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 |
|
A6 F21 I0 R1
|
2169 |
63.0 |
3952800 |
76.2% |
3012033 |
62.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,933,231 |
G→A |
28.6% |
N404N (AAC→AAT) |
lysS ← |
lysine tRNA synthetase, constitutive |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,933,231 | 0 | G | A | 28.6%
| 95.2
/ 42.9
| 63 | N404N (AAC→AAT) | lysS | lysine tRNA synthetase, constitutive |
| Reads supporting (aligned to +/- strand): ref base G (13/32); new base A (8/10); total (21/42) |
| Fisher's exact test for biased strand distribution p-value = 2.53e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.87e-01 |
TAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTACGACGCGCCAGCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGC > minE/1933161‑1933299
|
tAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAAcgtcg > 1:1676638/1‑71 (MQ=255)
aaGCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAAcgtcgt < 1:770120/70‑1 (MQ=255)
ccattACCGATTTCACGACCACCGATGAAGAATTCAAAACGGTCGGTGATTTCCGGGTTAACATCATTacg > 1:3628617/4‑71 (MQ=255)
ccGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTacg < 1:3698967/71‑1 (MQ=255)
attACCGATTTCACGACCACCGATGAAGAATTCAAAACGGTCGGTGATTTCCGGGTTAACATCATTacgg > 1:3154713/2‑69 (MQ=255)
aCCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTacgac > 1:3619747/1‑68 (MQ=255)
aCCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTACGAcgc < 1:368352/70‑1 (MQ=255)
aTTTCACGACCACCGATGAAGAATTCAAAACGGTCGGTGATTTCCGGGTTAACATCATTACGGCGTGCCAg < 1:670838/71‑1 (MQ=255)
aTTTCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTACGACGCGCCAg > 1:788704/1‑71 (MQ=255)
aTTTCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTACGACGCGCCAg > 1:3506037/1‑71 (MQ=255)
tttCACGACCACCGATGAAGAATTCAAAACGGTCGGTGATTTCCGGGTTAACATCATTACGGCGTGCCAGc < 1:3943499/71‑1 (MQ=255)
ttCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTACGACgcgc > 1:3070692/1‑66 (MQ=255)
tCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTACGACGCGCCAGCg < 1:1834786/70‑1 (MQ=255)
tCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTACGACGCGCCAGCg < 1:2078351/70‑1 (MQ=255)
cACGACCACCGATGAAGAATTCAAAACGGTCGGTGATTTCCGGGTTAACATCATTACGGCGTGCCAGCgg < 1:1340749/70‑1 (MQ=255)
aCGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTa > 1:2210341/1‑55 (MQ=255)
aCGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTACGACGCGCCAGCGga < 1:2053879/70‑1 (MQ=255)
gACCACCGATGAAGAATTCAAAACGGTCGGTGATTTCCGGGTTAACATCATTACGGCGTGCCAGCGggga > 1:3336015/1‑70 (MQ=255)
gACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTACGACGCGCCAGCg < 1:1943883/66‑1 (MQ=255)
gACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTACGACGCGCCAGCGgaga < 1:1762637/70‑1 (MQ=255)
gACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTACGACGCGCCAGCGgaga < 1:2000826/70‑1 (MQ=255)
gACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTACGACGCGCCAGCGgag > 1:2691720/1‑69 (MQ=255)
accaccAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTACGACGCGCCAGCGGAGaaa < 1:489697/71‑1 (MQ=255)
ccaccaATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTac < 1:1077931/52‑1 (MQ=255)
caccaATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTACGACGCGCCAGCGGAGAAAc < 1:2885904/70‑1 (MQ=255)
caccaATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTACGACGCGCCAGCGGAGAAACt < 1:986997/71‑1 (MQ=255)
cgaTGAAGAATTCAAAACGGTCGGTGATTTCCGGGTTAACATCATTACGGCGTGCCAGCGgggac < 1:2261431/63‑2 (MQ=255)
caATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTACGACGCGCCAGCGGAGAAACTTCt < 1:1541563/71‑1 (MQ=255)
gaTGAAGAATTCAAAACGGTCGGTGATTTCCGGGTTAACATCATTACGGCGTGCCAGCGGGGACACTTCTg < 1:990147/70‑1 (MQ=255)
gaTGAAGAATTCAAAACGGTCGGTGATTTCCGGGTTAACATCATTACGGCGTGCCAGCGGGGACACTTCTg < 1:2143574/70‑1 (MQ=255)
tGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTac < 1:119065/45‑1 (MQ=255)
tGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTac < 1:3267990/45‑1 (MQ=255)
gaagaaCTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTACGACGCGCCAGCGGAGAAACTTCTGCCg > 1:767057/1‑71 (MQ=255)
gaaTTCAAAACGGTCGGTGATTTCCGGGTTAACATCATTACGGCGTGCCAGCGGGGACACTTCTGCCGGa > 1:3235564/1‑70 (MQ=255)
attCAAAACGGTCGGTGATTTCCGGGTTAACATCATTACGGCGTGCCAGCGGGGACACTTCTGCCGGatat < 1:1320466/69‑1 (MQ=255)
cTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTACGAcgc < 1:3357586/43‑1 (MQ=255)
cTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTACGACGCGCCAGCGGAGAAACTTCTGCCGGATAtt < 1:3411527/71‑1 (MQ=255)
cAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTACGACGCGCCAGCGGAGAAACTTCTGCCgg < 1:722270/64‑1 (MQ=255)
cAAAACGGTCGGTGATTTCCGGGTTAACATCATTACGGCGTGCCAGCGGGGACACTTCTGCCGGATAtt < 1:704346/69‑1 (MQ=255)
aaaGCGGTCTGTGATTTCCGGGTTAACGTCGTTACGACGCGCCAGCGGAGAAACTTCTGCCGGATATTc < 1:1405310/69‑1 (MQ=255)
aaGCGGTCTGTGATTTCCGGGTTAACGTCGTTacga > 1:3196846/1‑36 (MQ=255)
aGCGGTCTGTGATTTCCGGGTTAACGTCGTTACGACGCGCCAGCgg > 1:809687/1‑46 (MQ=255)
aGCGGTCTGTGATTTCCGGGTTAACGTCGTTACGACGCGCCAGCgg > 1:3497264/1‑46 (MQ=255)
gCGGTCTGTGATTTCCGGGTTAACGGCGTTACGACGCGCCAGCGgaga < 1:2889304/48‑1 (MQ=255)
cggtcggtGATTTCCGGGTTAACATCATTACGGCGTGCCAGCGGGGACACTTCTGCCGGata > 1:245831/1‑62 (MQ=255)
cGGTCTGTGATTTCCGGGTTAACGTCGTTACGACGCGCCAGCGga < 1:3150566/45‑1 (MQ=255)
ggTCTGTGATTTCCGGGTTAACGTCGTTACGACGCGCCAGCGGAGAAACTTCTGCCGGATATTCAGTAATg < 1:147228/71‑1 (MQ=255)
ggTCGGTGATTTCCGGGTTAACATCATTACGGCGTGCCAGc < 1:2229912/41‑1 (MQ=19)
gTCTGTGATTTCCGGGTTAACGTCGTTACGACGCGCCAGCGGAGAAACTTCTGCCGGATATTCAGTAATGa < 1:1878731/71‑1 (MQ=255)
gTCGGTGATTTCCGGGTTAACATCATTACGGCGTGCCAGCGGGGACACTTCTGCCGGATATTCCGTAAtaa < 1:3803418/71‑3 (MQ=255)
tCTGTGATTTCCGGGTTAACGTCGTTACGACGCGCCAGCg < 1:1183831/40‑1 (MQ=255)
tCTGTGATTTCCGGGTTAACGTCGTTACGACGCGCCAGCg < 1:2258177/40‑1 (MQ=255)
tCTGTGATTTCCGGGTTAACGTCGTTACGACGCGCCAGCGGAGAAACtt < 1:2256603/49‑1 (MQ=255)
cggtgATTTCCGGGTTAACATCATTACGGCGTGCCAGCGGGGACACTTCTGCCGGATATTCCGTAATAAAg > 1:2340843/3‑71 (MQ=255)
tgtgATTTCCGGGTTAACGTCGTTACGACGCGCCAGCGGAGAAACTTCTGCCGGa < 1:1264421/55‑1 (MQ=255)
gcgATTTCCGGGTTAACGTCGTTACGACGCGCCAGCGGAGAAACTTCTGCCGGATATTCAGTaa < 1:3846345/62‑1 (MQ=255)
gATTTCCGGGTTAACGTCGTTACGACGCGCCAGCGga > 1:2496929/1‑37 (MQ=255)
aTTTCCGGGTTAACATCATTACGGCGTGCCAGCGGGGACACTTCTGCCGGATATTCCGTAATAAAGGTTgg > 1:3352935/1‑71 (MQ=255)
ccGGGTTAACATCATTACGGCGTGCCAGCGGGGACACTTCTGCCGGATATTCCGTAATAAAGGTTGGCTg > 1:2317851/1‑70 (MQ=255)
ggTTAACGTCGTTACGACGCGCCAGCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGt < 1:892255/61‑1 (MQ=255)
ggTTAACGTCGTTACGACGCGCCAGCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAAt > 1:3920323/1‑70 (MQ=255)
gTTAACGTCGTTACGACGCGCCAGCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAAt > 1:1595899/1‑69 (MQ=255)
ttAACGTCGTTACGACGCGCCAGCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTCg < 1:3165632/61‑1 (MQ=255)
ttAACGTCGTTACGACGCGCCAGCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAg < 1:1366373/71‑1 (MQ=255)
ttAACGTCGTTACGACGCGCCAGCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAg < 1:867695/71‑1 (MQ=255)
cgtcgtTACGACGCGCCAGCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGAtgt < 1:971606/71‑1 (MQ=255)
gtcgtTACGACGCGCCAGCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGAtgtg > 1:3734586/1‑71 (MQ=255)
tcgtTACGACGCGCCAGCGGAGAAACTTCTGCCGAATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGc < 1:2590603/71‑1 (MQ=255)
gtTACGACGCGCCAGCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGc > 1:1879522/1‑69 (MQ=255)
|
TAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTACGACGCGCCAGCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGC > minE/1933161‑1933299
|
| 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
