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 |
1,806,641 |
T→G |
100% |
A287A (GCT→GCG) |
emrB → |
multidrug efflux system protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,806,641 | 0 | T | G | 77.4%
| 61.6
/ 7.8
| 35 | A287A (GCT→GCG) | emrB | multidrug efflux system protein |
| Reads supporting (aligned to +/- strand): ref base T (3/5); new base G (1/26); total (4/31) |
| Fisher's exact test for biased strand distribution p-value = 3.02e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
TAAGTCGCGCAACTTCACCATCGGCTGCTTGTGTATCAGCCTCGCGTATATGCTCTACTTCGGCGCTATTGTTCTGCTGCCGCAGTTGTTGCAGGAGGTCTACGGTTACACGGCGACCTGGGCAGG > minE/1806575‑1806700
|
tAAGTCGCGCAACTTCACCATCGGCTGCTTGTGTATCAGCCTCGCGTATATGCTCTACTTCGGCGCTAt > 1:3343722/1‑69 (MQ=255)
tAAGTCGCGCAACTTCACCATCGGCTGCTTGTGTATCAGCCTCGCGTATATGCTCTACTTCGGCGCTAt > 1:179146/1‑69 (MQ=255)
ttCACCATCGGCTGCTTGTGTATCAGCCTCGCGTATATGCTCTACTTCGGCGCTATTGTTCtgctgc > 1:2927155/1‑67 (MQ=255)
cATCGGCTGCTTGTGTATCAGCCTCGCGTATATGCTCTACTTCGGCGCTATTGTTCTGCTGCCGCAgt < 1:888452/68‑1 (MQ=255)
cATCGGCTGCTTGTGTATCAGCCTCGCGTATATGCTCTACTTCGGCGCTATTGTTCTGCTGCCGCAgt < 1:2844540/68‑1 (MQ=255)
cATCGGCTGCTTGTGTATCAGCCTCGCGTATATGCTCTACTTCGGCGCTATTGTTCTGCTGCCGCAgt < 1:3115597/68‑1 (MQ=255)
cATCGGCTGCTTGTGTATCAGCCTCGCGTATATGCTCTACTTCGGCGCTATTGTTCTGCTGCCGCAgt < 1:808685/68‑1 (MQ=255)
cATCGGCTGCTTGTGTATCAGCCTCGCGTATATGCTCTACTTCGGCGCTATTGTTCTGCTGCCGCAgt < 1:829266/68‑1 (MQ=255)
ctctACTTCGGCGCGATTGTTCTGCTGCCGCAGTTGTTGCAGGAGGTCTACGGTTACACGGCGACGTg < 1:659010/68‑1 (MQ=255)
ctctACTTCGGCGCGATTGTTCTGCTGCCGCAGTTGTTGCAGGAGGTCTACGGTTACACGGCGACGTg < 1:351590/68‑1 (MQ=255)
ctctACTTCGGCGCGATTGTTCTGCTGCCGCAGTTGTTGCAGGAGGTCTACGGTTACACGGCGACGTg < 1:729407/68‑1 (MQ=255)
ctctACTTCGGCGCGATTGTTCTGCTGCCGCAGTTGTTGCAGGAGGTCTACGGTTACACGGCGACGTg < 1:791158/68‑1 (MQ=255)
ctctACTTCGGCGCGATTGTTCTGCTGCCGCAGTTGTTGCAGGAGGTCTACGGTTACACGGCGACGTg < 1:314547/68‑1 (MQ=255)
ctctACTTCGGCGCGATTGTTCTGCTGCCGCAGTTGTTGCAGGAGGTCTACGGTTACACGGCGACGTg < 1:3021056/68‑1 (MQ=255)
ctctACTTCGGCGCGATTGTTCTGCTGCCGCAGTTGTTGCAGGAGGTCTACGGTTACACGGCGACGTg < 1:2542426/68‑1 (MQ=255)
ctctACTTCGGCGCGATTGTTCTGCTGCCGCAGTTGTTGCAGGAGGTCTACGGTTACACGGCGACGTg < 1:2740791/68‑1 (MQ=255)
ctctACTTCGGCGCGATTGTTCTGCTGCCGCAGTTGTTGCAGGAGGTCTACGGTTACACGGCGACGTg < 1:1027944/68‑1 (MQ=255)
ctctACTTCGGCGCGATTGTTCTGCTGCCGCAGTTGTTGCAGGAGGTCTACGGTTACACGGCGACGTg < 1:1784382/68‑1 (MQ=255)
ctctACTTCGGCGCGATTGTTCTGCTGCCGCAGTTGTTGCAGGAGGTCTACGGTTACACGGCGACGTg < 1:113076/68‑1 (MQ=255)
ctctACTTCGGCGCGATTGTTCTGCTGCCGCAGTTGTTGCAGGAGGTCTACGGTTACACGGCGACGTg < 1:128157/68‑1 (MQ=255)
ctctACTTCGGCGCGATTGTTCTGCTGCCGCAGTTGTTGCAGGAGGTCTACGGTTACACGGCGACGTg < 1:1310191/68‑1 (MQ=255)
ctctACTTCGGCGCGATTGTTCTGCTGCCGCAGTTGTTGCAGGAGGTCTACGGTTACACGGCGACGTg < 1:1341728/68‑1 (MQ=255)
ctctACTTCGGCGCGATTGTTCTGCTGCCGCAGTTGTTGCAGGAGGTCTACGGTTACACGGCGACGTg < 1:1559605/68‑1 (MQ=255)
ctctACTTCGGCGCGATTGTTCTGCTGCCGCAGTTGTTGCAGGAGGTCTACGGTTACACGGCGACGTg < 1:1567260/68‑1 (MQ=255)
ctctACTTCGGCGCGATTGTTCTGCTGCCGCAGTTGTTGCAGGAGGTCTACGGTTACACGGCGACGTg < 1:2527267/68‑1 (MQ=255)
ctctACTTCGGCGCGATTGTTCTGCTGCCGCAGTTGTTGCAGGAGGTCTACGGTTACACGGCGACGTg < 1:1805481/68‑1 (MQ=255)
ctctACTTCGGCGCGATTGTTCTGCTGCCGCAGTTGTTGCAGGAGGTCTACGGTTACACGGCGACGTg < 1:1847038/68‑1 (MQ=255)
ctctACTTCGGCGCGATTGTTCTGCTGCCGCAGTTGTTGCAGGAGGTCTACGGTTACACGGCGACGTg < 1:196079/68‑1 (MQ=255)
ctctACTTCGGCGCGATTGTTCTGCTGCCGCAGTTGTTGCAGGAGGTCTACGGTTACACGGCGACGTg < 1:2019732/68‑1 (MQ=255)
ctctACTTCGGCGCGATTGTTCTGCTGCCGCAGTTGTTGCAGGAGGTCTACGGTTACACGGCGACGTg < 1:2045854/68‑1 (MQ=255)
ctctACTTCGGCGCGATTGTTCTGCTGCCGCAGTTGTTGCAGGAGGTCTACGGTTACACGGCGACGTg < 1:2154067/68‑1 (MQ=255)
ctctACTTCGGCGCGATTGTTCTGCTGCCGCAGTTGTTGCAGGAGGTCTACGGTTACACGGCGACGTg < 1:21774/68‑1 (MQ=255)
ctctACTTCGGCGCGATTGTTCTGCTGCCGCAGTTGTTGCAGGAGGTCTACGGTTACACGGAGACGTg < 1:7652/68‑1 (MQ=255)
tctACTTCGGCGCGATTGTTCTGCTGCCGCAGTTGTTGCAGGAGGTCTACGGTTACACGGCGACGTg < 1:495320/67‑1 (MQ=255)
ttCGGCGCGATTGTTATGCTGCCGCAGTTGTTGCAGGAGGTCTACGGTTACACGGCGACGTGGGCAgg > 1:349827/1‑68 (MQ=255)
|
TAAGTCGCGCAACTTCACCATCGGCTGCTTGTGTATCAGCCTCGCGTATATGCTCTACTTCGGCGCTATTGTTCTGCTGCCGCAGTTGTTGCAGGAGGTCTACGGTTACACGGCGACCTGGGCAGG > minE/1806575‑1806700
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
