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 I87 R1
|
7 |
17.1 |
1012950 |
96.1% |
973444 |
85.2 |
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%
| 77.2
/ NA
| 21 | R20C (CGC→TGC) | soxR | redox‑sensitive transcriptional activator SoxR |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (6/15); total (6/15) |
TCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAACGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAGCGGC > NZ_CP009273/4267370‑4267538
|
tCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGc < 1:258125/90‑1 (MQ=255)
tCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGc > 2:195642/1‑90 (MQ=255)
tCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGc < 2:183502/90‑1 (MQ=255)
aCTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGc > 1:163237/1‑90 (MQ=255)
ggTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATc < 1:482099/90‑1 (MQ=255)
aaaGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGgc < 2:4406/90‑1 (MQ=255)
gATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGc > 1:123463/1‑68 (MQ=255)
gATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGc < 2:123463/68‑1 (MQ=255)
cccGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGt < 1:275885/90‑1 (MQ=255)
aTTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGAtt < 1:102929/90‑1 (MQ=255)
aaaGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTAcc < 2:163237/90‑1 (MQ=255)
aGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAg < 2:312026/90‑1 (MQ=255)
aGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAg < 2:62171/90‑1 (MQ=255)
cgcTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTa < 2:179552/90‑1 (MQ=255)
ctgctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATc > 2:421496/1‑90 (MQ=255)
ccGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGGATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCg > 2:361788/1‑90 (MQ=255)
aGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGt < 2:210017/59‑1 (MQ=255)
aGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGt > 1:210017/1‑59 (MQ=255)
cGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAgcggc < 1:397650/90‑1 (MQ=255)
cGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAgcggc < 2:290448/90‑1 (MQ=255)
cGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAACCAgcggc < 1:5090/90‑1 (MQ=255)
|
TCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAACGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAGCGGC > NZ_CP009273/4267370‑4267538
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAACGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAGCGGCGATATAAACGTGA > NZ_CP009273/4267368‑4267551
|
CCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGC > SRR3722226.165585/1‑100 (MQ=60)
TCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGG < SRR3722226.262107/100‑1 (MQ=60)
GAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGctgtctcttata > SRR3722226.125296/1‑88 (MQ=60)
GGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCAT < SRR3722226.490952/100‑1 (MQ=60)
CCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAG < SRR3722226.280202/100‑1 (MQ=60)
ATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCC < SRR3722226.104497/100‑1 (MQ=60)
CCCCCGGGGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGctgtctcttatacacatctga > SRR3722226.212994/1‑79 (MQ=60)
CGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAGCGGCGATATAAACG < SRR3722226.404793/100‑1 (MQ=60)
CGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAACCAGCGGCGATATAAACG < SRR3722226.5179/100‑1 (MQ=60)
AATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGGTGATTACCAGTATCCGTAACAGCGGCAATCAGCGGCGATATAAACGTGA > SRR3722226.486486/1‑100 (MQ=60)
|
CCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAACGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAGCGGCGATATAAACGTGA > NZ_CP009273/4267368‑4267551
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
