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 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
374,053 |
G→T |
24.9% |
R301R (CGG→CGT) |
fepE → |
regulator of length of O‑antigen component of lipopolysaccharide chains |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 374,053 | 0 | G | T | 24.9%
| 116.6
/ 30.9
| 72 | R301R (CGG→CGT) | fepE | regulator of length of O‑antigen component of lipopolysaccharide chains |
| Reads supporting (aligned to +/- strand): ref base G (14/40); new base T (15/3); total (29/43) |
| Fisher's exact test for biased strand distribution p-value = 3.93e-05 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
ACGCAAACTGGAAATAGAAAAAGCGGTCACTGACGTTGCGGAACTGAACGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAATTTTACGCCGTTTAAATATC > minE/373987‑374120
|
aCGCAAACTGGAAATAGAAAAAGCGGTCACTGACGTTGCGGAACTGAACGGTGAATTACGTAATCGGc < 1:776078/68‑1 (MQ=255)
aCGCAAACTGGAAATAGAAAAAGCGGTCACTGACGTTGCGGAACTGAACGGTGAATTACGTAATCGGc < 1:3296176/68‑1 (MQ=255)
cGCAAACTGGAAATAGAAAAAGCGGTCACTGACGTTGCGGAACTGAACGGTGAATTACGTAATCGGCAg < 1:2231052/69‑1 (MQ=255)
aaCTGGAAATAGAAAAAGCGGTCACTGACGTTGCGGAACTGAACGGTGAATTACGTAATCGGCAGTATc < 1:936569/69‑1 (MQ=255)
aaCTGGAAATAGAAAAAGCGGTCACTGACGTTGCGGAACTGAACGGTGAATTACGTAATCGGCAGTATc < 1:2420005/69‑1 (MQ=255)
aaCTGGAAATAGAAAAAGCGGTCACTGACGTTGCGGAACTGAACGGTGAATTACGTAATCGGCAGTATc < 1:2901733/69‑1 (MQ=255)
aaCTGGAAATAGAAAAAGCGGTCACTGACGTTGCGGAACTGAACGGTGAATTACGTAATCGGCAGTATc < 1:2978027/69‑1 (MQ=255)
aaCTGGAAATAGAAAAAGCGGTCACTGACGTTGCGGAACTGAACGGTGAATTACGTAATCGGCAGTATc < 1:307886/69‑1 (MQ=255)
aaCTGGAAATAGAAAAAGCGGTCACTGACGTTGCGGAACTGAACGGTGAATTACGTAATCGGCAGTATc < 1:327101/69‑1 (MQ=255)
aCTGGAAATAGAAAAAGCGGTCACTGACGTTGCGGAACTGAACGGTGAATTACGTAATCGGCAGTATc < 1:84291/68‑1 (MQ=255)
aCTGGAAATAGAAAAAGCGGTCACTGACGTTGCGGAACTGAACGGTGAATTACGTAATCGGCAGTATc < 1:1460531/68‑1 (MQ=255)
tGGAAATAGAAAAAGCGGTCACTGACGTTGCGGAACTGAACGGTGAATTATGTAATCGGCAGTATCTTg < 1:1221410/69‑1 (MQ=255)
tGGAAATAGAAAAAGCGGTCACTGACGTTGCGGAACTGAACGGTGAATTACGTAATCGGCAGTATCTTg < 1:2254241/69‑1 (MQ=255)
tGGAAATAGAAAAAGCGGTCACTGACGTTGCGGAACTGAACGGTGAATTACGTAATCGGCAGTATCTTg < 1:2816177/69‑1 (MQ=255)
tGGAAATAGAAAAAGCGGTCACTGACGTTGCGGAACTGAACGGTGAATTACGTAATCGGCAGTATCTTg < 1:322627/69‑1 (MQ=255)
tGGAAATAGAAAAAGCGGTCACTGACGTTGCGGAACTGAACGGTGAATTACGTAATCGGCAGTATCTTg < 1:1541267/69‑1 (MQ=255)
tGGAAATAGAAAAAGCGGTCACTGACGTTGCGGAACTGAACGGTGAATTACGTAATCGGCAGTATCTTg < 1:1463102/69‑1 (MQ=255)
aaaGCGGTCACTGACGTTGCGGAACTGAACGGTGAATTACGTAATCgg < 1:152205/48‑1 (MQ=255)
aaaGCGGTCACTGACGTTGCGGAACTGAACGGTGAATTACGTAATCgg < 1:556089/48‑1 (MQ=255)
aaaGCGGTCACTGACGTTGCGGAACTGAACGGTGAATTACGTAATCgg < 1:1472670/48‑1 (MQ=255)
aaaGCGGTCACTGACGTTGCGGAACTGAACGGTGAATTACGTAATCgg < 1:2935222/48‑1 (MQ=255)
aaaGCGGTCACTGACGTTGCGGAACTGAACGGTGAATTACGTAATCgg < 1:228541/48‑1 (MQ=255)
aaaGCGGTCACTGACGTTGCGGAACTGAACGGTGAATTACGTAATCgg < 1:2302954/48‑1 (MQ=255)
aaaGCGGTCACTGACGTTGCGGAACTGAACGGTGAATTACGTAATCgg < 1:1054172/48‑1 (MQ=255)
aaaGCGGTCACTGACGTTGCGGAACTGAACGGTGAATTACGTAATCgg < 1:2171072/48‑1 (MQ=255)
aaaGCAGTCACTGACGTTGCGGAATTGAACGGTGAATTACGTAATCGTCAGTATCTAGTCGAGCAAtt > 1:2566120/1‑68 (MQ=255)
aaaGCAGTCACTGACGTTGCGGAATTGAACGGTGAATTACGTAATCGTCAGTATCTAGTCGAGCAAtt > 1:999151/1‑68 (MQ=255)
aaaGCAGTCACTGACGTTGCGGAATTGAACGGTGAATTACGTAATCGTCAGTATCTAGTCGAGCAAtt > 1:69747/1‑68 (MQ=255)
aaaGCAGTCACTGACGTTGCGGAATTGAACGGTGAATTACGTAATCGTCAGTATCTAGTCGAGCAAtt > 1:281772/1‑68 (MQ=255)
aaaGCAGTCACTGACGTTGCGGAATTGAACGGTGAATTACGTAATCGTCAGTATCTAGTCGAGCAAtt > 1:570703/1‑68 (MQ=255)
aaaGCAGTCACTGACGTTGCGGAATTGAACGGTGAATTACGTAATCGTCAGTATCTAGTCGAGCAAtt > 1:3068431/1‑68 (MQ=255)
aaaGCAGTCACTGACGTTGCGGAATTGAACGGTGAATTACGTAATCGTCAGTATCTAGTCGAGCAAtt > 1:3330600/1‑68 (MQ=255)
aaaGCAGTCACTGACGTTGCGGAATTGAACGGTGAATTACGTAATCGTCAGTATCTAGTCGAGCAAtt > 1:1639395/1‑68 (MQ=255)
aaaGCAGTCACTGACGTTGCGGAATTGAACGGTGAATTACGTAATCGTCAGTATCTAGTCGAGCAAtt > 1:1081348/1‑68 (MQ=255)
aaaGCAGTCACTGACGTTGCGGAATTGAACGGTGAATTACGTAATCGTCAGTATCTAGTCGAGCAAtt > 1:1469637/1‑68 (MQ=255)
aaaGCAGTCACTGACGTTGCGGAATTGAACGGTGAATTACGTAATCGTCAGTATCTAGTCGAGCAAtt > 1:164307/1‑68 (MQ=255)
aaaGCAGTCACTGACGTTGCGGAATTGAACGGTGAATTACGTAATCGTCAGTATCTAGTCGAGCAAtt > 1:2046198/1‑68 (MQ=255)
aaaGCAGTCACTGACGTTGCGGAATTGAACGGTGAATTACGTAATCGTCAGTATCTAGTCGAGCAAtt > 1:2164767/1‑68 (MQ=255)
aaaGCAGTCACTGACGTTGCGGAATTGAACGGTGAATTACGTAATCGTCAGTATCTAGTCGAGCAAt > 1:3224672/1‑67 (MQ=255)
aaaGCAGTCACTGACGTTGCGGAATTGAACGGTGAATTACGTAATCGTCAGTATCTAGTCGAGCAAt > 1:2823020/1‑67 (MQ=255)
aaGCGGTCACTGACGTTGCGGAACTGAACGGTGAATTACGTAATCgg < 1:3092971/47‑1 (MQ=255)
aCTGACGTTGCGGAACTGAACGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGca < 1:421085/69‑1 (MQ=255)
aCTGACGTTGCGGAACTGAACGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGca < 1:1633945/69‑1 (MQ=255)
aCTGACGTTGCGGAACTGAACGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGca < 1:3069638/69‑1 (MQ=255)
aCTGACGTTGCGGAACTGAACGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGca < 1:2906146/69‑1 (MQ=255)
cTGACGTTGCGGAACTGAACGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGca < 1:877622/68‑1 (MQ=255)
cTGACGTTGCGGAACTGAACGGCGAATTACGTAATCGGCATTATCTTGTCGAGCAATTAACAAAAGca < 1:3330849/68‑1 (MQ=255)
tGACGTTGCGGAACTGAACGGTGAATTACGTAATCGGCATTATCTTGTCGAGCAATTAACAAAAGca < 1:2455814/67‑1 (MQ=255)
gCGGAACTGAACGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAAtt < 1:2196004/50‑1 (MQ=255)
aattGAACGGTGAATTACGTAATCGTCAGTATCTAGTCGAGCAATTAACAAAAACAAATATCAACGAtg < 1:293724/66‑1 (MQ=255)
aattGAACGGTGAATTACGTAATCGTCAGTATCTAGTCGAGCAATTAACAAAAACAAATATCAACGAtg < 1:1984409/66‑1 (MQ=255)
gAACGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGaa > 1:42469/1‑69 (MQ=255)
gAACGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGaa > 1:1681594/1‑69 (MQ=255)
gAACGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGaa > 1:1630811/1‑69 (MQ=255)
gAACGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGaa > 1:2241079/1‑69 (MQ=255)
gAACGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGaa > 1:828126/1‑69 (MQ=255)
gAACGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATCTCAACGATGTGa > 1:991840/1‑68 (MQ=255)
cGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt < 1:2290931/69‑1 (MQ=255)
cGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt < 1:2344100/69‑1 (MQ=255)
cGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt < 1:1511416/69‑1 (MQ=255)
cGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt < 1:783135/69‑1 (MQ=255)
cGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt < 1:1984204/69‑1 (MQ=255)
cGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt < 1:2945646/69‑1 (MQ=255)
ggTGAATTACGTAATCGTCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt < 1:571464/68‑1 (MQ=255)
tGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt > 1:1172768/1‑66 (MQ=255)
tGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt < 1:1259591/66‑1 (MQ=255)
tGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt > 1:1159874/1‑66 (MQ=255)
tGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt > 1:1299900/1‑66 (MQ=255)
tGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt > 1:599236/1‑66 (MQ=255)
tGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt > 1:1812824/1‑66 (MQ=255)
tGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt > 1:2230816/1‑66 (MQ=255)
tGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt < 1:1497983/66‑1 (MQ=255)
tGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt < 1:342871/66‑1 (MQ=255)
tGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt > 1:1528649/1‑66 (MQ=255)
tGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt < 1:2581275/66‑1 (MQ=255)
tGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt > 1:2889572/1‑66 (MQ=255)
tGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt < 1:305411/66‑1 (MQ=255)
tGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt < 1:3047758/66‑1 (MQ=255)
tGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt < 1:1686795/66‑1 (MQ=255)
gAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAAttt < 1:3189397/65‑1 (MQ=255)
aaTCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAATTTTACGCCGTTTaaa < 1:2373372/69‑1 (MQ=255)
ggCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAATTTTACGCCGTTTAAATATc > 1:2536246/1‑69 (MQ=255)
|
ACGCAAACTGGAAATAGAAAAAGCGGTCACTGACGTTGCGGAACTGAACGGTGAATTACGTAATCGGCAGTATCTTGTCGAGCAATTAACAAAAGCACATGTCAACGATGTGAATTTTACGCCGTTTAAATATC > minE/373987‑374120
|
| 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
