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 I134 R1
|
6 |
21.3 |
1193788 |
96.3% |
1149617 |
85.7 |
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%
| 95.5
/ NA
| 25 | R20C (CGC→TGC) | soxR | redox‑sensitive transcriptional activator SoxR |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (10/15); total (10/15) |
CCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAACGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAGCGGC > NZ_CP009273/4267368‑4267538
|
ccTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCa > 1:139230/1‑90 (MQ=255)
cTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAg < 1:186998/90‑1 (MQ=255)
tCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGc < 2:401995/90‑1 (MQ=255)
tCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGc > 1:117073/1‑90 (MQ=255)
tCAAGTTAACTTGAGGTAAAGCGATTTATGCAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGc > 1:351260/1‑90 (MQ=255)
cTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCg < 1:261717/90‑1 (MQ=255)
aGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTAt > 1:466692/1‑90 (MQ=255)
ttATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCAtt < 2:466692/90‑1 (MQ=255)
aaGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGaa < 1:450955/90‑1 (MQ=255)
aaGAAATTACCCCGCATTAAAGCGCTGCTAACCCCAGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGaa < 1:181419/90‑1 (MQ=255)
tACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATgaaaggaaag > 1:473871/1‑90 (MQ=255)
cccGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGt < 1:52524/90‑1 (MQ=255)
cccGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGt < 2:419124/90‑1 (MQ=255)
cccGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGt < 2:139230/90‑1 (MQ=255)
cccGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGt < 1:40701/90‑1 (MQ=255)
ccGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGtt > 1:83067/1‑90 (MQ=255)
aGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAg < 2:228036/90‑1 (MQ=255)
aGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAg < 1:299467/90‑1 (MQ=255)
aGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAg < 2:530454/90‑1 (MQ=255)
gctgctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGGAAAGGGGTGATTACCAGGAt > 2:480530/1‑90 (MQ=255)
ctgctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTTTATGAAAAGAAAGGGGTGATTACCAGGATc > 2:329944/1‑90 (MQ=255)
ctgctAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGGTGATTACCAGTATc > 2:430053/1‑90 (MQ=255)
ccGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGGTGATTACCAGTATCCGTAACAGCg > 2:47495/1‑90 (MQ=255)
cGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAgcggc < 2:164626/90‑1 (MQ=255)
cGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAgcggc < 1:236571/90‑1 (MQ=255)
|
CCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAACGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAGCGGC > NZ_CP009273/4267368‑4267538
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 25 ≤ 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
GAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAACGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAGCGGCGATATAAACG > NZ_CP009273/4267358‑4267548
|
GAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCA > SRR3722002.140811/1‑100 (MQ=60)
GTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGC > SRR3722002.118405/1‑100 (MQ=60)
GTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGCAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGC > SRR3722002.355407/1‑100 (MQ=60)
ATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGG < SRR3722002.59186/100‑1 (MQ=60)
CTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCG < SRR3722002.189066/100‑1 (MQ=60)
AGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTAT > SRR3722002.472825/1‑100 (MQ=60)
CTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGC < SRR3722002.264444/100‑1 (MQ=60)
GAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGGAAAG > SRR3722002.480106/1‑100 (MQ=60)
AAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGT < SRR3722002.456837/100‑1 (MQ=60)
AAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCAGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGT < SRR3722002.183427/100‑1 (MQ=60)
AGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTT > SRR3722002.83954/1‑100 (MQ=60)
CCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAG < SRR3722002.53068/100‑1 (MQ=60)
CCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTAATTACCAG < SRR3722002.41124/100‑1 (MQ=60)
AGCGCTGCTAACCCCCGGCGAAGTGGCGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAAC < SRR3722002.302891/100‑1 (MQ=60)
CGAAATGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAGCGGCGATATAAACG < SRR3722002.239063/100‑1 (MQ=60)
|
GAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCTAACCCCCGGCGAAGTGGCGAAACGCAGCGGTGTGGCGGTATCGGCGCTGCATTTCTATGAAAGTAAAGGGTTGATTACCAGTATCCGTAACAGCGGCAATCAGCGGCGATATAAACG > NZ_CP009273/4267358‑4267548
|
| 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: ‑ |
