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 |
|
A4 F28 I1 R1
|
128 |
54.7 |
1845674 |
99.3% |
1832754 |
139.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
3,599,887 |
(A)5→6 |
intergenic (‑229/+42) |
livJ ← / ← rpoH |
branched chain amino acid/phenylalanine ABC transporter periplasmic binding protein/RNA polymerase, sigma 32 (sigma H) factor |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 3,599,882 | 1 | . | A | 97.6%
| 140.7
/ ‑3.4
| 41 | intergenic (‑224/+47) | livJ/rpoH | branched chain amino acid/phenylalanine ABC transporter periplasmic binding protein/RNA polymerase, sigma 32 (sigma H) factor |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base A (25/15); total (25/16) |
| Fisher's exact test for biased strand distribution p-value = 3.90e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01 |
GCTTTAGCAGCATACTCTGCTAAAACATACCCGATTTTTATGATATTGGAATAGCTATTTTGACAGTTTATTAACAATCTGCGTGGGGATTGGCGTTTTGCCGGAGGGGAAATTGATTATTACAGAGGCCCAAAAAAC‑AAAAACCCCGGACTCTCATCCAGGGTTCTCTGCTTAATAGCGGAAATTACGCTTCAATGGCAGCACGCAATTTTTTCATCGCGTTCTTTTCCAGCTGGCGTACACGCTCAGCGGAAACGCCGTAACGGTCAG > NC_000913/3599745‑3600014
|
gCTTTGGCAGAATACTCTGCTAAAACATACCCGATTTTTATGATATTGGAATAGCTATTTTGACAGTTTATTAACAATCTGCGTGGGGATTGGCGTTTTGCCGGAGGGGAAATTGATTATTACAGAGGCCCAaaaaac‑aa > 2:423848/1‑140 (MQ=255)
gCTTTAGCAGCATACTCTGCTAAAACATACCCGATTTTTATGATATTGGAATAGCTATTTTGACA‑TTTATTAACAATCTGCGTGGGGATTGGCGTTTTGCCGGAGGGGAAATTGATTATTACAGAGGCCCAaaaaac‑aaa > 1:348604/1‑140 (MQ=255)
cTTTAGCAGCATACTCTGCTAAAACATACCCGATTTTTATGATATTGGAATAGCTATTTTGACAGTTTATTAACAATCTGCGTGGGGATTGGCGTTTTGCCGGAGGGGAAATTGATTATTACAGAGGCCCAaaaaac‑aaa > 2:879707/1‑140 (MQ=255)
cTTTAGCAGCATACTCTGCTAAAACATACCCGATTTTTATGATATTGGAATAGCTATTTTGACAGTTTATTAACAATCTGCGTGGGGATTGGCGTTTTGCCGGAGGGGAAATTGATTATTACAGAGGCCCAaaaaac‑aaa > 1:834052/1‑140 (MQ=255)
cTTTAGCAGCATACTCTGCTAAAACATACCCGATTTTTATGATATTGGAATAGCTATTTTGACAGTTTATTAACAATCTGCGTGGGGATTGGCGTTTTGCCGGAGGGGAAATTGATTATTACAGAGGCCCAaaaaac‑aaa < 1:49469/140‑1 (MQ=255)
gcaTACTCTGCTAAAACATACCCGATTTTTATGATATTGGAATAGCTATTTTGACAGTTTATTAACAATCTGCGTGGGGATTGGCGTTTTGCCGGAGGGGAAATTGATTATTACAGAGGCCCAAAAAAC‑AAAAAaccccg < 2:628775/140‑3 (MQ=255)
aCTCTGCTAAAACATACCCGATTTTTATGATATTGGAATAGCTATTTTGACAGTTTATTAACAATCTGCGTGGGGATTGGCGTTTTGCCGGAGGGGAAATTGATTATTACAGAGGCCCAAAAAACAAAAAACCCCGGAct < 1:423848/140‑1 (MQ=255)
tAAAACATACCCGATTTTTATGATATTGGAATAGCTATTTTGACAGTTTATTAACAATCTGCGTGGGGATTGGCGTTTTGCCGGAGGGGAAATTGATTATTACAGAGGCCCAAAAAACAAAAAACCCCGGACTCTCATcc < 2:141338/140‑1 (MQ=255)
tAAAACATACCCGATTTTTATGATATTGGAATAGCTATTTTGACAGTTTATTAACAATCTGCGTGGGGATTGGCGTTTTGCCGGAGGGGAAATTGATTATTACAGAGGCCCAAAAAACAAAAAACCCAGGACTCTCATcc > 1:240098/1‑140 (MQ=255)
aaaaCATACCCGATTTTTATGATATTGGAATAGCTATTTTGACAGTTTATTAACAATCTGCGTGGGGATTGGCGTTTTGCCGGAGGGGAAATTGATTATTACAGAGGCCCAAAAAACAAAAAACCCCGGACTCTCATCCa < 2:251232/140‑1 (MQ=255)
aaaCATACCCGATTTTTATGATATTGGAATAGCTATTTTGACAGTTTATTAACAATCTGCGTGGGGATTGGCGTTTTGCCGGAGGGGAAATTGATTATTACAGAGGCCCAAAAAACAAAAAACCCCGGACTCTCATCCAg > 1:351366/1‑140 (MQ=255)
tACCCGATTTTTATGATATTGGAATAGCTATTTTGACA‑TTTATTAACAATCTGCGTGGGGATTGGCGTTTTGCCGGAGGGGAAATTGATTATTACAGAGGCCCAAAAAACAAAAAACCCCGGACTCTCATCCAGGGTtct < 2:348604/140‑1 (MQ=255)
aTTTTTATGATATTGGAATAGCTATTTTGACAGTTTATTAACAATCTGCGTGGGGATTGGCGTTTTGCCGGAGGGGAAATTGATTATTACAGAGGCCCAAAAAACAAAAAACCCCGGACTCTCATCCAGGGTTCTCTGCt > 2:132149/1‑140 (MQ=255)
ttttATGATATTGGAATAGCTATTTTGACAGTTTATTAACAATCTGCGTGGGGATTGGCGTTTTGCCGGAGGGGAAATTGATTATTACAGAGGCCCAAAAAACAAAAAACCCCGGACTCTCATCCAGGGTTCTCTGCTTa < 2:273735/140‑1 (MQ=255)
tGATATTGGAATAGCTATTTTGACAGTTTATTAACAATCTGCGTGGGGATTGGCGTTTTGCCGGAGGGGAAATTGATTATTACAGAGGCCCAAAAAACAAAAAACCCCGGACTCTCATCCAGGGTTCTCTGCTTAATAGc < 1:142755/140‑1 (MQ=255)
gATATTGGAATAGCTATTTTGACAGTTTATTAACAATCTGCGTGGGGATTGGCGTTTTGCCGGAGGGGAAATTGATTATTACAGAGGCCCAAAAAACAAAAAACCCCGGACTCTCATCCAGGGTTCTCTGCTTAATAGCg < 2:336061/140‑1 (MQ=255)
tatTGGAATAGCTATTTTGACAGTTTATTAACAATCTGCGTGGGGATTGGCGTTTTGCCGGAGGGGAAATTGATTATTACAGAGGCCCAAAAAACAAAAAACCCAGGACTCTCATCCAGGGTTCTCTGCTTAATAGCGGa < 2:240098/140‑1 (MQ=255)
ggAATAGCTATTTTGACAGTTTATTAACAATCTGCGTGGGGATTGGCGTTTTGCCGGAGGGGAAATTGATTATTACAGAGGCCCAAAAAACAAAAAACCCCGGACTCTCATCCAGGGTTCTCTGCTTAATAGCGGAAAtt > 1:230194/1‑140 (MQ=255)
gCTATTTTGACAGTTTATTAACAATCTGCGTGGGGATTGGCGTTTTGCCGGAGGGGAAATTGATTATTACAGAGGCCCAAAAAACAAAAAACCCCGGACTCTCATCCAGGGTTCTCTGCTTAATAGCGGAAATTACGCtt > 1:264176/1‑140 (MQ=255)
cTATTTTGACAGTTTATTAACAATCTGCGTGGGGATTGGCGTTTTGCCGGAGGGGAAATTGATTATTACAGAGGCCCAAAAAACAAAAAACCCCGGACTCTCATCCAGGGTTCTCTGCTTAATAGCGGAAATTACGCTTc > 1:660623/1‑140 (MQ=255)
tGCGTGGGGATTGGCGTTTTGCCGGAGGGGAAATTGATTATTACAGAGGCCCAAAAAACAAAAAACCCCGGACTCTCATCCAGGGTTCTCTGCTTAATAGCGGAAATTACGCTTCAATGGCAGCACGCAATTTTTTCATc < 1:132149/140‑1 (MQ=255)
tGCGTGGGGATTGGCGTTTTGCCGGAGGGGAAATTGATTATTACAGAGGCCCAAAAAACAAAAAACCCCGGACTCTCATCCAGGGTTCTCTGCTTAATAGCGGAAATTACGCTTCAATGGCAGCACGCAATTTTTTCATc > 1:70697/1‑140 (MQ=255)
gCGTGGGGATTGGCGTTTTGCCGGAGGGGAAATTGATTATTACAGAGGCCCAAAAAACAAAAAACCCCGGACTCTCATCCAGGGTTCTCTGCTTAATAGCGGAAATTACGCTTCAATGGCAGCACGCAATTTTTTCATcg > 1:44698/1‑140 (MQ=255)
aTTGGCGTTTTGCCGGAGGGGAAATTGATTATTACAGAGGCCCAAAAAACAAAAAACCCCGGACTCTCATCCAGGGTTCTCTGCTTAATAGCGGAAATTACGCTTCAATGGCAGCACGCAATTTTTTCATCGCGTTCttt > 2:425890/1‑140 (MQ=255)
ggCGTTTTGCCGGAGGGGAAATTGATTATTACAGAGGCCCAAAAAACAAAAAACCCCGGACTCTCATCCAGGGTTCTCTGCTTAATAGCGGAAATTACGCTTCAATGGCAGCACGCAATTTTTTCATCGCGTTCTTTTcc > 1:314680/1‑140 (MQ=255)
cGTTTTGCCGGAGGGGAAATTGATTATTACAGAGGCCCAAAAAACAAAAAACCCCGGACTCTCATCCAGGGTTCTCTGCTTAATAGCGGAAATTACGCTTCAATGGCAGCACGCAATTTTTTCATCGCGTTCTTTTCCAg < 1:425890/140‑1 (MQ=255)
ttttGCCGGAGGGGAAATTGATTATTACAGAGGCCCAAAAAACAAAAAACCCCGGACTCTCATCCAGGGTTCTCTGCTTAATAGCGGAAATTACGCTTCAATGGCAGCACGCAATTTTTTCATCGCGTTCTTTTCCAGCt < 1:144725/140‑1 (MQ=255)
ttttGCCGGAGGGGAAATTGATTATTACAGAGGCCCAAAAAACAAAAAACCCCGGACTCTCATCCAGGGTTCTCTGCTTAATAGCGGAAATTACGCTTCAATGGCAGCACGCAATTTTTTCATCGCGTTCTTTTCCAGCt < 2:44698/140‑1 (MQ=255)
tttGCCGGAGGGGAAATTGATTATTACAGAGGCCCAAAAAACAAAAAACCCCGGACTCTCATCCAGGGTTCTCTGCTTAATAGCGGAAATTACGCTTCAATGGCAGCACGCAATTTTTTCATCGCGtt > 2:652522/1‑128 (MQ=255)
tttGCCGGAGGGGAAATTGATTATTACAGAGGCCCAAAAAACAAAAAACCCCGGACTCTCATCCAGGGTTCTCTGCTTAATAGCGGAAATTACGCTTCAATGGCAGCACGCAATTTTTTCATCGCGtt < 1:652522/128‑1 (MQ=255)
tttGCCGGAGGGGAAATTGATTATTACAGAGACCCAAAAAACAAAAAACCCCGGACTCTCATCCAGGGTTCTCTGCTTAATAGCGGAAATTACGCTTCAATGGCAGCACGCAATTTTTTCATCGCGTTCTTTTCCAGCTg > 2:660271/1‑140 (MQ=255)
ttGCCGGAGGGGAAATTGATTATTACAGAGGCCCAAAAAACAAAAAACCCCGGACTCTCATCCAGGGTTCTCTGCTTAATAGCGGAAATTACGCTTCAATGGCAGCACGCAATTTTTTCATCGCGTTCTTTTCCAg > 1:724480/1‑136 (MQ=255)
ttGCCGGAGGGGAAATTGATTATTACAGAGGCCCAAAAAACAAAAAACCCCGGACTCTCATCCAGGGTTCTCTGCTTAATAGCGGAAATTACGCTTCAATGGCAGCACGCAATTTTTTCATCGCGTTCTTTTCCAg < 2:724480/136‑1 (MQ=255)
ttGCCGGAGGGGAAATTGATTATTACAGAGGCCCAAAAAACAAAAAACCCCGGACTCTCATCCAGGGTTCTCTGCTTAATAGCGGAAATTACGCTTCAATGGCAGCACGCAATTTTTTCATCGCGTTCTTTTCCAGCTgg > 1:107079/1‑140 (MQ=255)
ttGCCGGAGGGGAAATTGATTATTACAGAGGCCCAAAAAACAAAAAACCCCGGACTCTCATCCAGGGTTCTCTGCTTAATAGCGGAAATTACGCTTCAATGGCAGCACGCAATTTTTTCATCGCGTTCTTTTCCAGCTgg > 1:681289/1‑140 (MQ=255)
aaTTGATTATTACAGAGGCCCAAAAAACAAAAAACCCCGGACTCTCATCCAGGGTTCTCTGCTTAATAGCGGAAATTACGCTTCAATGGCAGCACGCAATTTTTTCATCGCGTTCTTTTCCAGCTGGCGTACACGCTCAg > 1:796688/1‑140 (MQ=255)
ttattaCAGAGGCCCAAAAAACAAAAAACCCCGGACTCTCATCCAGGGTTCTCTGCTTAATAGCGGAAATTACGCTTCAATGGCAGCACGCAATTTTTTCATCGCGTTCTTTTCCAGCTGGCGTACACGCTCAGCGGaaa > 1:381907/1‑140 (MQ=255)
ttattaCAGAGGCCCAAAAAACAAAAAACCCCGGACTCTCATCCAGGGTTCTCTGCTTAATAGCGGAAATTACGCTTCAATGGCAGCACGCAATTTTTTCATCGCGTTCTTTTCCAGCTGGCGTACACGCTCAGCGGaaa > 2:593540/1‑140 (MQ=255)
ttattaCAGAGGCCCAAAAAACAAAAAACCCCGGACTCTCATCCAGGGTTCTCTGCTTAATAGCGGAAATTACGCTTCAATGGCAGCACGCAATTTTTTCATCGCGTTCTTTTCCAGCTGGCGTACACGCTCAGCGGaaa > 2:133658/1‑140 (MQ=255)
ttattaCAGAGGCCCAAAAAACAAAAAACCCCGGACTCTCATCCAGGGTTCTCTGCTTAATAGCGGAAATTACGCTTCAATGGCAGCACGCAATTTTTTCATCGCGTTCTTTTCCAGCTGGCGTACACGCTCAGCGGaaa > 1:659028/1‑140 (MQ=255)
taCAGAGGCCCAAAAAACAAAAAACCCCGGACTCTCATCCAGGGTTCTCTGCTTAATAGCGGAAATTACGCTTCAATGGCAGCACGCAATTTTTTCATCGCGTTCTTTTCCAGCTGGCGTACACGCTCAGCGGAAACGcc > 2:713320/1‑140 (MQ=255)
cAGAGGCCCAAAAAACAAAAAACCCCGGACTCTCATCCAGGGTTCTCTGCTTAATAGCGGAAATTACGCTTCAATGGCAGCACGCAATTTTTTCATCGCGTTCTTTTCCAGCTGGCGTACACGCTCAGCGGAAACGCCGt > 1:581740/1‑140 (MQ=255)
agGCCCAAAAAACAAAAAACCCCGGACTCTCATCCAGGGTTCTCTGCTTAATAGCGGAAATTACGCTTCAATGGCAGCACGCAATTTTTTCATCGCGTTCTTTTCCAGCTGGCGTACACGCTCAGCGGAAACGCCGTAAc > 1:712620/1‑140 (MQ=255)
gCCCAAAAAACAAAAAACCCCGGACTCTCATCCAGGGTTCTCTGCTTAATAGCGGAAATTACGCTTCAATGGCAGCACGCAATTTTTTCATCGCGTTCTTTTCCAGCTGGCGTACACGCTCAGCGGAAACGCCGTAACgg > 2:215235/1‑140 (MQ=255)
gCCCAAAAAACAAAAAACCCCGGACTCTCATCCAGGGTTCTCTGCTTAATAGCGGAAATTACGCTTCAATGGCAGCACGCAATTTTTTCATCGCGTTCTTTTCCAGCTGGCGTACACGCTCAGCGGAAACGCCGTAACgg > 1:585177/1‑140 (MQ=255)
cccAAAAAACAAAAAACCCCGGACTCTCATCCAGGGTTCTCTGCTTAATAGCGGAAATTACGCTTCAATGGCAGCACGCAATTTTTTCATCGCGTTCTTTTCCAGCTGGCGTACACGCTCAGCGGAAACGCCGTAACGGt < 1:528218/140‑1 (MQ=255)
caaaaaacaaaaaaCCCCGGACTCTCATCCAGGGTTCTCTGCTTAATAGCGGAAATTACGCTTCAATGGCAGCACGCAATTTTTTCATCGCGTTCTTTTCCAGCTGGCGTACACGCTCAGCGGAAACGCCGTAACGGTCa > 1:9275/1‑140 (MQ=255)
aaaaaacaaaaaacCCCGGACTCTCATCCAGGGTTCTCTGCTTAATAGCGGAAATTACGCTTCAATGGCAGCACGCAATTTTTTCATCGCGTTCTTTTCCAGCTGGCGTACACGCTCAGCGGAAACGCCGTAACGGTCAg < 2:264176/140‑1 (MQ=255)
aaaaaacaaaaaacCCCGGACTCTCATCCAGGGTTCTCTGCTTAATAGCGGAAATTACGCTTCAATGGCAGCACGCAATTTTTTCATCGCGTTCTTTTCCAGCTGGCGTACACGCTCAGCGGAAACGCCGTAACGGTCAg < 2:314680/140‑1 (MQ=255)
|
GCTTTAGCAGCATACTCTGCTAAAACATACCCGATTTTTATGATATTGGAATAGCTATTTTGACAGTTTATTAACAATCTGCGTGGGGATTGGCGTTTTGCCGGAGGGGAAATTGATTATTACAGAGGCCCAAAAAAC‑AAAAACCCCGGACTCTCATCCAGGGTTCTCTGCTTAATAGCGGAAATTACGCTTCAATGGCAGCACGCAATTTTTTCATCGCGTTCTTTTCCAGCTGGCGTACACGCTCAGCGGAAACGCCGTAACGGTCAG > NC_000913/3599745‑3600014
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
