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 I142 R1
|
10 |
30.9 |
1778688 |
96.4% |
1714655 |
84.8 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,267,454 |
C→T |
R20C (CGC→TGC) |
soxR → |
redox‑sensitive transcriptional activator SoxR |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,267,454 | 0 | C | T | 100.0%
| 152.8
/ NA
| 39 | R20C (CGC→TGC) | soxR | redox‑sensitive transcriptional activator SoxR |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (25/14); total (25/14) |
CCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAACGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAGCG > NZ_CP009273/4267368‑4267536
|
ccTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCa > 2:47189/1‑90 (MQ=255)
ccTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCa > 1:451071/1‑90 (MQ=255)
ccTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCa > 2:44428/1‑90 (MQ=255)
tCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGc > 1:323657/1‑90 (MQ=255)
tCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGc < 1:352814/90‑1 (MQ=255)
tCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGc > 2:306266/1‑90 (MQ=255)
aaGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCgg < 1:327208/90‑1 (MQ=255)
gTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGgtg < 2:149226/90‑1 (MQ=255)
aGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTAt > 1:257320/1‑90 (MQ=255)
aGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTAt > 2:711238/1‑90 (MQ=255)
gATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGc > 1:4325/1‑90 (MQ=255)
aaGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGaa < 1:686113/90‑1 (MQ=255)
aaTTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTa > 1:61805/1‑90 (MQ=255)
aTTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTaa < 1:671652/90‑1 (MQ=255)
ttACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTaaa < 2:526082/90‑1 (MQ=255)
cGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGgcgc > 1:599778/1‑64 (MQ=255)
cGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGgcgc < 2:599778/64‑1 (MQ=255)
cGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGGATCGGCGCTGCATTTCTATGAAAGTAAAGGGGTg > 1:603315/1‑90 (MQ=255)
aaaGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTAcc < 2:829326/90‑1 (MQ=255)
aGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAg < 2:887081/90‑1 (MQ=255)
gctgctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAgggg > 1:677805/1‑76 (MQ=255)
gctgctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGt < 2:677805/77‑1 (MQ=255)
gctgctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTAt > 2:654588/1‑90 (MQ=255)
ctgctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATc > 1:421639/1‑90 (MQ=255)
gctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGgc > 1:800031/1‑48 (MQ=255)
gctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGgc < 2:800031/48‑1 (MQ=255)
gctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCCTTTCTTTGAAAGGAAAGGGGTGGTTACCAGTATCCg > 1:820426/1‑90 (MQ=255)
ccGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTTTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCg > 2:752344/1‑90 (MQ=255)
ccGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGaa > 1:83707/1‑56 (MQ=255)
ccGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGaa < 2:83707/56‑1 (MQ=255)
ccGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCg > 1:623328/1‑90 (MQ=255)
ggCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAgg > 2:474967/1‑62 (MQ=255)
ggCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAgg < 1:474967/62‑1 (MQ=255)
ggCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGc > 2:383848/1‑90 (MQ=255)
ggCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAAGAAAGGGGTGGTTACCAGTATCCGTAACAGCGGc > 1:608572/1‑90 (MQ=255)
ggCGAAGTGGCGAAATGCAGCGGTGTGGCGGGATCGGCGCTGCATTTTTATGAAAGAAAAAGGGTGATTACCAGGATCCGTAACAGCGGc > 1:548775/1‑90 (MQ=255)
aGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCa > 2:98972/1‑90 (MQ=255)
aGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTCCATTTCTATGAAAATAAAGGGGTGATTACCAGTATCCGTAACAGCGGCAATCa > 1:537863/1‑90 (MQ=255)
ggCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAgcg < 2:61805/90‑1 (MQ=255)
|
CCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAACGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAGCG > NZ_CP009273/4267368‑4267536
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 17 ≤ 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
GAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAACGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAGCGGCGATATAAACGTGATG > NZ_CP009273/4267358‑4267553
|
GAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCA > SRR3722011.457986/1‑100 (MQ=60)
GTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGC > SRR3722011.328217/1‑100 (MQ=60)
ATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGG < SRR3722011.4324/100‑1 (MQ=60)
TCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGG < SRR3722011.357718/100‑1 (MQ=60)
AAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTA < SRR3722011.331809/100‑1 (MQ=60)
AGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTAT > SRR3722011.261039/1‑100 (MQ=60)
GAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGC > SRR3722011.4387/1‑100 (MQ=60)
ATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTTTATGAAAGGA > SRR3722011.62679/1‑100 (MQ=60)
AAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGT < SRR3722011.697977/100‑1 (MQ=60)
GAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGGATCGGCGCTGCATTTttactgtctcttatacaca > SRR3722011.609860/1‑81 (MQ=60)
GAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGGATCGGCGCCGCATTTCTATGAAAGTAAAGGGGTG > SRR3722011.613475/1‑100 (MQ=60)
ATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATT < SRR3722011.683249/100‑1 (MQ=60)
gatgtgtataagagacagGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACC < SRR3722011.482320/82‑1 (MQ=60)
GCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTTTATGAAAGTAAAGGGGTGATTACCAGctg > SRR3722011.689527/1‑97 (MQ=60)
CATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGGATC > SRR3722011.427919/1‑100 (MQ=60)
TTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCctttcctgtctcttttaaacatctgacgctgccggcc > SRR3722011.814124/1‑63 (MQ=60)
TTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCCTTTCTTTGAAAGGAAAGGGGTGGTTACCAGTATCCG > SRR3722011.834911/1‑100 (MQ=60)
CTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTTTATGAAAGGAAAGGGgttggctcttttacacatctgacgg > SRR3722011.84898/1‑75 (MQ=60)
CTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGGTGATTACCAGGATCCGTAAAAGCG > SRR3722011.633899/1‑100 (MQ=60)
GCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTTTTTGAAAATAAAGGGGTGATTTCCAGTATCCtgtctctttta > SRR3722011.885200/1‑89 (MQ=60)
GCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAAGAAAGGGGTGGTTACCAGTATCCGTAACAGCGGC > SRR3722011.618843/1‑100 (MQ=60)
GCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGGATCGGCGCTGCATTTTTATGAAAGAAAAAGGGTGATTACCAGGATCCGTAACAGCGGC > SRR3722011.557672/1‑100 (MQ=60)
CCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTCCATTTCTATGAAAATAAAGGGGTGATTACCAGTATCCGTAACAGCGGCAATCA > SRR3722011.546508/1‑100 (MQ=60)
GGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGAAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAGCGGCGATATAAA > SRR3722011.111383/1‑100 (MQ=60)
TGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAGCGGCGATATAAACGTGATG < SRR3722011.406936/100‑1 (MQ=60)
|
GAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAACGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAGCGGCGATATAAACGTGATG > NZ_CP009273/4267358‑4267553
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
