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 F3 I122 R1
|
193 |
20.9 |
1228102 |
94.7% |
1163012 |
84.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,649,376 |
(T)5→4 |
coding (277/327 nt) |
hdeB ← |
acid‑activated periplasmic chaperone HdeB |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,649,372 | 0 | T | . | 100.0%
| 110.1
/ NA
| 26 | coding (281/327 nt) | hdeB | acid‑activated periplasmic chaperone HdeB |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base . (12/14); total (12/14) |
CAACTTGCTACTCCTTTTTACTTGCACCTCATTAATTCGGCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAATTTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTTGAGTGAGATCGGTTTCATTTAAAGTAACGGTATCGCCAC > NZ_CP009273/3649295‑3649456
|
cAACTTGCTACTCCTTTTTACTTGCACCTCATTAATTCGGCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGtt < 1:449074/90‑1 (MQ=255)
cAACTTGATAGTCCTGTTTACTTGCACCTCATAAATTCGGCAAGTCATTAGATGATTGATTTTTAAAGGTATACAAA‑TTTTCTGCGGGtt < 1:398719/90‑1 (MQ=255)
cTACTCCTTTTTACTTGCACCTCATTAATTCGGCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTa > 2:372777/1‑90 (MQ=255)
tACTCCTTTTTACTTGCACCTCATTAATTCGGCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTAc < 2:226263/90‑1 (MQ=255)
ttttACTTGCACCTCATTAATTCGGCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTc > 2:151605/1‑90 (MQ=255)
ttttACTTGCACCTCATTAATTCGGCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTc > 1:547534/1‑90 (MQ=255)
aCTTGCACCTCATTAATTCGGCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATc < 1:506841/90‑1 (MQ=255)
tGCACCTCATTAATTCGGCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACt > 2:326371/1‑90 (MQ=255)
tGCACCTCATTAATTCGGCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACt > 2:188809/1‑90 (MQ=255)
tGCACCTCATTAATTCGGCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACt > 1:342484/1‑90 (MQ=255)
tGCACCTCATTAATTCGGCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACt > 1:350972/1‑90 (MQ=255)
cTCATTAATTCGGCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAgg < 1:298759/90‑1 (MQ=255)
gCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTtgagtgag > 2:613835/1‑90 (MQ=255)
gCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTtgagtgag > 1:253218/1‑90 (MQ=255)
aTTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTTGAGTGAGATCGGtt < 1:77978/90‑1 (MQ=255)
aTTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTTGAGTGAGATCGGtt < 2:454231/90‑1 (MQ=255)
ttAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATc > 2:204838/1‑62 (MQ=255)
ttAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATc < 1:204838/62‑1 (MQ=255)
cTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTTGAGTGAGATCGGTTTCATTTaa < 1:293168/90‑1 (MQ=255)
ttGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTTGAGTGAGATCGGTTTCATTTaaa > 2:394809/1‑90 (MQ=255)
gTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTTGAGTGAGATCGGTTTCATTTAAAGTAACGGTATCGc > 1:472202/1‑90 (MQ=255)
tataCAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTTGAGTGAGATCGGTTTCATTTAAAGTAACGGTATCGcc < 1:394809/90‑1 (MQ=255)
tataCAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTTGAGTGAGATCGGTTTCATTTAAAGTAACGGTATCGcc < 1:326371/90‑1 (MQ=255)
taCAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTTGAGTGAGATCGGTTTCATTTAAAGTAACGGTATCGCCAc < 2:122002/90‑1 (MQ=255)
taCAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTTGAGTGAGATCGGTTTCATTTAAAGTAACGGTATCGCCAc < 1:222044/90‑1 (MQ=255)
taCAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTTGAGTGAGATCGGTTTCATTTAAAGTAACGGTATCGCCAc < 2:603237/90‑1 (MQ=255)
|
CAACTTGCTACTCCTTTTTACTTGCACCTCATTAATTCGGCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAATTTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTTGAGTGAGATCGGTTTCATTTAAAGTAACGGTATCGCCAC > NZ_CP009273/3649295‑3649456
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CAACTTGCTACTCCTTTTTACTTGCACCTCATTAATTCGGCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAATTTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTTGAGTGAGATCGGTTTCATTTAAAGTAACGGTATCGCCACCTTTATATAC > NZ_CP009273/3649295‑3649466
|
CAACTTGCTACTCCTTTTTACTTGCACCTCATTAATTCGGCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAG < SRR3721989.458445/100‑1 (MQ=60)
CAACTTGATAGTCCTGTTTACTTGCACCTCATAAATTCGGCAAGTCATTAGATGATTGATTTTTAAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAG < SRR3721989.406834/100‑1 (MQ=60)
TGCTACTCCTTTTTACTTGCACCTCATTAATTCGGCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTC > SRR3721989.559361/1‑100 (MQ=60)
CCTTTTTACTTGCACCTCATTAATTCGGCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACT > SRR3721989.349034/1‑100 (MQ=60)
CCTTTTTACTTGCACCTCATTAATTCGGCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACT > SRR3721989.357709/1‑100 (MQ=60)
gatgtgtataagagacagCGGCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAA < SRR3721989.208552/82‑1 (MQ=60)
ACTTGCACCTCATTAATTCGGCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAA < SRR3721989.517650/100‑1 (MQ=60)
CTCATTAATTCGGCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTTGAGTG < SRR3721989.304358/100‑1 (MQ=60)
CATTAATTCGGCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTTGAGTGAG > SRR3721989.257724/1‑100 (MQ=60)
ATTAGATGCTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTTGAGTGAGATCGGTTTCATTTAAAG < SRR3721989.79375/100‑1 (MQ=60)
CTTGATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTTGAGTGAGATCGGTTTCATTTAAAGTAACGGTA < SRR3721989.298599/100‑1 (MQ=60)
ATTTTTGAAGGTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTTGAGTGAGATCGGTTTCATTTAAAGTAACGGTATCGC > SRR3721989.482129/1‑100 (MQ=60)
GTATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTTGAGTGAGATCGGTTTCATTTAAAGTAACGGTATCGCCACCTTTATA > SRR3721989.591676/1‑100 (MQ=60)
TATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTTGAGTGAGATCGGTTTCATTTAAAGTAACGGTATCGCCACCTTTATAT < SRR3721989.332585/100‑1 (MQ=60)
TATACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTTGAGTGAGATCGGTTTCATTTAAAGTAACGGTATCGCCACCTTTATAT < SRR3721989.402812/100‑1 (MQ=60)
TACAAA‑TTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTTGAGTGAGATCGGTTTCATTTAAAGTAACGGTATCGCCACCTTTATATAC < SRR3721989.226060/100‑1 (MQ=60)
|
CAACTTGCTACTCCTTTTTACTTGCACCTCATTAATTCGGCAAGTCATTAGATGCTTGATTTTTGAAGGTATACAAATTTTTCTGCGGGTTTTTCTTACAGTATTCGATCACTTTAGGAATTTGAGTGAGATCGGTTTCATTTAAAGTAACGGTATCGCCACCTTTATATAC > NZ_CP009273/3649295‑3649466
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
