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 I195 R1
|
222 |
27.1 |
1551108 |
96.0% |
1489063 |
86.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,358,446 |
Δ1 bp |
coding (414/426 nt) |
nudI → |
nucleoside triphosphatase NudI |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,358,444 | 0 | A | . | 100.0%
| 67.9
/ NA
| 17 | coding (412/426 nt) | nudI | nucleoside triphosphatase NudI |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base . (12/5); total (12/5) |
CTACGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTGAAAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAGATTGAAAATTTAGTGGTTAACGAATTCCCCATCCAGA > NZ_CP009273/2358371‑2358524
|
cTACGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACaa > 1:16144/1‑90 (MQ=255)
cTACGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACaa > 1:650802/1‑90 (MQ=255)
tACGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAat > 1:392811/1‑90 (MQ=255)
tGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGt < 2:695855/78‑1 (MQ=255)
tGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGt > 1:695855/1‑78 (MQ=255)
gggTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGATAAACGTTACGTTTG‑AAGGtcttc < 1:436172/74‑1 (MQ=255)
gggTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGATAAACGTTACGTTTG‑AAGGtcttc > 2:436172/1‑74 (MQ=255)
aaaCCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAAtgatga > 1:194065/1‑83 (MQ=255)
aaaCCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAAtgatga < 2:194065/83‑1 (MQ=255)
gAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGACAGCCATTACTgg > 1:95990/1‑90 (MQ=255)
cTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCa > 2:497006/1‑90 (MQ=255)
ggTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAGa < 1:28022/90‑1 (MQ=255)
aTTATGATTTGAATGTCGCCACCCGAAAAACGTTACGGTTG‑AAGGGCGTCTGAACCAATGATGAAAGCCATTACTGTCTGTCAGATTGaa > 1:436891/1‑90 (MQ=255)
aTTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAGATTGAAAATTTa > 2:2882/1‑90 (MQ=255)
tttGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAGATTGAAAATTTAg < 2:504620/90‑1 (MQ=255)
gCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAGATTGAAAATTTAGTGGTTAACGa > 2:617020/1‑90 (MQ=255)
gttacgttTG‑AAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAGATTGAAAATTTAGTGGTTAACGAATTCCCCATCCAGa > 2:570470/1‑90 (MQ=255)
|
CTACGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTGAAAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAGATTGAAAATTTAGTGGTTAACGAATTCCCCATCCAGA > NZ_CP009273/2358371‑2358524
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ 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
AAATAAACGAAGAGTTTCAGGACTACGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTGAAAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAGATTGAAAATTTAGTGGTTAACGAATTCCCCATCCAGATAAACTTTGCCTTTTT > NZ_CP009273/2358349‑2358540
|
AAATAAACGAAGAGTTTCAGGACTACGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGT < SRR3722073.627712/100‑1 (MQ=60)
AGTTTCAGGACTACGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAA > SRR3722073.16552/1‑100 (MQ=60)
AGTTTCAGGACTACGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAA > SRR3722073.664178/1‑100 (MQ=60)
GTTTCAGGACTACGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAAT > SRR3722073.401177/1‑100 (MQ=60)
agaCAGGACTACGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGATAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATG < SRR3722073.445500/97‑1 (MQ=60)
GGACTACGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGct > SRR3722073.709988/1‑98 (MQ=60)
CGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGACAGCCAT > SRR3722073.197932/1‑100 (MQ=60)
GGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGACAGCCATTACTGG > SRR3722073.98104/1‑100 (MQ=60)
GATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGGTTG‑AAGGGCGTCTGAACCAATGATGAAAGCCATTACTGTCTGTCAGATTGAA > SRR3722073.446238/1‑100 (MQ=60)
GGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAGATTGAAAATTT < SRR3722073.28735/100‑1 (MQ=60)
TTTG‑AAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAGATTGAAAATTTAGTGGTTAACGAATTCCCCATCCAGATAAACTTTGCCTTTTT > SRR3722073.517182/1‑100 (MQ=60)
|
AAATAAACGAAGAGTTTCAGGACTACGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTGAAAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAGATTGAAAATTTAGTGGTTAACGAATTCCCCATCCAGATAAACTTTGCCTTTTT > NZ_CP009273/2358349‑2358540
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
