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 |
|
A12 F28 I1 R1
|
227 |
52.0 |
1764248 |
99.3% |
1751898 |
138.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
1,594,256 |
(C)8→10 |
pseudogene (3831/5422 nt) |
yneO ← |
AIDA‑I family autotransporter YneO |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 1,594,248 | 1 | . | C | 98.1%
| 177.8
/ ‑3.2
| 52 | pseudogene (3839/5422 nt) | yneO | AIDA‑I family autotransporter YneO |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base C (26/25); total (27/25) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.32e-01 |
| * | NC_000913 | 1,594,248 | 2 | . | C | 82.7%
| 146.2
/ 26.4
| 52 | pseudogene (3839/5422 nt) | yneO | AIDA‑I family autotransporter YneO |
| Reads supporting (aligned to +/- strand): ref base . (4/5); new base C (23/20); total (27/25) |
| Fisher's exact test for biased strand distribution p-value = 7.22e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.21e-01 |
GACACGCAGTGCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTT‑‑‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAGCTACGCTCAGT > NC_000913/1594114‑1594378
||
cacacGCAGTGCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTT‑‑‑ccccc < 1:63166/139‑1 (MQ=255)
aGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCcgtcgt > 1:820732/1‑140 (MQ=255)
aGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCcgtcgt > 1:428396/1‑140 (MQ=255)
aGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCcgtcgt > 1:252251/1‑140 (MQ=255)
cATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATAcgc > 1:363478/1‑140 (MQ=255)
tCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCcgcg < 1:168151/140‑1 (MQ=255)
ccTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGaa > 2:462111/1‑140 (MQ=255)
tGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATc < 2:493223/140‑1 (MQ=255)
gtggtgACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCgttg > 1:528352/1‑140 (MQ=255)
tggtgACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCgttgtt < 1:599734/140‑1 (MQ=255)
ggtgACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCgttgtt < 2:437483/140‑1 (MQ=255)
ggtgACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTCATACGCCGCGGAATCgttgtt < 2:628357/140‑1 (MQ=255)
gtgACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCgttgtt > 2:420186/1‑139 (MQ=255)
gtgACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCgttgtt < 1:420186/139‑1 (MQ=255)
gtgACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTa < 2:323114/140‑1 (MQ=255)
gtgACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTa > 1:442746/1‑140 (MQ=255)
gtgACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTaa > 2:663773/1‑140 (MQ=255)
ccGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGa > 1:21504/1‑140 (MQ=255)
aTCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCg < 1:462111/140‑1 (MQ=255)
ttAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCa < 2:442746/140‑1 (MQ=255)
tAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCac > 2:689075/1‑140 (MQ=255)
tAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCac > 2:601704/1‑140 (MQ=255)
tAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCac > 1:708588/1‑140 (MQ=255)
tAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCac > 2:281583/1‑140 (MQ=255)
tAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCacc > 2:481604/1‑140 (MQ=255)
gtgtTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccgct < 1:281583/140‑1 (MQ=255)
gtgtTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccgct < 2:820732/140‑1 (MQ=255)
tgtTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccgctac < 1:663773/140‑1 (MQ=255)
tgtTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccgctac < 2:876506/140‑1 (MQ=255)
tgtTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccgctac < 1:481604/140‑1 (MQ=255)
gtTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccgctac < 1:689075/140‑1 (MQ=255)
ttGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccgctac < 1:169533/140‑1 (MQ=255)
gCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATa < 2:428396/140‑1 (MQ=255)
ccATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATAc > 1:809090/1‑140 (MQ=255)
ccATATTAATGGCAGAGTCGGAACCGAAAGCAATTT‑‑‑CCCCCCCCCCAACGATATCCGTCGAACCCTAAAACGCCCGGAAATCGTTTTTAAAGGCCAGCATCCCGGTACCCAGTTTTTCCCCACAACCCCTACCGCGGaac > 2:815855/1‑138 (MQ=255)
ggCAGAGTCGGAACCGAAAGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCAt > 1:347059/1‑140 (MQ=255)
ggCAGAGTCGGAACCGAAAGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCAt > 1:754731/1‑140 (MQ=255)
ggCAGAGTCGGAACCGAAAGCAATTTC‑‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATc > 2:657538/1‑140 (MQ=255)
agagTCGGAACCGAAAGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGc < 2:363478/140‑1 (MQ=255)
gagTCGGAACCGAAAGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGcc < 2:754731/140‑1 (MQ=255)
gagCCGGAACCGAAAGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGcc < 2:34780/140‑1 (MQ=255)
gggcGGAACCGAAAGCAATTTCCCCCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGcc < 1:815855/137‑1 (MQ=255)
agTCGGAACCGAAAGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCa > 1:683220/1‑134 (MQ=255)
agTCGGAACCGAAAGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCa < 2:683220/134‑1 (MQ=255)
agTCGGAACCGAAAGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGccc > 1:798905/1‑140 (MQ=255)
agTCGGAACCGAAAGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGcc < 2:207268/139‑1 (MQ=255)
agTCGGAACCGAAAGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGcc > 1:207268/1‑139 (MQ=255)
agTCGGAACCGAAAGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGGACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGccc > 1:489029/1‑140 (MQ=255)
aaaGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAGCTACGCTCa > 2:676209/1‑140 (MQ=255)
aaGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAGCTACGCTCAg > 2:230738/1‑140 (MQ=255)
aaGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAGCTACGCTCAg > 2:155069/1‑140 (MQ=255)
aaGCAATTTC‑‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAGCTACGCTCAGt < 1:657538/140‑1 (MQ=255)
aGCAATTTCC‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAGCTACGCTCAGt < 1:642970/140‑1 (MQ=255)
||
GACACGCAGTGCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTT‑‑‑CCCCCCCC‑‑‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAGCTACGCTCAGT > NC_000913/1594114‑1594378
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
