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 F2 I228 R1
|
214 |
26.5 |
1448192 |
97.1% |
1406194 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,649,723 |
G→C |
intergenic (‑71/+45) |
hdeB ← / ← hdeA |
acid‑activated periplasmic chaperone HdeB/acid‑activated periplasmic chaperone HdeA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,649,723 | 0 | G | C | 96.8%
| 95.9
/ ‑3.2
| 31 | intergenic (‑71/+45) | hdeB/hdeA | acid‑activated periplasmic chaperone HdeB/acid‑activated periplasmic chaperone HdeA |
| Reads supporting (aligned to +/- strand): ref base G (0/1); new base C (15/15); total (15/16) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.71e-01 |
AGAGATGAAATATTCATTTTGTAACCCATTCAATATAGAGATTATATATGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGGCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGAATTACATATCTTTCTTAATTTTGTCCCATTCGCCTTTAACTTT > NZ_CP009273/3649636‑3649809
|
agagaTGAAATATTCATTTTGTAACCCATTCAATATAGAGATTATATATGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGccc < 2:606969/90‑1 (MQ=255)
agagaTGAAATATTCATTTTGTAACCCATTCAATATAGAGATTATATATGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGccc < 2:554714/90‑1 (MQ=255)
agagaTGAAATATTCATTTTGTAACCCATTCAATATAGAGATTATATATGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGccc > 1:414338/1‑90 (MQ=255)
agaaaTGAAATATTCATTTTGTAACCCATTCAATATAGAGATTATATATGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGccc < 2:323543/90‑1 (MQ=255)
gggaTGAAATATTCATTTTGTAACCCATTCAATATAGAGATTATATATGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGCCCt < 1:340035/88‑1 (MQ=255)
agaTGAAATATTCATTTTGTAACCCATTCAATATAGAGATTATATATGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGCCCTg > 2:700369/1‑90 (MQ=255)
gaTGAAATATTCATTTTGTAACCCATTCAATATAGAGATTATATATGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGCCCTGt < 2:522170/90‑1 (MQ=255)
tGAAATATTCATTTTGTAACCCATTCAATATAGAGATTATATATGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGCCCTGTTc < 2:166749/90‑1 (MQ=255)
aaaTATTCATTTTGTAACCCATTCAATATAGAGATTATATATGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGCCCTGTTCaa < 2:253773/90‑1 (MQ=255)
ttCATTTTGTAACCCATTCAATATAGAGATTATATATGAACAGGAGGAATAGCTGCTTTTAAAGAGGATATTCCGCCCTGTTCAATATGc < 2:537148/90‑1 (MQ=255)
cATTTTGTAACCCATTCAATATAGAGATTATATATGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGCCCTGTTCAATATGCaa < 1:213286/90‑1 (MQ=255)
cATTTTGTAACCCATTCAATATAGAGATTATATATGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGCCCTGTTCAATATGCaa < 2:605299/90‑1 (MQ=255)
cATTTTGTAACCCATTCAATATAGAGATTATATATGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGCCCTGTTCAATATGCaa < 1:700369/90‑1 (MQ=255)
tAACCCATTCAATATAGAGATTATATATGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGGCCTGTTCAATATGCAAGGAAGTa < 1:45034/90‑1 (MQ=255)
aaCCCATTCAATATAGAGATTATATATGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGCCCTGTTCAATATGCAAGGAAGTAc < 2:272849/90‑1 (MQ=255)
cATTCAATATAGAGATTATATATGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGCCCTGTTCAATATGCAAGGAAGTACGATg > 1:419475/1‑90 (MQ=255)
ttCAATATAGAGATTATATATGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGCCCTGTTCAATATGCAAGGAAGTACGATGTa > 1:77833/1‑90 (MQ=255)
gagaTTATATATGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGCCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTcc > 2:159576/1‑90 (MQ=255)
agaTTATATATGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGCCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTccc < 2:77833/90‑1 (MQ=255)
agaTTATATATGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGCCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTccc < 1:675702/90‑1 (MQ=255)
agaTTATATATGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGCCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTccc < 1:240235/90‑1 (MQ=255)
tatataTGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGCCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGaa > 2:266323/1‑90 (MQ=255)
tatataTGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGCCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGaa > 2:407766/1‑90 (MQ=255)
tatataTGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGCCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGaa > 1:422982/1‑90 (MQ=255)
tatataTGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGCCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGaa > 1:374898/1‑90 (MQ=255)
tatataTGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGCCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGaa > 1:130138/1‑90 (MQ=255)
gAACAGGAGGATTAGCTGCTTTTAAAGAAGATATTCCGCCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGAATTACata > 1:488056/1‑90 (MQ=255)
gAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGCCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGAATTACata > 2:603653/1‑90 (MQ=255)
aaTAGCTGCTTTTAAAGAAGATATTCCGCCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGAATTACATATCTTTCTTaa > 1:246519/1‑90 (MQ=255)
aGCTGCTTTTAAAGAAGATATTCCGCCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGAATTACATATCTTTCTTAAttt < 1:445818/90‑1 (MQ=255)
gctTTTAAAGAAGATATTCCGCCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGAATTACATATCTTTCTTAATTTTGTc > 1:255104/1‑90 (MQ=255)
ttttAAAGAAGATATTCCGCCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGAATTACATATCTTTCTTAATTTTGTccc > 1:653829/1‑90 (MQ=255)
ttttAAAGAAGATATTCCGCCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGAATTACATATCTTTCTTAATTTTGTccc > 1:184649/1‑90 (MQ=255)
tAAAGAAGATATTCCGCCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGAATTACATATCTTTCTTAATTTTGTCCCAtt < 2:579170/90‑1 (MQ=255)
ccGCCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGAATTACATATCTTTCTTAATTTTGTCCCATTCGCCTTTAACttt < 2:255104/90‑1 (MQ=255)
|
AGAGATGAAATATTCATTTTGTAACCCATTCAATATAGAGATTATATATGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGGCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGAATTACATATCTTTCTTAATTTTGTCCCATTCGCCTTTAACTTT > NZ_CP009273/3649636‑3649809
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ 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
CGCTTTACGGAGAGATGAAATATTCATTTTGTAACCCATTCAATATAGAGATTATATATGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGGCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGAATTACATATCTTTCTTAATTTTGTCCCATTCGCCTTTAACTTTATCTT > NZ_CP009273/3649626‑3649814
|
ataagagacagGAGATGAAATATTCATTTTGTAACCCATTCAATATAGAGATTATATATGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGCCC < SRR3722112.442665/89‑1 (MQ=60)
CGCTTTACGGAGAGATGAAATATTCATTTTGTAACCCATTCAATATAGAGATTATATATGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGCCC > SRR3722112.419818/1‑100 (MQ=60)
GGGATGAAATATTCATTTTGTAACCCATTCAATATAGAGATTATATATGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGCCCTGTTCAATATG < SRR3722112.344226/100‑1 (MQ=60)
CATTTTGTAACCCATTCAATATAGAGATTATATATGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGCCCTGTTCAATATGCAAGGAAGTACGA < SRR3722112.711314/100‑1 (MQ=60)
CATTTTGTAACCCATTCAATATAGAGATTATATATGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGCCCTGTTCAATATGCAAGGAAGTACGA < SRR3722112.215860/100‑1 (MQ=60)
TTTTGTAACCCATTCAATATAGAGATTATATATGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGCCCTGTTCAATATGCAAGGAAGTACGATG > SRR3722112.425033/1‑100 (MQ=60)
TTGTAACCCATTCAATATAGAGATTATATATGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGCCCTGTTCAATATGCAAGGAAGTACGATGTA > SRR3722112.78779/1‑100 (MQ=60)
TAACCCATTCAATATAGAGATTATATATGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGGCCTGTTCAATATGCAAGGAAGTACGATGTAACG < SRR3722112.45578/100‑1 (MQ=60)
ATATAGAGATTATATATGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGCCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGAA > SRR3722112.379742/1‑100 (MQ=60)
ATATAGAGATTATATATGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGCCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGAA > SRR3722112.428615/1‑100 (MQ=60)
ATATAGAGATTATATATGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGCCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGAA > SRR3722112.131754/1‑100 (MQ=60)
AGATTATATATGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGCCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGAATTACAT < SRR3722112.243091/100‑1 (MQ=60)
AGATTATATATGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGCCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGAATTACAT < SRR3722112.686260/100‑1 (MQ=60)
GATTATATATGAACAGGAGGATTAGCTGCTTTTAAAGAAGATATTCCGCCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGAATTACATA > SRR3722112.495095/1‑100 (MQ=60)
GAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGCCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGAATTACATATCTTTCTTAA > SRR3722112.249438/1‑100 (MQ=60)
AGGAATAGCTGCTTTTAAAGAAGATATTCCGCCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGAATTACATATCTTTCTTAATTTTGTC > SRR3722112.258117/1‑100 (MQ=60)
nnnnnnnnnnnnnnnnnnnnAGATATTCCGCCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGAATTACATATCTTTCTTAATTTNNNNC < SRR3722112.590415/80‑1 (MQ=60)
GAATAGCTGCTTTTAAAGAAGATATTCCGCCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGAATTACATATCTTTCTTAATTTTGTCCC > SRR3722112.664028/1‑100 (MQ=60)
GAATAGCTGCTTTTAAAGAAGATATTCCGCCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGAATTACATATCTTTCTTAATTTTGTCCC > SRR3722112.186910/1‑100 (MQ=60)
AGCTGCTTTTAAAGAAGATATTCCGCCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGAATTACATATCTTTCTTAATTTTGTCCCATTC < SRR3722112.452013/100‑1 (MQ=60)
ATATTCCGCCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGAATTACATATCTTTCTTAATctgtctcttatacacatctgacgctgccg > SRR3722112.24535/1‑71 (MQ=60)
|
CGCTTTACGGAGAGATGAAATATTCATTTTGTAACCCATTCAATATAGAGATTATATATGAACAGGAGGAATAGCTGCTTTTAAAGAAGATATTCCGGCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGAATTACATATCTTTCTTAATTTTGTCCCATTCGCCTTTAACTTTATCTT > NZ_CP009273/3649626‑3649814
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
