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 F8 I0 R2
|
296 |
77.6 |
4260404 |
88.1% |
3753415 |
61.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,858,845 |
G→A |
48.0% |
S373S (TCG→TCA) |
amiB → |
N‑acetylmuramoyl‑l‑alanine amidase II |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,858,845 | 0 | G | A | 48.0%
| 9.7
/ 106.9
| 74 | S373S (TCG→TCA) | amiB | N‑acetylmuramoyl‑l‑alanine amidase II |
| Reads supporting (aligned to +/- strand): ref base G (27/11); new base A (26/9); total (54/20) |
| Fisher's exact test for biased strand distribution p-value = 7.98e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.44e-01 |
CAGTTGCAACGCATTGGCGAAATACATAAACGTCGACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCGCCGGATATCCCATCAGTACTGGTCGAAACCGGTTTTATCAGCAACAACAGCGAAGAACGTTTGCTGGC > minE/2858777‑2858913
|
cagtTGCAACGCATTGGCGAAATACATAAACGTCGACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCGcc > 1:3011485/1‑71 (MQ=255)
cagtTGCAACGCATTGGCGAAATACATAAACGTCGACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCGcc > 1:3797954/1‑71 (MQ=255)
cagtTGCAACGCATTGGCGAAATACATAAACGTCGACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCGcc > 1:1438971/1‑71 (MQ=255)
agtTGCAACGCATTGGCGAAATACATAAACGTCGACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCGCCg > 1:2605344/1‑71 (MQ=255)
agtTGCAACGCATTGGCGAAATACATAAACGTCGACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCGCCg < 1:3732902/71‑1 (MQ=255)
agtTGCAACGCATTGGCGAAATACATAAACGTCGACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCGCCg > 1:3326846/1‑71 (MQ=255)
agtTGCAACGCATTGGCGAAATACATAAACGTCGACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCGCCg > 1:3236554/1‑71 (MQ=255)
ttGCAACGCATTGGCGAAATACATAAACGTCGACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCGCCGGa > 1:3367135/1‑71 (MQ=255)
tGCAACGCATTGGCGAAATACATAAACGTCGACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCGCCGGa > 1:3537013/1‑70 (MQ=255)
tGCAACGCATTGGCGAAATACATAAACGTCGACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCGCCGGa > 1:1509870/1‑70 (MQ=255)
tGCAACGCATTGGCGAAATACATAAACGTCGACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCGCCGGa > 1:515267/1‑70 (MQ=255)
tGCAACGCATTGGCGAAATACATAAACGTCGACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCGCCGGa > 1:282672/1‑70 (MQ=255)
tGCAACGCATTGGCGAAATACATAAACGTCGACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCGCCGGa > 1:373736/1‑70 (MQ=255)
gCAACGCATTGGCGAAATACATAAACGTCGACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCGCCGGata > 1:601172/1‑71 (MQ=255)
gCAACGCATTGGCGAAATACATAAACGTCGACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCGCCGGata > 1:4193489/1‑71 (MQ=255)
gCAACGCATTGGCGAAATACATAAACGTCGACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCGCCGGata > 1:4173073/1‑71 (MQ=255)
gCAACGCATTGGCGAAATACATAAACGTCGACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCACCGGata > 1:1402661/1‑71 (MQ=255)
gCAACGCATTGGCGAAATACATAAACGTCGACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCACCGGata > 1:1605428/1‑71 (MQ=255)
ggCGAAATACATAAACGTCGACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCGCCGGATATCCCATCAg > 1:810047/1‑70 (MQ=255)
ggCGAAATACATAAACGTCGACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCGCCGGATATCCCATCAg > 1:648343/1‑70 (MQ=255)
ggCGAAATACATAAACGTCGACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCACCGGATATCCCATCAg < 1:1095563/70‑1 (MQ=255)
ggCGAAATACATAAACGTCGACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCACCGGATATCCCATCAg > 1:1604754/1‑70 (MQ=255)
ggCGAAATACATAAACGTCGACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCACCGGATATCCCATCAg < 1:2081406/70‑1 (MQ=255)
ggCGAAATACATAAACGTCGACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCACCGGATATCCCATCAg < 1:2275351/70‑1 (MQ=255)
ggCGAAATACATAAACGTCGACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCACCGGATATCCCATCAg < 1:2397939/70‑1 (MQ=255)
gCGAAATACATAAACGTCGACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCGCCGGATATCCCATCAGt < 1:3810026/70‑1 (MQ=255)
gCGAAATACATAAACGTCGACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCGCCGGATATCCCATCAGt < 1:2056032/70‑1 (MQ=255)
gCGAAATACATAAACGTCGACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCGCCGGATATCCCATCAGt < 1:1032561/70‑1 (MQ=255)
gAAATACATAAACGTCGACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCGCCGGATATCCCATCAg < 1:909013/67‑1 (MQ=255)
aaaCGTCGACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCACCGGATATCCCATCAGTACTGGTCGAAAc > 1:3203864/1‑71 (MQ=255)
aaaCGTCGACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCACCGGATATCCCATCAGTACTGGTCGAAAc > 1:2853317/1‑71 (MQ=255)
aaCGTCGACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCACCGGATATCCCAt > 1:1042587/1‑54 (MQ=255)
aaCGTCGACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCACCGGATATCCCAt > 1:474600/1‑54 (MQ=255)
aaCGTCGACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCACCGGATATCCCAt > 1:1706938/1‑54 (MQ=255)
aaCGTCGACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCACCGGATATCCCATCAGTACTGGTCGAAAcc > 1:854839/1‑71 (MQ=255)
aaCGTCGACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCACCGGATATCCCATCAGTACTGGTCGAAAcc > 1:3400329/1‑71 (MQ=255)
aaCGTCGACCAGAACACGCCAGCCTTGGCGTTCTGAGCTCACCGGATATCCCAt > 1:2645835/1‑54 (MQ=39)
gACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCACCGGATATCCCATCAGTACTGGTCGAAACCGGtttt < 1:1239869/71‑1 (MQ=255)
cAGAACACGCCAGCCTTGGCGTTCTGCGCTCACCGGATATCCCATCAGTACTGGTCGAAACCGGTTTTATc < 1:633178/71‑1 (MQ=255)
gAACACTCCAGCCTTGGCGTTCTGCGCTCGCCGGATATCCCATCAGTACTGGTCGAAACCGGTTTTATCAg > 1:905105/1‑71 (MQ=255)
gAACACGCCAGCCTTGGCGTTCTGCGCTCGCCGGATATCCCATCAGTACTGGTCGAAACCGGTTTTATCAg > 1:771932/1‑71 (MQ=255)
gAACACGCCAGCCTTGGCGTTCTGCGCTCGCCGGATATCCCATCAGTACTGGTCGAAACCGGTTTTATCAg > 1:1552527/1‑71 (MQ=255)
gAACACGCCAGCCTTGGCGTTCTGCGCTCGCCGGATATCCCATCAGTACTGGTCGAAACCGGTTTTATCAg > 1:477005/1‑71 (MQ=255)
gAACACGCCAGCCTTGGCGTTCTGCGCTCGCCGGATATCCCATCAGTACTGGTCGAAACCGGTTTTATCAg > 1:1276659/1‑71 (MQ=255)
cacGCCAGCCTTGGCGTTCTGCGCTCGCCGGATATCCCATCAGTACTGGTCGAAACCGGTTTTATCAGcaa > 1:3087195/1‑71 (MQ=255)
cacGCCAGCCTTGGCGTTCTGCGCTCGCCGGATATCCCATCAGTACTGGTCGAAACCGGTTTTATCAGcaa > 1:2924890/1‑71 (MQ=255)
acGCCAGCCTTGGCGTTCTGCGCTCACCGGATATCCCATCAGTACTGGTCGAAACCGGTTTTATCAGcaac < 1:3388120/71‑1 (MQ=255)
acGCCAGCCTTGGCGTTCTGCGCTCACCGGATATCCCATCAGTACTGGTCGAAACCGGTTTTATCAGcaac < 1:524966/71‑1 (MQ=255)
gCCTTGGCGTTCTGCGCTCGCCGGATATCCCATCAGTACTGGTCGAAACCGGTTTTATCAGCAACAACAGc > 1:2805851/1‑71 (MQ=255)
gCCTTGGCGTTCTGCGCTCACCGGATATCCCATCAGTACTGGTCGAAACCGGTTTTAt > 1:2630778/1‑58 (MQ=255)
gCCTTGGCGTTCTGCGCTCACCGGATATCCCATCAGTACTGGTCGAAACCGGTTTTAt > 1:1697541/1‑58 (MQ=255)
gCCTTGGCGTTCTGCGCTCACCGGATATCCCATCAGTACTGGTCGAAACCGGTTTTAt > 1:3338200/1‑58 (MQ=255)
gCCTTGGCGTTCTGCGCTCACCGGATATCCCATCAGTACTGGTCGAAACCGGTTTTAt > 1:1172009/1‑58 (MQ=255)
gCCTTGGCGTTCTGCGCTCACCGGATATCCCATCAGTACTGGTCGAAACCGGTTTTAt > 1:1228197/1‑58 (MQ=255)
gCCTTGGCGTTCTGCGATCGCCGGATATCCCATCAGTACTGGTCGAAACCGGTTTTATCAGCAACAACAGc > 1:746183/1‑71 (MQ=255)
cTTGGCGTTCTGCGCTCCCCGGATATCCCATCAGTACTGGTCGAAACCGGtt > 1:1639454/1‑52 (MQ=255)
cTTGGCGTTCTGCGCTCACCGGATATCCCATCAGTACTGGTCGAAACCGGtt > 1:1131239/1‑52 (MQ=255)
cTTGGCGTTCTGCGCTCACCGGATATCCCATCAGTACTGGTCGAAACCGGtt > 1:4146375/1‑52 (MQ=255)
cTTGGCGTTCTGCGCTCACCGGATATCCCATCAGTACTGGTCGAAACCGGtt > 1:181323/1‑52 (MQ=255)
cTTGGCGTTCTGCGCTCACCGGATATCCCATCAGTACTGGTCGAAACCGGtt > 1:3447433/1‑52 (MQ=255)
ggCGTTCTGCGCTCGCCGGATATCCCATCAGTACTGGTCGAAACCGGTTTTATCAGCAACAACAGCgaag < 1:1447780/70‑1 (MQ=255)
ggCGTTCTGCGCTCGCCGGATATCCCATCAGTACTGGTCGAAACCGGTTTTATCAGCAACAACAGCgaa < 1:69122/69‑1 (MQ=255)
cGTTCTGCGCTCACCGGATATCCCATCAGTACTGGTCGAAACCGGTTTTATCAGCAACAACAGCGAAGAAc < 1:2112580/71‑1 (MQ=255)
gTTCTGCGCTCGCCGGATATCCCATCAGTACTGGTc < 1:2807883/36‑1 (MQ=255)
gTTCTGCGCTCGCCGGATATCCCATCAGTACTGGTc < 1:645374/36‑1 (MQ=255)
cTGCGCTCACCGGATATCCCATCAGTACTGGTCGAAACCGGTTTTATCAGCAACAACAGCgaagaa > 1:298941/1‑66 (MQ=255)
cTGCGCTCACCGGATATCCCATCAGTACTGGTCGAAACCGGTTTTATCAGCAACAACAGCGAAGCACGttt > 1:4105248/1‑71 (MQ=255)
cTGCGCTCACCGGATATCCCATCAGTACTGGTCGAAACCGGTTTTATCAGCAACAACAGCGAAGAACGttt > 1:4100295/1‑71 (MQ=255)
cTGCGCTCACCGGATATCCCATCAGTACTGGTCGAAACCGGTTTTATCAGCAACAACAGCGAAGAACGttt > 1:569747/1‑71 (MQ=255)
cTGCGCTCACCGGATATCCCATCAGTACTGGTCGAAACCGGTTTTATCAGCAACAACAGCGAAGAACGttt > 1:2907452/1‑71 (MQ=255)
cTGCGCTCACCGGATATCCCATCAGTACTGGTCGAAACCGGTTTTATCAGCAACAACAGCGAAGAACGttt > 1:2928128/1‑71 (MQ=255)
cgcTCGCCGGATATCCCATCAGTACTGGTCGAAACCGGTTTTATCAGCAACAACAGCGAAGAACGttt < 1:1578460/68‑1 (MQ=255)
cgcTCGCCGGATATCCCATCAGTACTGGTCGAAACCGGTTTTATCAGCAACAACAGCGAAGAACGttt < 1:310453/68‑1 (MQ=255)
cGCCGGATATCCCATCAGTACTGGTCGAAACCGGTTTTATCAGCAACAACAGCGAAGAACGTTTGCTGgc > 1:3303518/1‑70 (MQ=255)
|
CAGTTGCAACGCATTGGCGAAATACATAAACGTCGACCAGAACACGCCAGCCTTGGCGTTCTGCGCTCGCCGGATATCCCATCAGTACTGGTCGAAACCGGTTTTATCAGCAACAACAGCGAAGAACGTTTGCTGGC > minE/2858777‑2858913
|
| 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
