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 |
|
A2 F17 I0 R2
|
278 |
43.2 |
2215644 |
94.6% |
2095999 |
61.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,283,783 |
G→T |
14.2% |
L39M (CTG→ATG) |
oxyR ← |
DNA‑binding transcriptional dual regulator |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,283,783 | 0 | G | T | 14.2%
| 143.4
/ 6.5
| 49 | L39M (CTG→ATG) | oxyR | DNA‑binding transcriptional dual regulator |
| Reads supporting (aligned to +/- strand): ref base G (21/21); new base T (3/4); total (24/25) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.97e-01 |
TTCCCGCCTGGGTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATCTGCCGCACGCCGAAAAT > minE/2283714‑2283848
|
ttCCCGCCTGGGTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGc > 1:1682939/1‑71 (MQ=255)
cccGCCTGGGTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCATCt > 1:1638856/1‑70 (MQ=255)
gCCTGGGTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTAc > 1:398796/1‑70 (MQ=255)
cTGGGTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGaa < 1:1179213/71‑1 (MQ=255)
cTGGGTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGaa < 1:1551630/71‑1 (MQ=255)
cTGGGTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGaa < 1:102755/71‑1 (MQ=255)
gggTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACg < 1:1485762/67‑1 (MQ=255)
gggTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACg < 1:1691707/67‑1 (MQ=255)
gggTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGaa < 1:1238530/69‑1 (MQ=255)
acaacaCTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCATCTTACGAATTTGCCCg < 1:569865/71‑1 (MQ=255)
acacTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCt > 1:2029710/1‑70 (MQ=255)
acTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGc > 1:1281624/1‑51 (MQ=255)
acTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAg > 1:45023/1‑71 (MQ=255)
cTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGc > 1:1673220/1‑71 (MQ=255)
tttAAGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCATCTTACGAATTTGCCCGCTAAGCg > 1:2136686/1‑71 (MQ=255)
tACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGaa > 1:1837849/1‑54 (MQ=255)
tACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAAtt > 1:640498/1‑56 (MQ=255)
ctgCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCg < 1:1887100/68‑1 (MQ=255)
cGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCg < 1:9633/70‑1 (MQ=255)
tGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACg < 1:962364/46‑1 (MQ=255)
cGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAAtt > 1:217586/1‑45 (MQ=255)
cGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTaa < 1:197629/70‑1 (MQ=255)
cGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAAc < 1:1547913/71‑1 (MQ=255)
gCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACg < 1:737376/71‑1 (MQ=255)
cTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGt < 1:199313/71‑1 (MQ=255)
cAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTgg < 1:1894254/70‑1 (MQ=255)
gCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGc > 1:103891/1‑41 (MQ=255)
aaCATCACGCCCAGCTCATCTTCCATCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGa < 1:1316241/71‑1 (MQ=255)
aaCATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAgg > 1:1009171/1‑70 (MQ=255)
aaCATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGa < 1:1286993/71‑1 (MQ=255)
cATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTaa < 1:1878675/44‑1 (MQ=255)
aTCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATc > 1:1536426/1‑71 (MQ=255)
cACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATCTg > 1:2197826/1‑71 (MQ=255)
aCGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATCTGc > 1:798452/1‑71 (MQ=255)
cccAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATCTGCCg > 1:983111/1‑70 (MQ=255)
ccAGCTCATCTTCCATCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATCTGCCGCa < 1:295551/71‑1 (MQ=255)
gCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAgg < 1:1884211/57‑1 (MQ=255)
cTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAgg < 1:42843/56‑1 (MQ=255)
cTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAgg < 1:1450385/56‑1 (MQ=255)
cATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATCTGCCGCACGCCg > 1:1997078/1‑70 (MQ=255)
aTCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATCTGCCGCACGCCGa < 1:1109367/70‑1 (MQ=255)
tCTTCCATCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTgg < 1:1983665/48‑1 (MQ=255)
tCTTCCATCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATCTGCCGAACGCCGaa > 1:347989/1‑70 (MQ=255)
cTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATCTGCCGCACGCCGaaaa > 1:906740/1‑71 (MQ=255)
ttCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTaa > 1:1928930/1‑41 (MQ=255)
ttCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAAt > 1:1936503/1‑53 (MQ=255)
ttCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAAt > 1:700910/1‑53 (MQ=255)
ttCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATCTGCCGCACGCCGAAAAt > 1:839558/1‑71 (MQ=255)
cAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATCTGCCGCACGCCGaaa < 1:1597717/66‑1 (MQ=255)
|
TTCCCGCCTGGGTGAACAACACTTTACGGCTGGTCCGCTCCAGCAACATCACGCCCAGCTCATCTTCCAGCTTACGAATTTGCCCGCTAAGCGTCGGCTGGCTAACGTGGCAGGAATCTGCCGCACGCCGAAAAT > minE/2283714‑2283848
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
