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 |
|
A5 F1 I1 R1
|
770 |
51.4 |
2439994 |
93.8% |
2288714 |
110.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,288,561 |
(C)7→6 |
pseudogene (354/2525 nt) |
yejO ← |
pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,288,555 | 0 | C | . | 97.8%
| 176.5
/ ‑2.9
| 45 | pseudogene (360/2525 nt) | yejO | pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system |
| Reads supporting (aligned to +/- strand): ref base C (0/0); major base . (21/23); minor base A (1/0); total (22/23) |
| Fisher's exact test for biased strand distribution p-value = 4.89e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01 |
TTTGTTCCGAATACCTCCATGGCCCGCGTGGTTGTTTTAATAGCACCGCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGGCCCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTGCCGCGCCACCCATTTGAACAATTTGATAACCG > NC_000913/2288425‑2288688
|
tttGTTCCGAATACCTCCATGGCCCGCGTGGTTGTTTTAATAGCACCGCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGGccccccatc > 1:796393/1‑136 (MQ=255)
cTCCATGGCCCGCGTGGTTGTTTTAATAGCACCGCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTa > 1:468568/1‑139 (MQ=255)
ggCCCGCTTGGGTGTTTTAAGAGCCCCGCCTTCTTTCTTATCTACCGCAAATTGAAAGCCCCGCTCTTTAACCTCCAGTAGTCCTCCATTTTCGATGGCGAAAAAGACGG‑CCGCCCATCTTTTTCAACGATTATGcgcc < 1:27252/139‑1 (MQ=255)
ggCCCGCGTGGTTGTTTTAATAGCACCGCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGcgcc < 1:889997/139‑1 (MQ=255)
gCCCGCGTGGTTGTTTTAATAGCACCGCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCATCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGcgccc < 1:872972/139‑1 (MQ=255)
cccGCGTGGTTGTTTTAATAGCACCGCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGcgcccg > 2:1101191/1‑139 (MQ=255)
gTGGTTGTTTTAATAGCACCGCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCttt > 2:832489/1‑139 (MQ=255)
ggTTGTTTTAATAGCACCGCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTaa < 1:832489/139‑1 (MQ=255)
aGCACCGCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCAt > 2:263076/1‑139 (MQ=255)
aCCGCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCg < 2:796393/139‑1 (MQ=255)
aCCGCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCg > 1:997801/1‑139 (MQ=255)
gCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTg < 2:572037/139‑1 (MQ=255)
ccTGCTTTCTGATCTACCGCAAATGCCAATCCCCCCTCTTTAACCTCCAGTACCCCTCCCTTTTCGATCGCGACAAAGAC‑CACGCCCAATCTTTTTCAACGATTAAGCGCCCGCCTTTAATTGTGGTATCATTCCCTgc > 1:262972/1‑139 (MQ=255)
cTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCATGGTATCATTCGCTgcg > 2:931079/1‑139 (MQ=255)
tGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAAc < 2:468568/139‑1 (MQ=255)
tACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTa > 2:411942/1‑139 (MQ=255)
ccGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGc < 2:988298/139‑1 (MQ=255)
cGCAAATGCAAGTCCCCCCTCTTTAACCGCCACTAGTCATCCGTTTTCGATAGCGACTAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCAGTCGCTGCGCCATAAACCTGTAGca < 1:1030268/139‑1 (MQ=255)
cGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGca < 2:747569/139‑1 (MQ=255)
cGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGca < 2:1097549/139‑1 (MQ=255)
cGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCACCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGAAGca < 1:931079/139‑1 (MQ=255)
caaatgcaaatCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAg > 2:363741/1‑135 (MQ=255)
caaatgcaaatCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAg < 1:363741/135‑1 (MQ=255)
caaatgcaaatCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGcaca < 1:9940/139‑1 (MQ=255)
aatgcaaatCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTg < 2:350549/117‑1 (MQ=255)
aatgcaaatCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTg > 1:350549/1‑117 (MQ=255)
aatgcaaatCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACAcc > 1:1165312/1‑139 (MQ=255)
tgcaaatCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTg > 2:869177/1‑115 (MQ=255)
tgcaaatCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTg < 1:869177/115‑1 (MQ=255)
ccccTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCt > 1:85727/1‑105 (MQ=255)
ccccTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCt < 2:85727/105‑1 (MQ=255)
ccTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTa > 2:1213480/1‑139 (MQ=255)
agtagtCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTGCcgc > 2:506209/1‑139 (MQ=255)
gtCCTCCCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATCGAGCGTAGTCTGGTTTGCCGCGCCa > 1:319242/1‑139 (MQ=255)
cctccCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTGCCGCGCCa > 1:330021/1‑137 (MQ=255)
cctccCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTGCCGCGCCa < 2:330021/137‑1 (MQ=255)
ctccCTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTGCCGCGCCAccc > 1:556440/1‑139 (MQ=255)
cccTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTGCCGCGCCACCCAt > 1:960887/1‑139 (MQ=255)
cccTTTTCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTGCCGCGCCACCCAt > 2:199666/1‑139 (MQ=255)
ttttCGATAGCGACAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTGCCGCGCCACCCATTTg < 2:556440/139‑1 (MQ=255)
aCAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTg < 2:451617/111‑1 (MQ=255)
aCAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTg > 1:451617/1‑111 (MQ=255)
aCAAAGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTGCCGCGCCACCCATTTGAACAATTTGATa > 1:123239/1‑139 (MQ=255)
aGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTGCCGCGCCACCCATTTGAACAATTTGATAACCg < 1:1213480/139‑1 (MQ=255)
aGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTGCCGCGCCACCCATTTGAACAATTTGATAACCg < 1:1101191/139‑1 (MQ=255)
aGACGG‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTGCCGCGCCACCCATTTGAACAATTTGATAACCg < 2:123239/139‑1 (MQ=255)
|
TTTGTTCCGAATACCTCCATGGCCCGCGTGGTTGTTTTAATAGCACCGCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACGGCCCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTGCCGCGCCACCCATTTGAACAATTTGATAACCG > NC_000913/2288425‑2288688
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
