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 |
715,819 |
A→G |
28.9% |
G112G (GGT→GGC) |
mdtH ← |
predicted drug efflux system |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 715,819 | 0 | A | G | 28.9%
| 32.8
/ 13.9
| 38 | G112G (GGT→GGC) | mdtH | predicted drug efflux system |
| Reads supporting (aligned to +/- strand): ref base A (14/13); new base G (8/3); total (22/16) |
| Fisher's exact test for biased strand distribution p-value = 2.96e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.18e-01 |
GCTGCTGTGGACGGATTAATTTCACCACCAGCGCCGAACGCGGCGGATCAAACAACGTGCCACCGAGTCCCGAGAGCAGGCATGAAAACCACAATAGCCACGGTTCGTGGGCGATACCCATTGTGGCGAA > minE/715758‑715887
|
gctgctGTGGACGGATTAATTTCACCACCAGCGCCGAACGCGGCGGATCAAACAACGTGCCACCGAGTc < 1:1313315/69‑1 (MQ=255)
gctgctGTGGACGGATTAATTTCACCACCAGCGCCGAACGCGGCGGATCAAACAACGTGCCACCGAGTc < 1:2954352/69‑1 (MQ=255)
gctgctGTGGACGGATTAATTTCACCACCAGCGCCGAACGCGGCGGATCAAACAACGTGCCACCGAGTc < 1:1444978/69‑1 (MQ=255)
tgctgTGGACGGATTAATTTCACCACCAGCGCCGAACGCGGCGGATCAAACAACGTGCCACCGAGTccc < 1:279340/69‑1 (MQ=255)
tgctgTGGACGGATTAATTTCACCACCAGCGCCGAACGCGGCGGATCAAACAACGTGCCACCGAGTccc < 1:2544816/69‑1 (MQ=255)
tgctgTGGACGGATTAATTTCACCACCAGCGCCGAACGCGGCGGATCAAACAACGTGCCACCGAGTccc < 1:2489028/69‑1 (MQ=255)
ttAATTTCACCACCAGCGCCGAACGCGGCGGATCAAACAACGTGCCACCGAGTCCCGAGAGCAGGCAt > 1:3054358/1‑68 (MQ=255)
ttCACCACCAGCGCCGAACGCGGCGGATCAAACAACGTGCCACCGAGTCCCga > 1:791692/1‑53 (MQ=255)
ttCACCACCAGCGCCGAACGCGGCGGATCAAACAACGTGCCACCGAGTCCCga > 1:1403184/1‑53 (MQ=255)
ttCACCACCAGCGCCGAACGCGGCGGATCAAACAACGTGCCACCGAGTCCCga > 1:1491791/1‑53 (MQ=255)
ttCACCACCAGCGCCGAACGCGGCGGATCAAACAACGTGCCACCGAGTCCCga > 1:641075/1‑53 (MQ=255)
ttCACCACCAGCGCCGAACGCGGCGGATCAAACAACGTGCCAACGAGTCCCga > 1:2879006/1‑53 (MQ=255)
tCACCACCAGCGCCGAACGCGTAGGATCAAACAACGTGCCGCCGAGTCCCAAAAGCAGGCATGAAAAc > 1:375638/1‑68 (MQ=255)
tCACCACCAGCGCCGAACGCGGCGGATCAAACAACGTGCCACCGAGTCCCGAGAGCAGGCATGaa < 1:1907210/65‑1 (MQ=255)
tCACCACCAGCGCCGAACGCGGCGGATCAAACAACGTGCCACCGAGTCCCGAGAGCAGGCATGaa < 1:654127/65‑1 (MQ=255)
tCACCACCAGCGCCGAACGCGGCGGATCAAACAACGTGCCACCGAGTCCCGAGAGCAGGCATGAAAAc > 1:441052/1‑68 (MQ=255)
tCACCACCAGCGCCGAACGCGGCGGATCAAACAACGTGCCACCGAGTCCCGAGAGCAGGCATGAAAAc > 1:757332/1‑68 (MQ=255)
tCACCACCAGCGCCGAACGCGGCGGATCAAACAACGTGCCACCGAGTCCCGAGAGCAGGCATGAAAAc > 1:1409528/1‑68 (MQ=255)
tCACCACCAGCGCCGAACGCGGCGGATCAAACAACGTGCCACCGAGTCCCGAGAGCAGGCATGAAAAc > 1:1339182/1‑68 (MQ=255)
tCACCACCAGCGCCGAACGCGGAGGATCAAACAACGTGCCGCCGAGTCCCGAAAGCAGGCATGAAAAc > 1:1656413/1‑68 (MQ=255)
tCACCACCAGCGCCGAACGCGGAGGATCAAACAACGTGCCGCCGAGTCCCGAAAGCAGGCATGAAAAc > 1:508763/1‑68 (MQ=255)
tCACCACCAGCGCCGAACGCGGAGGATCAAACAACGTGCCGCCGAGTCCCGAAAGCAGGCATGAAAAc > 1:1954332/1‑68 (MQ=255)
tCACCACCAGCGCCGAACGCGGAGGATCAAACAACGTGCCGCCGAGTCCCGAAAGCAGGCATGAAAAc > 1:3387286/1‑68 (MQ=255)
tCACCACCAGCGCCGAACGCGGAGGATCAAACAACGTGCCGCCGAGTCCCGAAAGCAGGCATGAAAAc > 1:2335429/1‑68 (MQ=255)
tCACCACCAGCGCCGAACGCGGAGGATCAAACAACGTGCCGCCGAGTCCCGAAAGCAGGCATGAAAAc > 1:3219828/1‑68 (MQ=255)
tCACCACCAGCGCCGAACGCGGAGGATCAAACAACGTGCCGCCGAGTCCCGAAAGCAGGCATGAAAAc > 1:1431507/1‑68 (MQ=255)
aaCGCGGCGGATCAAACAACGTGCCACCGAGTCCCGAGAGCAGGCATGAAAACCACAATAGCCACGGtt < 1:2403148/69‑1 (MQ=255)
aaCGCGGCGGATCAAACAACGTGCCACCGAGTCCCGAGAGCAGGCATGAAAACCACAATAGCCACGGtt < 1:2580304/69‑1 (MQ=255)
aCGCGGCGGATCAAACAACGTGCCACCGAGTCCCGAGAGCAGGCATGAAAACCACAATAGGCACGGTTc > 1:811836/1‑69 (MQ=255)
aCGCGGCGGATCAAACAACGTGCCACCGAGTCCCGAGAGCAGGCATGAAAACCACAATAGCCACGGtt < 1:1941055/68‑1 (MQ=255)
aCGCGGCGGATCAAACAACGTGCCACCGAGTCCCGAGAGCAGGCATGAAAACCACAATAGCCACGGTTc > 1:1089102/1‑69 (MQ=255)
aCGCGGCGGATCAAACAACGTGCCACCGAGTCCCGAGAGCAGGCATGAAAACCACAATAGCCACGGTTc > 1:1777493/1‑69 (MQ=255)
aCGCGGCGGATCAAACAACGTGCCACCGAGTCCCGAGAGCAGGCATGAAAACCACAATAGCCACGGTTc > 1:1447844/1‑69 (MQ=255)
cggATCAAACAACGTGCCACCGAGTCCCGAGAGCAGGCATGAAAACCACAATAGCCACGGTTCGTGGGc < 1:261376/69‑1 (MQ=255)
cggATCAAACAACGTGCCACCGAGTCCCGAGAGCAGGCATGAAAACCACAATAGCCACGGTTCGTGGGc < 1:1363302/69‑1 (MQ=255)
acaacGTGCCGCCGAGTCCCGAAAGCAGGCATGAAAACCACAGTAGCCACGGTTCGTGGGCGATACCCa < 1:2284287/69‑1 (MQ=255)
acaacGTGCCGCCGAGTCCCGAAAGCAGGCATGAAAACCACAGTAGCCACGGTTCGTGGGCGATACCCa < 1:1515507/69‑1 (MQ=255)
caacGTGCCGCCGAGTCCCGAAAGCAGGCATGAAAACCACAGTAGCCACGGTTCGTGGGCGATACCCa < 1:1850691/68‑1 (MQ=255)
aCCGAGTCCCGAGAGCAGGCATGAAAACCACAATAGCCACGGTTCGTGGGCGATACCCATTGTGGCGaa < 1:2025629/69‑1 (MQ=255)
aCCGAGTCCCGAGAGCAGGCATGAAAACCACAATAGCCACGGCTCGTGGGCGATACCCATTGTGGCGaa < 1:962136/69‑1 (MQ=255)
|
GCTGCTGTGGACGGATTAATTTCACCACCAGCGCCGAACGCGGCGGATCAAACAACGTGCCACCGAGTCCCGAGAGCAGGCATGAAAACCACAATAGCCACGGTTCGTGGGCGATACCCATTGTGGCGAA > minE/715758‑715887
|
| 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
