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 |
|
A24 F30 I1 R1
|
17 |
36.3 |
1245384 |
98.8% |
1230439 |
138.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
4,568,243 |
C→A |
A93S (GCC→TCC) |
mdtM ← |
multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 4,568,243 | 0 | C | A | 97.3%
| 124.1
/ ‑3.6
| 37 | A93S (GCC→TCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| Reads supporting (aligned to +/- strand): ref base C (0/1); new base A (20/16); total (20/17) |
| Fisher's exact test for biased strand distribution p-value = 4.59e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01 |
TTGATCCCTTTTGTCTGTCCGAACGCCTCCTGCACCGTGACATAACCAACGGTGGCAATAAAACAGATACTGGTGCCCTGAATTGCACGCGCGATAAGAAACTGTGTCATAGACGTTGTGAACATTGTCGCGGCGCAGGCAAGGGTAAAAATTAGCGCCCCGGTAATCAGCACCGGCCTGCGGCCAATTCTGTCGGAAAGCGGCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGA > NC_000913/4568110‑4568376
|
ttGATCCCTTTTGTCTGTCCGAACGCCTCCTGCACCGTGACATAACCAACGGTGGCAATAAAACAGATACTGGTGCCCTGAATTGCACGCGCGATAAGAAACTGTGTCATAGACGTTGTGAACATTGTCGCGGAGCAGGc < 1:22970/140‑1 (MQ=255)
cTTTTGTCTGTCCGAACGCCTCCTGCACCGTGACATAACCAACGGTGGCAATAAAACAGATACTGGTGCCCTGAATTGCACGCGCGATAAGAAACTGTGTCATAGACGTTGTGAACATTGTCGCGGAGCAGGCAAGGGTa > 2:396824/1‑140 (MQ=255)
cTTTTGTCTGTCCGAACGCCTCCTGCACCGTGACATAACCAACGGTGGCAATAAAACAGATACTGGTGCCCTGAATTGCACGCGCGATAAGAAACTGTGTCATAGACGTTGTGAACATTGTCGCGGAGCAGGCAAGGGTa > 2:584535/1‑140 (MQ=255)
tcCGAACGCCTCCTGCACCGTGACATAACCAACGGTGGCAATAAAACAGATACTGGTGCCCTGAATTGCACGCGCGATAAGAAACTGTGTCATAGACGTTGTGAACATTGTCGCGGAGCAGGCAAGGGTAAAAATTAgcg < 1:412887/140‑1 (MQ=255)
tcCGAACGCCTCCTGCACCGTGACATAACCAACGGTGGCAATAAAACAGATACTGGTGCCCTGAATTGCACGCGCGATAAGAAACCGTGTCATAGACGTTGTGAACATTGTCGCGGAGCAGGc < 2:445772/123‑1 (MQ=255)
tcCGAACGCCTCCTGCACCGTGACATAACCAACGGTGGCAATAAAACAGATACTGGTGCCCTGAATTGCACGCGCGATAAGAAACCGTGTCATAGACGTTGTGAACATTGTCGCGGAGCAGGc > 1:445772/1‑123 (MQ=255)
aaCGCCTCCTGCACCGTGACATAACCAACGGTGGCAATAAAACAGATACTGGTGCCCTGAATTGCACGCGCGATAAGAAACTGTGTCATAGACGTTGTGAACATTGTCGCGGAGCAGGCAAGGGTAAAAATTAGCGcccc > 2:556625/1‑140 (MQ=255)
aCGCCTCCTGCACCGTGACATAACCAACGGTGGCAATAAAACAGATACTGGTGCCCTGAATTGCACGCGCGATAAGAAACTGTGTCATAGACGTTGTGAACATTGTCGCGGAGCAGGCAAGGGTAAAAATTAGCGCCCCg < 1:479571/140‑1 (MQ=255)
cGCCTCCTGCACCGTGACATAACCAACGGTGGCAATAAAACAGATACTGGTGCCCTGAATTGCACGCGCGATAAGAAACTGTGTCATAGACGTTGTGAACATTGTCGCGGAGCAGGCAAGGGTAAAAATTAGCGCCCCgg < 1:396824/140‑1 (MQ=255)
ctGCACCGTGACATAACCAACGGTGGCAATAAAACAGATACTGGTGCCCTGAATTGCACGCGCGATAAGAAACTGTGTCATAGACGTTGTGAACATTGTCGCGGAGCAGGCAAGGGTAAAAATTAGCGCCCCGGTAATCa > 2:520720/1‑140 (MQ=255)
cACCGTGACATAACCAACGGTGGCAATAAAACAGATACTGGTGCCCTGAATTGCACGCGCGATAAGAAACTGTGTCATAGACGTTGTGAACATTGTCGCGGAGCAGGCAAGGGTAAAAATTAGCGCCCCGGTAATCAGCa > 2:190640/1‑140 (MQ=255)
gTGACATAACCAACGGTGGCAATAAAACAGATACTGGTGCCCTGAATTGCACGCGCGATAAGAAACTGTGTCATAGACGTTGTGAACATTGTCGCGGAGCAGGCAAGGGTAAAAATTAGCGCCCCGGTAATCAGCACCgg > 1:259176/1‑140 (MQ=255)
gTGACATAACCAACGGTGGCAATAAAACAGATACTGGTGCCCTGAATTGCACGCGCGATAAGAAACTGTGTCATAGACGTTGTGAACATTGTCGCGGAGCAGGCAAGGGTAAAAATTAGCGCCCCGGTAATCAGCACCgg > 1:215762/1‑140 (MQ=255)
cATAACCAACGGTGGCAATAAAACAGATACTGGTGCCCTGAATTGCACGCGCGATAAGAAACTGTGTCATAGACGTTGTGAACATTGTCGCGGAGCAGGCAAGGGTAAAAATTAGAGCCCCg > 1:338213/1‑122 (MQ=255)
cATAACCAACGGTGGCAATAAAACAGATACTGGTGCCCTGAATTGCACGCGCGATAAGAAACTGTGTCATAGACGTTGTGAACATTGTCGCGGAGCAGGCAAGGGTAAAAATTAGAGCCCCg < 2:338213/122‑1 (MQ=255)
aCGGTGGCAATAAAACAGATACTGGTGCCCTGAATTGCACGCGCGATAAGAAACTGTGTCATAGACGTTGTGAACATTGTCGCGGAGCAGGCAAGGGTAAAAATTAGCGCCCCGGTAATCAGCACCGGCCt > 1:400105/1‑131 (MQ=255)
aCGGTGGCAATAAAACAGATACTGGTGCCCTGAATTGCACGCGCGATAAGAAACTGTGTCATAGACGTTGTGAACATTGTCGCGGAGCAGGCAAGGGTAAAAATTAGCGCCCCGGTAATCAGCACCGGCCt < 2:400105/131‑1 (MQ=255)
gTGGCAATAAAACAGATACTGGTGCCCTGAATTGCACGCGCGATAAGAAACTGTGTCATAGACGTTGTGAACATTGTCGCGGAGCAGGCAAGGGTAAAAATTAGCGCCCCGGTAATCAGCACCGGCCTGCGGCCAATTCt > 2:418892/1‑140 (MQ=255)
gCAATAAAACAGATACTGGTGCCCTGAATTGCACGCGCGATAAGAAACTGTGTCATAGACGTTGTGAACATTGTCGCGGAGCAGGCAAGGGTAAAAATTAGCGCCCCGGTAATCAGCACCGGCCTGCGGCCAATTCTGTc > 1:66316/1‑140 (MQ=255)
cAATAAAACAGATACTGGTGCCCTGAATTGCACGCGCGATAAGAAACTGTGTCATAGACGTTGTGAACATTGTCGCGGAGCAGGCAAGGGTAAAAATTAGCGCCCCGGTAATCAGCACCGGCCTGCGGCCAATTCTGTCg > 1:476093/1‑140 (MQ=255)
cAGATACTGGTGCCCTGAATTGCACGCGCGATAAGAAACTGTGTCATAGACGTTGTGAACATTGTCGCGGAGCAGGCAAGGGTAAAAATTAGCGCCCCGGTAATCAGCACCGGCCTGCGGCCAATTCTGTCGGAAAGCgg < 1:584535/140‑1 (MQ=255)
aTACTGGTGCCCTGAATTGCACGCGCGATAAGAAACTGTGTCATAGACGTTGTGAACATTGTCGCGGAGCAGGCAAGGGTAAAAATTAGCGCCCCGGTAATCAGCACCGGCCTGCGGCCAATTCTGTCGGAAAGCGGccc > 2:33999/1‑140 (MQ=255)
tGCCCTGAATTGCACGCGCGATAAGAAACTGTGTCATAGACGTTGTGAACATTGTCGCGGAGCAGGCAAGGGTAAAAATTAGCGCCCCGGTAATCAGCACCGGCCTGCGGCCAATTCTGTCGGAAAGCGGCCCCagcagc < 1:190640/140‑1 (MQ=255)
tGCCCTGAATTGCACGCGCGATAAGAAACTGTGTCATAGACGTTGTGAACATTGTCGCGGAGCAGGCAAGGGTAAAAATTAGCGCCCCGGTAATCAGCACCGGCCTGCGGCCAATTCTGTCGGAAAGCGGCCCCagcagc < 2:522756/140‑1 (MQ=255)
aaTTGCACGCGCGATAAGAAACTGTGTCATAGACGTTGTGAACATTGTCGCGGAGCAGGCAAGGGTAAAAATTAGCGCCCCGGTAATCAGCACCGGCCTGCGGCCAATTCTGTCGGAAAGCGGCCCCAGCAGCCACTGTa < 2:215762/140‑1 (MQ=255)
gcgATAAGAAACTGTGTCATAGACGTTGTGAACATTGTCGCGGAGCAGGCAAGGGTAAAAATTAGCGCCCCGGTAATCAGCACCGGCCTGCGGCCAATTCTGTCGGAAAGCGGCCCCAGCAGCCACTGTAACGCCATAcc < 1:520720/140‑1 (MQ=255)
gATAAGAAACTGTGTCATAGACGTTGTGAACATTGTCGCGGAGCAGGCAAGGGTAAAAATTAGCGCCCCGGTAATCAGCACCGGCCTGCGGCCAATTCTGTCGGAAAGCGGCCCCAGCAGCCACTGTAACGCCATACCGc < 1:289932/140‑1 (MQ=255)
tgtCATAGACGTTGTGAACATTGTCGCGGAGCAGGCAAGGGTAAAAATTAGCGCCCCGGTAATCAGCACCGGCCTGCGGCCAATTCTGTCGGAAAGCGGCCCCAGCAGCCACTGTAACGCCATAcc > 2:292920/1‑126 (MQ=255)
tgtCATAGACGTTGTGAACATTGTCGCGGAGCAGGCAAGGGTAAAAATTAGCGCCCCGGTAATCAGCACCGGCCTGCGGCCAATTCTGTCGGAAAGCGGCCCCAGCAGCCACTGTAACGCCATAcc < 1:292920/126‑1 (MQ=255)
tgtCATAGACGTTGTGAACATTGTCGCGGAGCAGGCAAGGGTAAAAATTAGCGCCCCGGTAATCAGCACCGGCCTGCGGCCAATTCTGTCGGAAAGCGGCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATaga > 2:323751/1‑140 (MQ=255)
tCATAGACGTTGTGAACATTGTCGCGGAGCAGGCAAGGGTAAAAATTAGCGCCCCGGTAATCAGCACCGGCCTGCGGCCAATTCTGTCGGAAAGCGGCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAgaga < 2:66316/140‑1 (MQ=255)
gTTGTGAACATTGTCGCGGAGCAGGCAAGGGTAAAAATTAGCGCCCCGGTAATCAGCACCGGCCTGCGGCCAATTCTGTCGGAAAGCGGCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGgc > 1:224888/1‑140 (MQ=255)
tgtgAACATTGTCGCGGAGCAGGCAAGGGTAAAAATTAGCGCCCCGGTAATCAGCACCGGCCTGCGGCCAATTCTGTCGGAAAGCGGCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGgcag > 2:487994/1‑140 (MQ=255)
ttGTCGCGGCGCAGGCAAGGGTAAAAATTAGCGCCCCGGTAATCAGCACCGGCCTGCGGCCAATTCTGTCGGAAAGCGGCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGcc < 1:235402/140‑1 (MQ=255)
tGTCGCGGAGCAGGCAAGGGTAAAAATTAGCGCCCCGGTAATCAGCACCGGCCTGCGGCCAATTCTGTCGGAAAGCGGCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCa > 2:44331/1‑140 (MQ=255)
tCGCGGAGCAGGCAAGGGTAAAAATTAGCGCCCCGGTAATCAGCACCGGCCTGCGGCCAATTCTGTCGGAAAGCGGCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGa < 1:44331/140‑1 (MQ=255)
tCGCGGAGCAGGCAAGGGTAAAAATTAGCGCCCCGGTAATCAGCACCGGCCTGCGGCCAATTCTGTCGGAAAGCGGCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGa > 2:238521/1‑140 (MQ=255)
|
TTGATCCCTTTTGTCTGTCCGAACGCCTCCTGCACCGTGACATAACCAACGGTGGCAATAAAACAGATACTGGTGCCCTGAATTGCACGCGCGATAAGAAACTGTGTCATAGACGTTGTGAACATTGTCGCGGCGCAGGCAAGGGTAAAAATTAGCGCCCCGGTAATCAGCACCGGCCTGCGGCCAATTCTGTCGGAAAGCGGCCCCAGCAGCCACTGTAACGCCATACCGCCAGCAAGATAGAGACTGACGGCAGCAGGGGCCAGA > NC_000913/4568110‑4568376
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
