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 |
2,517,491 |
T→G |
67.9% |
G528G (GGA→GGC) |
spoT ← |
bifunctional (p)ppGpp synthetase II and guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,517,491 | 0 | T | G | 67.9%
| 86.4
/ 43.4
| 73 | G528G (GGA→GGC) | spoT | bifunctional (p)ppGpp synthetase II and guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase |
| Reads supporting (aligned to +/- strand): ref base T (9/14); new base G (17/32); total (27/46) |
| Fisher's exact test for biased strand distribution p-value = 7.95e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.23e-01 |
GAGGCGTCCCCATGTTGCAGATTTTTCGCGACCACCACGCTCATTGCGTTACCAAGTCCGATTTCTGCCAGCAGATCGTCAAGCGTTGCCAGCTTCATGCGATCCAGCTCGCGCTGAATATT > minE/2517435‑2517556
|
gAGGCGTCCCCATGTTGCAGATTTTTCGCGACCACCACGCTCATTGCGTTACCAAGTCCGATTTCTGcc > 1:2023797/1‑69 (MQ=255)
gAGGCGTCCCCATGTTGCAGATTTTTCGCGACCACCACGCTCATTGCGTTACCAAGTCCGATTTCTGcc > 1:1099419/1‑69 (MQ=255)
gAGGCGTCCCCATGTTGCAGATTTTTCGCGACCACCACGCTCATTGCGTTACCAAGTCCGATTTCTGcc > 1:1736600/1‑69 (MQ=255)
gTCCCCATGTTGCAGATTTTTCGCGACCACCACGCTCATTGCGTTACCAAGTCCGATTTCTGCcagcag < 1:2390680/69‑1 (MQ=255)
gTCCCCATGTTGCAGATTTTTCGCGACCACCACGCTCATTGCGTTACCAAGTCCGATTTCTGCcagcag < 1:1668686/69‑1 (MQ=255)
ttttCGCGACCACCACGCTCATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGCGTTGcc > 1:726176/1‑68 (MQ=255)
ttttCGCGACCACCACGCTCATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGCGTTGcc > 1:3268308/1‑68 (MQ=255)
ttttCGCGACCACCACGCTCATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGCGTTGcc > 1:2517105/1‑68 (MQ=255)
ttttCGCGACCACCACGCTCATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGCGTTGcc > 1:2599092/1‑68 (MQ=255)
ttttCGCGACCACCACGCTCATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGCGTTGcc > 1:361927/1‑68 (MQ=255)
ttttCGCGACCACCACGCTCATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGCGTTGcc > 1:2866766/1‑68 (MQ=255)
ttttCGCGACCACCACGCTCATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGCGTTGcc > 1:1960459/1‑68 (MQ=255)
ttttCGCGACCACCACGCTCATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGCGTTGcc > 1:3190186/1‑68 (MQ=255)
ttttCGCGACCACCACGCTCATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGCGTTGcc > 1:1739639/1‑68 (MQ=255)
ttttCGCGACCACCACGCTCATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGCGTTGcc > 1:1174208/1‑68 (MQ=255)
ttttCGCGACCACCACGCTCATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGCGTTGcc > 1:1685842/1‑68 (MQ=255)
ttttCGCGACCACCACGCTCATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGCGTTGcc > 1:667565/1‑68 (MQ=255)
ttttCGCGACCACCACGCTCATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGCGTTGcc > 1:1692231/1‑68 (MQ=255)
tttCGCGACCACCACGCTCATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGCGTTGCCAg > 1:604463/1‑69 (MQ=255)
tttCGCGACCACCACGCTCATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGCGTTGCCAg > 1:460637/1‑69 (MQ=255)
tttCGCGACCACCACGCTCATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGCGTTGCCAg > 1:1510973/1‑69 (MQ=255)
tttCGCGACCACCACGCTCATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGCGTTGCCAg > 1:1528791/1‑69 (MQ=255)
gcgACCACCACGCTCATTGCGTTACCAAGTCCGATTTCTGCCAGCAGATCGTCAAGCGTTGCCAGCtt < 1:1517555/68‑1 (MQ=255)
gcgACCACCACGCTCATTGCGTTACCAAGTCCGATTTCTGCCAGCAGATCGTCAAGCGTTGCCAGCtt < 1:810121/68‑1 (MQ=255)
gcgACCACCACGCTCATTGCGTTACCAAGTCCGATTTCTGCCAGCAGATCGTCAAGCGTTGCCAGCtt < 1:3303132/68‑1 (MQ=255)
gcgACCACCACGCTCATTGCGTTACCAAGTCCGATTTCTGCCAGCAGATCGTCAAGCGTTGCCAGCtt < 1:2777303/68‑1 (MQ=255)
cgACCACCACGCTCATTGCGTTACCAAGTCCGATTTCTGCCAGCAGATCGTCAAGCGTTGTCAGCtt < 1:440513/67‑1 (MQ=255)
gCTCATTGCGTTACCAAGTCCGATTTCTGCCAGCAGATCGTCAAGCGTTGCCAGCTTTATGCGATCCAg < 1:3047077/69‑1 (MQ=255)
gCTCATTGCGTTACCAAGTCCGATTTCTGCCAGCAGATCGTCAAGCGCTGCCAGCTTCATGCGATCCAg < 1:1397103/69‑1 (MQ=255)
cTCATTGCGTTACCAAGTCCGATTTCTGCCAGCAGATCGTCAAGCGTTGCCAGc > 1:2309665/1‑54 (MQ=255)
cATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGc < 1:3259361/43‑1 (MQ=255)
cATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGc < 1:2933767/43‑1 (MQ=255)
cATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGc < 1:453801/43‑1 (MQ=255)
cATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGc < 1:3295298/43‑1 (MQ=255)
cATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGc < 1:3370405/43‑1 (MQ=255)
cATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGc < 1:3427638/43‑1 (MQ=255)
cATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGc < 1:2670984/43‑1 (MQ=255)
cATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGc < 1:546028/43‑1 (MQ=255)
cATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGc < 1:613921/43‑1 (MQ=255)
cATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGc < 1:816858/43‑1 (MQ=255)
cATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGc < 1:835266/43‑1 (MQ=255)
cATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGc < 1:902264/43‑1 (MQ=255)
cATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGc < 1:1895517/43‑1 (MQ=255)
cATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGc < 1:1112990/43‑1 (MQ=255)
cATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGc < 1:1113055/43‑1 (MQ=255)
cATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGc < 1:1284374/43‑1 (MQ=255)
cATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGc < 1:1506666/43‑1 (MQ=255)
cATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGc < 1:1605107/43‑1 (MQ=255)
cATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGc < 1:174115/43‑1 (MQ=255)
cATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGc < 1:1788711/43‑1 (MQ=255)
cATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGc < 1:1874294/43‑1 (MQ=255)
cATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGc < 1:286420/43‑1 (MQ=255)
cATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGc < 1:2042921/43‑1 (MQ=255)
cATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGc < 1:2153608/43‑1 (MQ=255)
cATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGc < 1:231766/43‑1 (MQ=255)
cATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGc < 1:2848815/43‑1 (MQ=255)
cATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGc < 1:2733687/43‑1 (MQ=255)
cATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGc < 1:2703828/43‑1 (MQ=255)
cATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGc < 1:2356614/43‑1 (MQ=255)
cATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGc < 1:2352620/43‑1 (MQ=255)
cATTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGc < 1:2313718/43‑1 (MQ=255)
aTTGCGTTACCAAGGCCGATTTCTGCCAGCAGATCGTCAAGc < 1:625709/42‑1 (MQ=255)
gCGTTACCAAGTCCGATTTCTGCCAGCAGATCGTCAAGCGTTGCCAGCTTCATGCGATCCAGCTcgcg > 1:1831067/1‑68 (MQ=255)
aCCAAGTCCGATTTCTGCCAGCAGATCGTCAAGCGTTGCCAGCTTCATGCGATCCAGCTCGCGCTGAat > 1:2508321/1‑69 (MQ=255)
aCCAAGTCCGATTTCTGCCAGCAGATCGTCAAGCGTTGCCAGCTTCATGCGATCCAGCTCGCGCTGAat > 1:3138113/1‑69 (MQ=255)
aCCAAGTCCGATTTCTGCCAGCAGATCGTCAAGCGTTGCCAGCTTCATGCGATCCAGCTCGCGCTGAat > 1:1186609/1‑69 (MQ=255)
aCCAAGACCGATTTCTGCCAGCAGATCGTCAAGCGTTGCCAGCTTCATGCGATCCAGCTCGCGCTGaa > 1:550/1‑68 (MQ=255)
cAAGTCCGATTTCTGCCAGCAGATCGTCAAGCGTTGCCAGCTTCATGCGATCCAGCTCGCGCTGAata < 1:571252/68‑1 (MQ=255)
aaGTCCGATTTCTGCCAGCAGATCGTCAAGCGTTGCCAGCTTCATGCGATCCAGCTCGCGCTGAATAtt < 1:3242368/69‑1 (MQ=255)
aaGTCCGATTTCTGCCAGCAGATCGTCAAGCGTTGCCAGCTTCATGCGATCCAGCTCGCGCTGAATAtt > 1:2672277/1‑69 (MQ=255)
aaGTCCGATTTCTGCCAGCAGATCGTCAAGCGTTGCCAGCTTCATGCGATCCAGCTCGCGCTGAATAtt < 1:621183/69‑1 (MQ=255)
aaGTCCGATTTCTGCCAGCAGATCGTCAAGCGTTGCCAGCTTCATGCGATCCAGCTCGCGCTGAATAtt < 1:3087370/69‑1 (MQ=255)
aaGTCCGATTTCTGCCAGCAGATCGTCAAGCGTTGCCAGCTTCATGCGATCCAGCTCGCGCTGAATAtt < 1:1177740/69‑1 (MQ=255)
|
GAGGCGTCCCCATGTTGCAGATTTTTCGCGACCACCACGCTCATTGCGTTACCAAGTCCGATTTCTGCCAGCAGATCGTCAAGCGTTGCCAGCTTCATGCGATCCAGCTCGCGCTGAATATT > minE/2517435‑2517556
|
| 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
