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 |
|
A1 F1 I2 R1
|
524 |
31.4 |
1748232 |
97.8% |
1709770 |
80.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
4,567,357 |
+A |
coding (1163/1233 nt) |
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 | 4,567,353 | 1 | . | A | 96.2%
| 85.6
/ ‑2.7
| 26 | coding (1167/1233 nt) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base A (10/15); total (11/15) |
| Fisher's exact test for biased strand distribution p-value = 4.23e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01 |
GGATCGCGCAAAAATCACTGCTCCTCCACTAGCTCGGCTGCCTGATGCTGGCGCACGCGATTGAGCAATCCCGCCAGGGTG‑AAA‑ACGACGATAACGCCCGCCACAACGGCTAACAGATGAAACGGCAAGCGACCGCCGTTAAACCATAGCCAGCG > NC_000913/4567273‑4567427
|
ggATCGCGCAAAAATCACTGCTCCTCCACTAGCTCGGCTGCCTGATGCTGGCGCACGCGATTGAGCAATCCCGCCAGGGTg < 1:842270/81‑1 (MQ=255)
aaaaTCACTGCTCCTCCACTAGCTCGGCTGCCTGATGCTGGCGCACGCGATTGAGCAATCCCGCCAGGGTGAAAA‑acgacg < 1:842271/81‑1 (MQ=255)
aaaaTCACTGCTCCTCCACTAGCTCGGCTGCCTGATGCTGGCGCACGCGATTGAGCAATCCCGCCAGGGTGAAAA‑acgacg < 2:842273/81‑1 (MQ=255)
aaaaTCACTGCTCCTCCACTAGCTCGGCTGCCTGATGCTGGCGCACGCGATTGAGCAATCCCGCCAGGGTGAAAA‑acgacg < 2:842272/81‑1 (MQ=255)
ctcctcCACTAGCTCGGCTGCCTGATGCTGGCGCACGCGATTGAGCAATCCCGCCAGGGTGAAAA‑ACGACGATAAcgcccg < 2:842274/81‑1 (MQ=255)
cctccACTAGCTCGGCTGCCTGATGCTGGCGCACGCGATTGAGCAATCCCGCCAGGGTGAAAA‑ACGACGATAAcgcccgc > 2:842314/1‑80 (MQ=255)
cctccACTAGCTCGGCTGCCTGATGCTGGCGCACGCGATTGAGCAATCCCGCCAGGGTGAAAA‑ACGACGATAAcgcccgc > 1:842306/1‑80 (MQ=255)
ctccACTAGCTCGGCTGCCTGATGCTGGCGCACGCGATTGAGCAATCCCGCCAGGGTGAAAA‑ACGACGATAAcgcccgc < 2:842276/79‑1 (MQ=255)
ctccACTAGCTCGGCTGCCTGATGCTGGCGCACGCGATTGAGCAATCCCGCCAGGGTGAAAA‑ACGACGATAACGCCCGCca < 1:842275/81‑1 (MQ=255)
cACTAGCTCGGCTGCCTGATGCTGGCGCACGCGATTGAGCAATCCCGCCAGGGTGAAAA‑ACGACGATAACGCCCGCCACaa < 2:842277/81‑1 (MQ=255)
aGCTCGGCTGCCTGATGCTGGCGCACGCGATTGAGCAATCCCGCCAGGGTGAAAA‑ACGACGATAACGCCCGCCACAACGGc > 1:842312/1‑81 (MQ=255)
cGGCTGCCTGATGCTGGCGCACGCGATTGAGCAATCCCGCCAGGGTGAAAA‑ACGACGATAACGCCCGCCACAACGGCTaa > 1:842309/1‑80 (MQ=255)
ggCTGCCTGATGCTGGCGCACGCGATTGAGCAATCCCGCCAGGGTGAAAA‑ACGACGATAACGCCCGCCACAACGGCTAACa < 1:842278/81‑1 (MQ=255)
ggCTGCCTGATGCTGGCGCACGCGATTGAGCAATCCCGCCAGGGTG‑AAATACGACGATAACGCCCGCCACAACGGCTaa > 2:842313/1‑79 (MQ=255)
gCTGCCTGATGCTGGCGCACGCGATTGAGCAATCCCGCCAGGGTGAAAA‑ACGACGATAACGCCCGCCACAACGGCTAACAg < 1:842279/81‑1 (MQ=255)
tGCCTGATGCTGGCGCACGCGATTGAGCAATCCCGCCAGGGTGAAAA‑ACGACGATAACGCCCGCCACAACGGCTAACAGAt > 2:842307/1‑81 (MQ=255)
cTGATGCTGGCGCACGCGATTGAGCAATCCCGCCAGGGTGAAAA‑ACGACGATAACGCCCGCCACAACGGCTAACAGATGaa < 1:842280/81‑1 (MQ=255)
tGGCGCACGCGATTGAGCAATCCCGCCAGGGTGAAAA‑ACGACGATAACGCCCGCCACAACGGCTAACAGATGAAACGGc > 1:842317/1‑79 (MQ=255)
tGGCGCACGCGATTGAGCAATCCCGCCAGGGTGAAAA‑ACGACGATAACGCCCGCCACAACGGCTAACAGATGAAACGGc > 2:842310/1‑79 (MQ=255)
gcgcACGCGATTGAGCAATCCCGCCAGGGTGAAAA‑ACGACGATAACGCCCGCCACAACGGCTAACAGATGAAACGGCAAg < 1:842282/80‑1 (MQ=255)
gcgcACGCGATTGAGCAATCCCGCCAGGGTGAAAA‑ACGACGATAACGCCCGCCACAACGGCTAACAGATGAAACGGCAAGc < 2:842281/81‑1 (MQ=255)
cgATTGAGCAATCCCGCCAGGGTGAAAA‑ACGACGATAACGCCCGCCACAACGGCTAACAGATGAAACGGCAAGCGAccgcc > 1:842316/1‑81 (MQ=255)
aTTGAGCAATCCCGCCAGGGTGAAAA‑ACGACGATAACGCCCGCCACAACGGCTAACAGATGAAACGGCAAGCGACCGCCGt < 2:842283/81‑1 (MQ=255)
aaTCCCGCCAGGGTGAAAA‑ACGACGATAACGCCCGCCACAACGGCTAACAGATGAAACGGCAAGCGACCGCCGTTAAACCa > 1:842301/1‑81 (MQ=255)
aTCCCGCCAGGGTGAAAA‑ACGACGATAACGCCCGCCACAACGGCTAACAGATGAAACGGCAAGCGACCGCCGTTAAACCa > 1:842320/1‑80 (MQ=255)
ccGCCAGGGTGAAAA‑ACGACGATAACGCCCGCCACAACGGCTAACAGATGAAACGGCAAGCGACCGCCGTTAAACCATAg < 2:842284/80‑1 (MQ=255)
aGGGTGAAAA‑ACGACGATACCGCCCGCCACAACGGCTAACAGATGAAACGGCAAGCGACCGCCGTTAAACCATAGCCAGCg < 2:842285/81‑1 (MQ=255)
|
GGATCGCGCAAAAATCACTGCTCCTCCACTAGCTCGGCTGCCTGATGCTGGCGCACGCGATTGAGCAATCCCGCCAGGGTG‑AAA‑ACGACGATAACGCCCGCCACAACGGCTAACAGATGAAACGGCAAGCGACCGCCGTTAAACCATAGCCAGCG > NC_000913/4567273‑4567427
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
