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 F17 I0 R1
|
71 |
95.7 |
2922988 |
91.7% |
2680379 |
65.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
656,044 |
T→C |
100% |
F44L (TTC→CTC) |
ycbS → |
predicted outer membrane usher protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 656,044 | 0 | T | C | 79.0%
| 34.5
/ 6.1
| 19 | F44L (TTC→CTC) | ycbS | predicted outer membrane usher protein |
| Reads supporting (aligned to +/- strand): ref base T (4/0); new base C (0/15); total (4/15) |
| Fisher's exact test for biased strand distribution p-value = 2.58e-04 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.38e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
TTTGTGTCGGCAGCGTTCAATGCACAAGCTGAAACCTGGTTCGATCCTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACA > minE/655990‑656096
|
tttGTGTCGGCAGCGTTCAATGCACAAGCTGAAACCTGGTTCGATCCTGCTTTTTTCAAAga > 1:183472/1‑62 (MQ=255)
tttGTGTCGGCAGCGTTCAATGCACAAGCTGAAACCTGGTTCGATCCTGCTTTTTTCAAAGATGATACCt > 1:2252913/1‑70 (MQ=255)
tgtgTCGGCAGCGTTCAATGCACAAGCTGAAACCTGGTTCGATCCTGCTTTTTTCAAAGATGATCCCTCaa > 1:1453427/1‑71 (MQ=255)
tgtgTCGGCAGCGTTCAATGCACAAGCTGAAACCTGGTTCGATCCTGCTTTTTTCAAAGATGATCCCTCaa > 1:2180887/1‑71 (MQ=255)
gTTCGATCCTGCTTTTCTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACa < 1:2145208/69‑1 (MQ=255)
gTTCGATCCTGCTTTTCTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACa < 1:494339/69‑1 (MQ=255)
gTTCGATCCTGCTTTTCTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACa < 1:381850/69‑1 (MQ=255)
gTTCGATCCTGCTTTTCTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACa < 1:2405010/69‑1 (MQ=255)
gTTCGATCCTGCTTTTCTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACa < 1:2382286/69‑1 (MQ=255)
gTTCGATCCTGCTTTTCTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACa < 1:2379433/69‑1 (MQ=255)
gTTCGATCCTGCTTTTCTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACa < 1:2276746/69‑1 (MQ=255)
gTTCGATCCTGCTTTTCTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACa < 1:2227129/69‑1 (MQ=255)
gTTCGATCCTGCTTTTCTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACa < 1:102089/69‑1 (MQ=255)
gTTCGATCCTGCTTTTCTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACa < 1:1937403/69‑1 (MQ=255)
gTTCGATCCTGCTTTTCTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACa < 1:1790798/69‑1 (MQ=255)
gTTCGATCCTGCTTTTCTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACa < 1:1629366/69‑1 (MQ=255)
gTTCGATCCTGCTTTTCTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACa < 1:1605367/69‑1 (MQ=255)
gTTCGATCCTGCTTTTCTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACa < 1:1238338/69‑1 (MQ=255)
gTTCGATCCTGCTTTTCTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACa < 1:1155392/69‑1 (MQ=255)
|
TTTGTGTCGGCAGCGTTCAATGCACAAGCTGAAACCTGGTTCGATCCTGCTTTTTTCAAAGATGATCCCTCAATGGTGGCCGATTTGTCTCGTTTCGAAAAAGGACA > minE/655990‑656096
|
| 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
