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 |
2,587,673 |
T→C |
58.5% |
T262T (ACA→ACG) |
mdtE ← |
multidrug resistance efflux transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,587,673 | 0 | T | C | 58.5%
| 25.9
/ 51.3
| 73 | T262T (ACA→ACG) | mdtE | multidrug resistance efflux transporter |
| Reads supporting (aligned to +/- strand): ref base T (6/24); new base C (21/21); total (27/46) |
| Fisher's exact test for biased strand distribution p-value = 1.34e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01 |
AAGTCACCATTTGGGTTGGGGAAAATCGCCCGTAACGTCACGGAGCCCGTGGTTTCATCCACTGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGCTGTAGCGTTTACCATTTTCCAGATTGAGCTGTA > minE/2587611‑2587740
|
aaGTCACCATTTGGGTTGGGGAAAATCGCCCGTAACGTCACGGAGCCCGTGGTTTCATCCACTgtcggg > 1:185266/1‑69 (MQ=255)
aaGTCACCATTTGGGTTGGGGAAAATCGCCCGTAACGTCACGGAGCCCGTGGTTTCATCCACTgtcggg > 1:1306720/1‑69 (MQ=255)
cATTTGGGTTGGGGAAAATCGCCCGTAACGTCATGGAGCCCGTGGTTTCATCCACTGTCGGGTCGgag < 1:3000914/68‑1 (MQ=255)
cATTTGGGTTGGGGAAAATCGCCCGTAACGTCACGGAGCCCGTGGTTTCATCCACTGTCGGGTCGgag < 1:417889/68‑1 (MQ=255)
cGCCCGTAACGTCACGGAGCCCGTGGTTTCTTCCACTGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTg < 1:1328335/69‑1 (MQ=255)
cGCCCGTAACGTCACGGAGCCCGTGGTTTCATCCACTGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTg < 1:866804/69‑1 (MQ=255)
cGCCCGTAACGTCACGGAGCCCGTGGTTTCATCCACTGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTg < 1:83754/69‑1 (MQ=255)
cGCCCGTAACGTCACGGAGCCCGTGGTTTCATCCACTGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTg < 1:811649/69‑1 (MQ=255)
cGCCCGTAACGTCACGGAGCCCGTGGTTTCATCCACTGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTg < 1:1206353/69‑1 (MQ=255)
cGCCCGTAACGTCACGGAGCCCGTGGTTTCATCCACTGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTg < 1:1926257/69‑1 (MQ=255)
cGCCCGTAACGTCACGGAGCCCGTGGTTTCATCCACTGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTg < 1:2011693/69‑1 (MQ=255)
cGCCCGTAACGTCACGGAGCCCGTGGTTTCATCCACTGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTg < 1:910986/69‑1 (MQ=255)
cGCCCGTAACGTCACGGAGCCCGTGGTTTCATCCACTGTCGGCTCGGAGAATTTCAGCGTGCCGGTCTg < 1:1570443/69‑1 (MQ=255)
gTAACGTCACGGAGCCCGTGGTTTCATCCACCGTCGGGTCGGAGAAtt < 1:991902/48‑1 (MQ=255)
gTAACGTCACGGAGCCCGTGGTTTCATCCACCGTCGGGTCGGAGAAtt < 1:1873584/48‑1 (MQ=255)
gTAACGTCACGGAGCCCGTGGTTTCATCCACCGTCGGGTCGGAGAAtt < 1:2415763/48‑1 (MQ=255)
gTAACGTCACGGAGCCCGTGGTTTCATCCACCGTCGGGTCGGAGAAtt < 1:2804427/48‑1 (MQ=255)
gTAACGTCACGGAGCCCGTGGTTTCATCCACCGTCGGGTCGGAGAAtt < 1:3229291/48‑1 (MQ=255)
gTAACGTCACGGAGCCCGTGGTTTCATCCACCGTCGGGTCGGAGAAtt < 1:3355392/48‑1 (MQ=255)
gTAACGTCACGGAGCCCGTGGTTTCATCCACCGTCGGGTCGGAGAAtt < 1:392807/48‑1 (MQ=255)
gTAACGTCACGGAGCCCGTGGTTTCATCCACCGTCGGGTCGGAGAAtt < 1:1008955/48‑1 (MQ=255)
gTAACGTCACGGAGCCCGTGGTTTCATCCACCGTCGGGTCGGAGAAtt < 1:508156/48‑1 (MQ=255)
gTAACGTCACGGAGCCCGTGGTTTCATCCACCGTCGGGTCGGAGAAtt < 1:693378/48‑1 (MQ=255)
gTAACGTCACGGAGCCCGTGGTTTCATCCACCGTCGGGTCGGAGAAtt < 1:790973/48‑1 (MQ=255)
gTAACGTCACGGAGCCCGTGGTTTCATCCACCGTCGGGTCGGAGAAtt < 1:1793409/48‑1 (MQ=255)
gTAACGTCACGGAGCCCGTGGTTTCATCCACCGTCGGGTCGGAGAAtt < 1:1000994/48‑1 (MQ=255)
gTAACGTCACGGAGCCCGTGGTTTCATCCACCGTCGGGTCGGAGAAtt < 1:1317105/48‑1 (MQ=255)
gTAACGTCACGGAGCCCGTGGTTTCATCCACCGTCGGGTCGGAGAAtt < 1:1321097/48‑1 (MQ=255)
gTAACGTCACGGAGCCCGTGGTTTCATCCACCGTCGGGTCGGAGAAtt < 1:1324475/48‑1 (MQ=255)
gTAACGTCACGGAGCCCGTGGTTTCATCCACCGTCGGGTCGGAGAAtt < 1:134816/48‑1 (MQ=255)
gTAACGTCACGGAGCCCGTGGTTTCATCCACCGTCGGGTCGGAGAAtt < 1:1376796/48‑1 (MQ=255)
gTAACGTCACGGAGCCCGTGGTTTCATCCACCGTCGGGTCGGAGAAtt < 1:1506368/48‑1 (MQ=255)
gTAACGTCACGGAGCCCGTGGTTTCATCCACCGTCGGGTCGGAGAAtt < 1:1841391/48‑1 (MQ=255)
gTAACGTCACGGAGCCCGTGGTTTCATCCACCGTCGGGTCGGAGAAtt < 1:1725323/48‑1 (MQ=255)
gTAACGTCACGGAGCCCGTGGTTTCATCCACAGTCGGGTCGGAGAAtt < 1:3169605/48‑1 (MQ=255)
gTCACGGAGCCCGTGGTTTCATCCACTGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGCTGTAGCg < 1:21138/68‑1 (MQ=255)
gTCACGGAGCCCGTGGTTTCATCCACTGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGCTGTAGCg < 1:1204937/68‑1 (MQ=255)
ggTTTCATCCACTGTCGGGTTGGAGAATTTCAGCGTGCCGGTCTGGCTGTAGCGTTTACCATTTTCCAg < 1:2344097/69‑1 (MQ=255)
ggTTTCATCCACTGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGCTGTAGCGTTTACCATTTTCCAg < 1:2138441/69‑1 (MQ=255)
ggTTTCATCCACTGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGCTGTAGCGTTTACCATTTTCCAg < 1:1418123/69‑1 (MQ=255)
ggTTTCATCCACTGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGCTGTAGCGTTTACCATTTTCCAg < 1:1430114/69‑1 (MQ=255)
ggTTTCATCCACTGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGCTGTAGCGTTTACCATTTTCCAg < 1:3178914/69‑1 (MQ=255)
ggTTTCATCCACTGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGCTGTAGCGTTTACCATTTTCCAg < 1:2542163/69‑1 (MQ=255)
ggTTTCATCCACTGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGCTGTAGCGTTTACCATTTTCCAg < 1:2596977/69‑1 (MQ=255)
ggTTTCATCCACTGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGCTGTAGCG‑TTACCATTTTCCAg < 1:1443334/68‑1 (MQ=255)
gTTTCATCCACTGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGCTGTAGCGTTTACCATTTTCCAGa > 1:2702675/1‑69 (MQ=255)
gTTTCATCCACTGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGCTGTAGCGTTTACCATTTTCCAGa > 1:2354922/1‑69 (MQ=255)
gTTTCATCCACTGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGCTGTAGCGTTTACCATTTTCCAGa > 1:3129476/1‑69 (MQ=255)
aTCCACCGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGGCGTAACGTTTACCATTTTCCAGATTGAg > 1:1546154/1‑69 (MQ=255)
aTCCACCGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGCCGTAACGTTTACCATTTTcc > 1:1346458/1‑61 (MQ=255)
aTCCACCGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGCCGTAACGTTTACCATTTTCCAGATTGa > 1:3279920/1‑68 (MQ=255)
aTCCACCGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGCCGTAACGTTTACCATTTTCCAGATTGa > 1:3390262/1‑68 (MQ=255)
aTCCACCGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGCCGTAACGTTTACCATTTTCCAGATTGAg > 1:53074/1‑69 (MQ=255)
aTCCACCGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGCCGTAACGTTTACCATTTTCCAGATTGAg > 1:667615/1‑69 (MQ=255)
aTCCACCGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGCCGTAACGTTTACCATTTTCCAGATTGAg > 1:669185/1‑69 (MQ=255)
aTCCACCGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGCCGTAACGTTTACCATTTTCCAGATTGAg > 1:1112156/1‑69 (MQ=255)
aTCCACCGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGCCGTAACGTTTACCATTTTCCAGATTGAg > 1:790031/1‑69 (MQ=255)
aTCCACCGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGCCGTAACGTTTACCATTTTCCAGATTGAg > 1:978791/1‑69 (MQ=255)
aTCCACCGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGCCGTAACGTTTACCATTTTCCAGATTGAg > 1:3192152/1‑69 (MQ=255)
aTCCACCGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGCCGTAACGTTTACCATTTTCCAGATTGAg > 1:2248026/1‑69 (MQ=255)
aTCCACCGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGCCGTAACGTTTACCATTTTCCAGATTGAg > 1:2202871/1‑69 (MQ=255)
aTCCACCGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGCCGTAACGTTTACCATTTTCCAGATTGAg > 1:2995316/1‑69 (MQ=255)
aTCCACCGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGCCGTAACGTTTACCATTTTCCAGATTGAg > 1:2969939/1‑69 (MQ=255)
aTCCACCGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGCCGTAACGTTTACCATTTTCCAGATTGAg > 1:2836769/1‑69 (MQ=255)
aTCCACCGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGCCGTAACGTTTACCATTTTCCAGATTGAg > 1:2476623/1‑69 (MQ=255)
aTCCACCGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGCCGTAACGTTTACCATTTTCCAGATTGAg > 1:2407440/1‑69 (MQ=255)
aTCCACCGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGCCGTAACGTTTACCATTTTCCAGATTGAg > 1:2292017/1‑69 (MQ=255)
aTCCACCGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGCCGTAACGTTTACCATTTTCCAGATTGAg > 1:2264476/1‑69 (MQ=255)
aTCCACCGTCGGGTCGGAGAATTTCAGCGTGCCCGTCTg > 1:1685114/1‑39 (MQ=38)
cACTGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGCTGTAGCGTTTACCATTTTCCAg > 1:2013957/1‑60 (MQ=255)
cACTGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGCTGTAGCGTTTACCATTTTCCAGATTGAGCTg < 1:3046563/69‑1 (MQ=255)
cACTGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGCTGTAGCGTTTACCATTTTCCAGATTGAGCTg < 1:2057577/69‑1 (MQ=255)
cTGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGCTGTAGCGTTTACCATTTTCCAGATTGAGCTGTa < 1:757554/69‑1 (MQ=255)
|
AAGTCACCATTTGGGTTGGGGAAAATCGCCCGTAACGTCACGGAGCCCGTGGTTTCATCCACTGTCGGGTCGGAGAATTTCAGCGTGCCGGTCTGGCTGTAGCGTTTACCATTTTCCAGATTGAGCTGTA > minE/2587611‑2587740
|
| 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
