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 |
|
A1 F5 I102 R1
|
278 |
39.1 |
2251254 |
95.8% |
2156701 |
87.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
771,797 |
A→G |
intergenic (+64/‑1) |
tolR → / → tolA |
colicin uptake protein TolR/cell envelope integrity protein TolA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 771,797 | 0 | A | G | 100.0%
| 115.0
/ NA
| 32 | intergenic (+64/‑1) | tolR/tolA | colicin uptake protein TolR/cell envelope integrity protein TolA |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (19/13); total (19/13) |
TGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGAGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGGCGC > NZ_CP009273/771717‑771882
|
tGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGGGTCAAAgg > 2:2786/1‑91 (MQ=255)
gCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAAc > 2:202663/1‑91 (MQ=255)
gCAGCCTATCTAAACATCTGCGTGTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAAc < 1:647523/91‑1 (MQ=255)
aTCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACaa > 1:203456/1‑91 (MQ=255)
tCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACaaa < 2:474012/91‑1 (MQ=255)
aCATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGAc > 2:762355/1‑91 (MQ=255)
cTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGc > 1:260939/1‑91 (MQ=255)
cTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGc > 1:414280/1‑91 (MQ=255)
cTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGc > 2:47402/1‑91 (MQ=255)
cTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGc > 1:870114/1‑91 (MQ=255)
gTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCaa > 2:936892/1‑91 (MQ=255)
gTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCaa > 2:349334/1‑91 (MQ=255)
cttgcttgAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGc > 2:916836/1‑91 (MQ=255)
cttgcttgAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGc < 2:296111/91‑1 (MQ=255)
tgcttgAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGa > 2:983920/1‑91 (MQ=255)
gcttgAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAACCGACAAGCTCAAGCGGGCGAt > 2:114759/1‑91 (MQ=255)
ttgAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGTGGGCGATaa < 1:762355/91‑1 (MQ=255)
ttgAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATaa < 1:428935/91‑1 (MQ=255)
gagCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGGGTCAAAGGCACCCGAACAAAACGACAAGATCAAGCGGGCGATAATTATTTca > 1:343016/1‑91 (MQ=255)
gCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTcagc < 2:227935/91‑1 (MQ=255)
gCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTcagc < 2:609170/91‑1 (MQ=255)
ggTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGt < 1:157447/91‑1 (MQ=255)
gTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGtg < 1:1032180/91‑1 (MQ=255)
gAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTc > 1:596585/1‑91 (MQ=255)
gAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTc > 2:381416/1‑91 (MQ=255)
cAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATc < 2:936591/91‑1 (MQ=255)
gTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCtt > 2:508108/1‑91 (MQ=255)
aaCCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTgcggc < 2:537030/91‑1 (MQ=255)
aCCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTgcggcg > 2:381722/1‑91 (MQ=255)
aCCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTgcggcg > 2:220413/1‑91 (MQ=255)
ccGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGgcgc < 2:851712/91‑1 (MQ=255)
ccGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGgcgc < 2:27723/91‑1 (MQ=255)
|
TGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGAGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGGCGC > NZ_CP009273/771717‑771882
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGAGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCA > NZ_CP009273/771707‑771867
|
GTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGG < SRR3722125.903556/101‑1 (MQ=60)
TTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGC < SRR3722125.855988/101‑1 (MQ=60)
GTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCctg > SRR3722125.752844/1‑98 (MQ=60)
GACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAA > SRR3722125.207470/1‑101 (MQ=60)
GCAGCCTATCTAAACATCTGCGTGTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAAC < SRR3722125.661486/101‑1 (MQ=60)
ATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGC > SRR3722125.266186/1‑101 (MQ=60)
ATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGC > SRR3722125.423017/1‑101 (MQ=60)
ATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGC > SRR3722125.889330/1‑101 (MQ=60)
TCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCctgtctcttatacacatctcc > SRR3722125.691805/1‑80 (MQ=60)
GCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGGGTCAAAGGCACCCGAACAAAACGACAAGATCAAGCGGGCGATAATTATTTCA > SRR3722125.350147/1‑101 (MQ=60)
TTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGTGGGCGATAATTATTTCAGC < SRR3722125.778875/101‑1 (MQ=60)
TTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGC < SRR3722125.437984/101‑1 (MQ=60)
GGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTC < SRR3722125.160458/101‑1 (MQ=60)
GGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTC > SRR3722125.609411/1‑101 (MQ=60)
GTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCA < SRR3722125.1055321/101‑1 (MQ=60)
|
GTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGAGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCA > NZ_CP009273/771707‑771867
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
