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 |
1,689,310 |
T→G |
47.1% |
D38A (GAT→GCT) |
yfhJ ← |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,689,310 | 0 | T | G | 47.1%
| ‑6.2
/ 81.8
| 68 | D38A (GAT→GCT) | yfhJ | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (17/19); new base G (24/8); total (41/27) |
| Fisher's exact test for biased strand distribution p-value = 2.61e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.74e-01 |
ATCGCTTCGAGGATTTTCTCGTTGGATGCCTGCGGGTCGTCGTCGAAATCTTCCAGATCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAAGATCGGGATACGCATCGTA > minE/1689253‑1689377
|
aTCGCTTCGAGGATTTTCTCGTTGGTTGCCTGCGGGTCGTCGTCGAAATCTTCCAGATCGCAAATCCa > 1:2689957/1‑68 (MQ=255)
aTCGCTTCGAGGATTTTCTCGTTGGATGCCTGCGGGTCGTCGTCGAAATCTTCCAGATCGCAAATcc > 1:2746900/1‑67 (MQ=255)
aTCGCTTCGAGGATTTTCTCGTTGGATGCCTGCGGGTCGTCGTCGAAATCTTCCAGATCGCAAATCCa > 1:1712242/1‑68 (MQ=255)
tcgATGCCTGCGGGTCGTCGTCGAAATCTTCCAGAGCGCAAATCCACTGATGCATATCGGTGAATCg < 1:1169314/65‑1 (MQ=255)
tcgATGCCTGCGGGTCGTCGTCGAAATCTTCCAGAGCGCAAATCCACTGATGCATATCGGTGAATCg < 1:1705123/65‑1 (MQ=255)
tcgATGCCTGCGGGTCGTCGTCGAAATCTTCCAGAGCGCAAATCCACTGATGCATATCGGTGAATCg < 1:2869137/65‑1 (MQ=255)
tcgATGCCTGCGGGTCGTCGTCGAAATCTTCCAGAGCGCAAATCCACTGATGCATATCGGTGAATCg < 1:376781/65‑1 (MQ=255)
tcgATGCCTGCGGGTCGTCGTCGAAATCTTCCAGAGCGCAAATCCACTGATGCATATCGGTGAATCg < 1:1497021/65‑1 (MQ=255)
tcgATGCCTGCGGGTCGTCGTCGAAATCTTCCAGAGCGCAAATCCACTGATGCATATCGGTGAATCg < 1:136966/65‑1 (MQ=255)
tcgATGCCTGCGGGTCGTCGTCGAAATCTTCCAGAGCGCAAATCCACTGATGCATATCGGTGAATCg < 1:1106810/65‑1 (MQ=255)
tcgATGCCTGCGGGTCGTCGTCGAAATCTTCCAGAGCGCAAATCCACTGATGCATATCGGTGAATCg < 1:959772/65‑1 (MQ=255)
gtcgtcgAAATCTTCCAGATCGCAAATCCACTGATGCATATCGGTGAATCg > 1:1489234/1‑51 (MQ=255)
gtcgtcgAAATCTTCCAGATCGCAAATCCACTGATGCATATCGGTGAATCGa > 1:636799/1‑52 (MQ=255)
gAAATCTTCCAGATCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAAGATCgg > 1:2117749/1‑68 (MQ=255)
gAAATCTTCCAGATCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAAGATCgg > 1:2471048/1‑68 (MQ=255)
gAAATCTTCCAGATCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAAGATCgg > 1:2758257/1‑68 (MQ=255)
gAAATCTTCCAGATCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAAGATCgg > 1:243050/1‑68 (MQ=255)
gAAATCTTCCAGATCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAAGATCgg > 1:3290958/1‑68 (MQ=255)
gAAATCTTCCAGATCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAAGATCgg > 1:370233/1‑68 (MQ=255)
gAAATCTTCCAGATCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAAGATCgg > 1:533181/1‑68 (MQ=255)
gAAATCTTCCAGATCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAAGATCgg > 1:1288284/1‑68 (MQ=255)
gAAATCTTCCAGATCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAAGATCgg > 1:626247/1‑68 (MQ=255)
gAAATCTTCCAGATCGCAAATCCACTGATGCATATCGGCGAATCGAACCGTTTTCGGATCAAGATCgg > 1:1584901/1‑68 (MQ=255)
gAAATCTTCCAGATCGCAAATCCACTGAAGCATATCGGTCAATCGAACCGTTTTCGGATCAAGATCgg > 1:1809416/1‑68 (MQ=255)
aaaaTCTTCCAGATCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAAGATCgg > 1:2556060/2‑68 (MQ=255)
aaTCTTCCAGATCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAAGATCGGGa < 1:2757952/68‑1 (MQ=255)
aaTCTTCCAGATCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAAGATCGGGa < 1:1607219/68‑1 (MQ=255)
aaTCTTCCAGATCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAAGATCGGGa < 1:3086909/68‑1 (MQ=255)
aaTCTTCCAGATCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAAGATCGGGa < 1:3051523/68‑1 (MQ=255)
aaTCTTCCAGATCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAAGATCGGGa < 1:302250/68‑1 (MQ=255)
aaTCTTCCAGATCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAAGATCGGGa < 1:2246527/68‑1 (MQ=255)
aaTCTTCCAGATCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAAGATCGGGa < 1:2924030/68‑1 (MQ=255)
aaTCTTCCAGATCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAAGATCGGGa < 1:168407/68‑1 (MQ=255)
aaTCTTCCAGATCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAAGATCGGGa < 1:2646063/68‑1 (MQ=255)
aaTCTTCCAGATCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAAGATCGGGa < 1:254313/68‑1 (MQ=255)
aaTCTTCCAGATCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAAGATCGGGa < 1:2291031/68‑1 (MQ=255)
aaTCTTCCAGATCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAAGATCGGGa < 1:863473/68‑1 (MQ=255)
aaTCTTCCAGATCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAAGATCGGGa < 1:2220698/68‑1 (MQ=255)
aTCTTCGAGAGCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAATATCAGGATa > 1:440273/1‑69 (MQ=255)
aTCTTCCAGATCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAAGATCGGGATa < 1:1776835/69‑1 (MQ=255)
aTCTTCCAGATCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAAGATCGGGATa < 1:2891307/69‑1 (MQ=255)
aTCTTCCAGATCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAAGATCGGGATa < 1:1528806/69‑1 (MQ=255)
aTCTTCCAGAGCGCGAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAATATCAGGATa > 1:2359243/1‑69 (MQ=255)
aTCTTCCAGAGCGCAAATCCACTGATGCATATCGGTGAATCGaa > 1:2737395/1‑44 (MQ=255)
aTCTTCCAGAGCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAATATCAGGATa > 1:2929173/1‑69 (MQ=255)
aTCTTCCAGAGCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAATATCAGGATa > 1:585492/1‑69 (MQ=255)
aTCTTCCAGAGCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAATATCAGGATa > 1:1285224/1‑69 (MQ=255)
aTCTTCCAGAGCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAATATCAGGATa > 1:644951/1‑69 (MQ=255)
aTCTTCCAGAGCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAATATCAGGATa > 1:710212/1‑69 (MQ=255)
aTCTTCCAGAGCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAATATCAGGATa > 1:1526306/1‑69 (MQ=255)
aTCTTCCAGAGCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAATATCAGGATa > 1:1178137/1‑69 (MQ=255)
aTCTTCCAGAGCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAATATCAGGATa > 1:1282633/1‑69 (MQ=255)
aTCTTCCAGAGCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAATATCAGGATa > 1:3332120/1‑69 (MQ=255)
aTCTTCCAGAGCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAATATCAGGATa > 1:978079/1‑69 (MQ=255)
aTCTTCCAGAGCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAATATCAGGATa > 1:3190278/1‑69 (MQ=255)
aTCTTCCAGAGCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAATATCAGGATa > 1:3092274/1‑69 (MQ=255)
aTCTTCCAGAGCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAATATCAGGATa > 1:3012744/1‑69 (MQ=255)
aTCTTCCAGAGCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAATATCAGGATa > 1:2778982/1‑69 (MQ=255)
aTCTTCCAGAGCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAATATCAGGATa > 1:2065933/1‑69 (MQ=255)
aTCTTCCAGAGCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAATATCAGGATa > 1:2086788/1‑69 (MQ=255)
aTCTTCCAGAGCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAATATCAGGATa > 1:2224905/1‑69 (MQ=255)
aTCTTCCAGAGCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAATATCAGGATa > 1:2357111/1‑69 (MQ=255)
aTCTTCCAGAGCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAATATCAGGATa > 1:2332531/1‑69 (MQ=255)
aTCTTCCAGAGCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAATATCAGGATa > 1:2286603/1‑69 (MQ=255)
aTCTTCCAGAGCGCAAATCCACTGATCCATATCGGTGAATCGAACCGTTTTCGGATCAATATCAGGa > 1:1362533/1‑67 (MQ=255)
aTCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAAGATCGGGATACGCATCGTa < 1:2897586/69‑1 (MQ=255)
aTCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAAGATCGGGATACGCATCGTa < 1:604146/69‑1 (MQ=255)
aTCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAAGATCGGGATACGCATCGTa < 1:1814683/69‑1 (MQ=255)
|
ATCGCTTCGAGGATTTTCTCGTTGGATGCCTGCGGGTCGTCGTCGAAATCTTCCAGATCGCAAATCCACTGATGCATATCGGTGAATCGAACCGTTTTCGGATCAAGATCGGGATACGCATCGTA > minE/1689253‑1689377
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
