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 |
|
A6 F21 I0 R1
|
2169 |
63.0 |
3952800 |
76.2% |
3012033 |
62.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,714,607 |
C→A |
21.9% |
L275L (CTG→CTT) |
yphG ← |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,714,607 | 0 | C | A | 21.9%
| 120.4
/ 17.7
| 50 | L275L (CTG→CTT) | yphG | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base C (22/17); new base A (7/4); total (29/21) |
| Fisher's exact test for biased strand distribution p-value = 7.41e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.89e-01 |
GCCAAATTCACTGTGTCCCCAACTCCACTGTTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCGTACTGCGATTTTTCGGCCATA > minE/1714541‑1714673
|
gCCAAATTCACTGTGTCCCCAACTCCACTGTTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTgcagc > 1:3196770/1‑70 (MQ=255)
gCCAAATTCACTGTGTCCCCAACTCCACTGTTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTgcag > 1:2278071/1‑69 (MQ=255)
ccAAATTCACTGTGTCCCCAACTCCACTGTTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTgaagca > 1:1571722/1‑70 (MQ=255)
cAAATTCACTGTGTCCCCAACTCCACTGTTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCaaa < 1:1016785/71‑1 (MQ=255)
aaaTTCACTGTGTCCCCAACTCCACTGTTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCAAAc < 1:581484/71‑1 (MQ=255)
aTTCACTGTGTCCCCAACTCCACTGTTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGAAGCAAACCg > 1:294347/1‑71 (MQ=255)
cACTGTGTCCCCAACTCCACTGTTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTgcag > 1:1372064/1‑61 (MQ=255)
cACTGTGTCCCCAACTCCACTGTTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCAAACCGcc < 1:1972205/70‑1 (MQ=255)
cTGTGTCCCCAACTCCACTGTTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGAAGCaaa > 1:116721/1‑63 (MQ=255)
tgtgTCCCCAACTCCACTGTTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCAAACCGCCATCt > 1:346090/1‑71 (MQ=255)
gtgtCCCCAACTCCACTGTTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCAAACCGCCATCtt > 1:620312/1‑71 (MQ=255)
tgtCCCCAACTCCACTGTTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCAAACCGCCATCtt > 1:965002/1‑70 (MQ=255)
tgtCCCCAACTCCACTGTTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCAAACCGCCATCt < 1:2744827/69‑1 (MQ=255)
gtCCCCAACTCCACTGTTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCAAACCGCCATCTTCa > 1:1700383/1‑71 (MQ=255)
cACTGTTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGAcacc < 1:670422/70‑1 (MQ=255)
cACTGTTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGAAGCAAACCGCCAt > 1:2164881/1‑55 (MQ=255)
aCTGTTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGAcacca > 1:3523313/1‑70 (MQ=255)
cTGTTTTTTACCTGGCGCAATATGGTGGTTGTCAACGTGCAGCAAACCGCCATCTTCATCGTGACACCAcg < 1:449969/71‑1 (MQ=255)
cTGTTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGAcacca > 1:434209/1‑69 (MQ=255)
cTGTTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGACACCAcg > 1:1994196/1‑71 (MQ=255)
ttttttACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCaaa > 1:3949273/1‑43 (MQ=255)
ttttttACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGac > 1:3243988/1‑62 (MQ=255)
ttttttACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGACACCACgcgc > 1:3658265/1‑71 (MQ=255)
ttttttACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGACACCACgcgc > 1:2758876/1‑71 (MQ=255)
ttttACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGcc > 1:2361784/1‑70 (MQ=255)
ggCGCAATATGGTGGTTGGCAACGTGAAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATc > 1:2004903/1‑71 (MQ=255)
gcgcAATATGGTGGTTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCg < 1:3075844/71‑1 (MQ=255)
gcgcAATATGGTGGTTGGCAACGTGAAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCg < 1:2767864/71‑1 (MQ=255)
cgcAATATGGTGGTTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCg < 1:3306513/70‑1 (MQ=255)
cgcAATATGGTGGTTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCg > 1:2758112/1‑70 (MQ=255)
cgcAATATGGTGGTTGGCAACGTGAAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCg > 1:2135219/1‑70 (MQ=255)
cgcAATATGGTGGTTGGCAACGTGAAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCg > 1:2455152/1‑70 (MQ=255)
gcAATATGGTGGTTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCGTa < 1:2433591/71‑1 (MQ=255)
atatGGTGGTTGGCAACGTTAAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACaaa < 1:3306881/62‑1 (MQ=255)
atatGGTGGTTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCGTACTg > 1:1192774/1‑71 (MQ=255)
atatGGTGGTTGGCAACGTGAAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACaaa < 1:2150719/62‑1 (MQ=255)
tggtggTTGGCAACGTGAAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCGTACTGCg < 1:1487932/70‑1 (MQ=255)
ggtggtTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCGTACTGCGAt > 1:142981/1‑71 (MQ=255)
gtggtTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCGTACTGCGAt < 1:3478107/70‑1 (MQ=255)
ggtTGGCAACGTGAAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCGTACTGCGAtttt > 1:2508574/1‑71 (MQ=255)
gtTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCGTACTGCGAttttt < 1:1176103/71‑1 (MQ=255)
tGGCAACGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCGTACTGCGAttt < 1:1497518/67‑1 (MQ=255)
gCAACGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCGTa > 1:3203840/1‑56 (MQ=255)
gCAACGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCGTACTGCGATTTTTCGGc > 1:2039694/1‑71 (MQ=255)
aaCGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCGTACTGCGATTTTTc < 1:3696889/66‑1 (MQ=255)
aCGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACa < 1:2452475/45‑1 (MQ=255)
aCGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCGTACTGCGATTTTTc > 1:2597831/1‑65 (MQ=255)
aCGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCGTACTGCGATTTTTc > 1:905231/1‑65 (MQ=255)
aCGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCGTACTGCGATTTTTCGGCCat < 1:1548109/71‑1 (MQ=255)
aCGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCGTACTGCGATTTTTCGGCCa > 1:534611/1‑70 (MQ=255)
aCGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCGTACTGCGATTTTTCGGCCa > 1:930037/1‑70 (MQ=255)
cGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCGTACTGCGATTTTTCGGCCata > 1:3030141/1‑71 (MQ=255)
cGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCGTACTGCGATTTTTCGGCCata < 1:2318861/71‑1 (MQ=255)
gTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCg < 1:75113/49‑1 (MQ=255)
|
GCCAAATTCACTGTGTCCCCAACTCCACTGTTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCGTACTGCGATTTTTCGGCCATA > minE/1714541‑1714673
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
