTCAGCAGCGTCTGCTTTCTGATATCTCTCACGAGCTgc > 1:1177490/1‑71 (MQ=255)
cgcTGGAGCGCATGATGACCTCTCAGCAGCGTCTGCTTTCTGat < 1:1197089/44‑1 (MQ=255)
cgcTGGAGCGCATGATGACCTCTCAGCAGCGTCTGCTTTCTGat < 1:395264/44‑1 (MQ=255)
gcgcATGATGACCTCTCAGCAGCGTCTGCTTTCTGATATCTCTCACGAGCTGCGCACCCCGCTGACGCGTc > 1:1576587/1‑71 (MQ=255)
tgaCCTCTCAGCAGCGTCTGCTTTCTGATATCTCTCACGAGCTGCGCACCCCGCTGACGCGTCTGCAACTg < 1:1630223/71‑1 (MQ=255)
|
TCCTTGCCGCAGGTGCCAGTTTTAACCAGATGGTCACCGCGCTGGAGCGCATGATGACCTCTCAGCAGCGTCTGCTTTCTGATATCTCTCACGAGCTGCGCACCCCGCTGACGCGTCTGCAACTG > W3110S.gb/3532358‑3532482
|
| 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
