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 |
587,628 |
A→G |
F336S (TTC→TCC) |
nrfB ← |
cyclic di‑3',5'‑guanylate‑activated glycosyltransferase NrfB |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 587,628 | 0 | A | G | 100.0%
| 81.2
/ NA
| 24 | F336S (TTC→TCC) | nrfB | cyclic di‑3',5'‑guanylate‑activated glycosyltransferase NrfB |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (9/15); total (9/15) |
AAGTTACTGATTGCCCCTTTGCGGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGAAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGATC > NZ_CP009273/587541‑587708
|
aaGTTACTGATTGCCCCTTTGCGGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGgaaa > 1:634169/1‑91 (MQ=255)
aCTGATTGCCCCTTTGCGGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATg < 1:75788/91‑1 (MQ=255)
gATTGCCCCTTTGCGGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCg > 2:444752/1‑91 (MQ=255)
aTTGCCCCTTTGCGGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCga < 1:101910/91‑1 (MQ=255)
ttGCCCCATTGCGGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCgat > 2:186054/1‑91 (MQ=255)
gCCCCTTTGCGGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCgatga > 1:923283/1‑91 (MQ=255)
cTTTGCGGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCa > 1:697356/1‑91 (MQ=255)
ttGCGGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGc > 2:106274/1‑91 (MQ=255)
gCGGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCgg > 2:214431/1‑91 (MQ=255)
tagtTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAg < 2:634169/91‑1 (MQ=255)
gCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGaaaa > 1:870906/1‑91 (MQ=255)
aGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTAt > 2:1041438/1‑91 (MQ=255)
ttATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTcgc < 1:659631/91‑1 (MQ=255)
tATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTcgcg > 2:788254/1‑91 (MQ=255)
aTGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCgcgc < 1:813010/91‑1 (MQ=255)
aTGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCgcgc < 1:564493/91‑1 (MQ=255)
aTGGGTTTTAAAGCCTTAGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCgcgc < 1:786557/91‑1 (MQ=255)
tGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGcgca < 2:78583/91‑1 (MQ=255)
tggTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGcgcac < 1:472445/90‑1 (MQ=255)
gTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGcgcacgc < 2:246919/91‑1 (MQ=255)
gTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGcgcacgc < 2:318447/91‑1 (MQ=255)
gTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGcgcacgc < 1:219111/91‑1 (MQ=255)
aaaGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGATc < 2:895667/91‑1 (MQ=255)
aaaGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGATc < 1:917810/91‑1 (MQ=255)
aaaGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGATc < 1:911620/91‑1 (MQ=255)
|
AAGTTACTGATTGCCCCTTTGCGGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGAAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGATC > NZ_CP009273/587541‑587708
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 30 ≤ 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
GAAGCTGACAAAGTTACTGATTGCCCCTTTGCGGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGAAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGATCATGTTTGATG > NZ_CP009273/587531‑587718
|
GAAGCTGACAAAGTTACTGATTGCCCCTTTGCGGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAA > SRR3722125.647833/1‑101 (MQ=60)
GTGACTGATTGCCCCTTTGCGGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGA > SRR3722125.943782/1‑101 (MQ=60)
ACTGATTGCCCCTTTGCGGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCC < SRR3722125.77195/101‑1 (MQ=60)
CTGATTGCCCCTTTGCGGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCA > SRR3722125.712384/1‑101 (MQ=60)
ATTGCCCCTTTGCGGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCG < SRR3722125.103823/101‑1 (MQ=60)
CGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCtgtctcttatacacatctccgagcccacga > SRR3722125.18300/1‑71 (MQ=60)
AAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAA > SRR3722125.890143/1‑101 (MQ=60)
tcggagatgtgtataagagacagGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTGGCG < SRR3722125.84237/78‑1 (MQ=60)
TTATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGAT < SRR3722125.673863/101‑1 (MQ=60)
ATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGATCA < SRR3722125.576576/101‑1 (MQ=60)
ATGGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGATCA < SRR3722125.830813/101‑1 (MQ=60)
ATGGGTTTTAAAGCCTTAGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGATCA < SRR3722125.803704/101‑1 (MQ=60)
TGGTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGATCATG < SRR3722125.482406/101‑1 (MQ=60)
GTTTTAAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGATCATGTT < SRR3722125.223436/101‑1 (MQ=60)
AAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGATCATGTTTGATG < SRR3722125.931819/101‑1 (MQ=60)
AAAGCCTTGGGAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGATCATGTTTGATG < SRR3722125.938174/101‑1 (MQ=60)
|
GAAGCTGACAAAGTTACTGATTGCCCCTTTGCGGTCGCGCCAGAGAAAGTAGTTCAGCGTCAGGCTGGAGGTCCATTTATGGGTTTTAAAGCCTTGGAAAACAATGCCGATGATCCAGCGGGATTTTTGTCGAACCGCAGTCGAAAAGGTATCGGGGAAATATTCGCGCACGCAGATCATGTTTGATG > NZ_CP009273/587531‑587718
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
