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 |
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%
| 59.8
/ NA
| 15 | coding (412/426 nt) | nudI | nucleoside triphosphatase NudI |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base . (9/6); total (9/6) |
AGTTTCAGGACTACGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTGAAAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAGATTGAAAATTTAGTGGTTAACGAATTCCCCATC > NZ_CP009273/2358361‑2358520
|
agTTTCAGGACTACGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGtct < 2:343810/90‑1 (MQ=255)
tttCAGGACTACGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGtcttc < 2:328747/90‑1 (MQ=255)
aCGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAatg > 1:636251/1‑90 (MQ=255)
tCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTc > 2:418827/1‑90 (MQ=255)
tCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTc > 2:675820/1‑90 (MQ=255)
cTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCa > 2:499584/1‑90 (MQ=255)
ggTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAGa > 2:395714/1‑90 (MQ=255)
cATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAGATTGa > 2:188108/1‑90 (MQ=255)
aTTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAGATTGaa < 1:395714/90‑1 (MQ=255)
gAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAGATTGAAAATTTAGTgg > 2:562391/1‑90 (MQ=255)
tGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAGATTGAAAATTTAGTGGTTa < 1:181091/90‑1 (MQ=255)
tGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAGATTGAAAATTTAGTGGTTa > 2:298686/1‑90 (MQ=255)
tCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAGATTGAAAATTTAGTGGTTAAc > 1:299649/1‑90 (MQ=255)
aaaaCGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAGATTGAAAATTTAGTGGTTAACGAATTCCCCAt < 2:212071/90‑1 (MQ=255)
aaccgttacgttTG‑AAGGTCTTCTGTAAAAATGATGACAGCCATTACTGGCTGTCAGATTGAAAATTTAGTGGTTAACGAATTCCCCATc < 1:387270/87‑1 (MQ=255)
|
AGTTTCAGGACTACGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTGAAAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAGATTGAAAATTTAGTGGTTAACGAATTCCCCATC > NZ_CP009273/2358361‑2358520
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ 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
TTTCAGGACTACGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTGAAAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAGATTGAAAATTTAGTGGTTAACGAATTCCCCATCCAGATAAACTTTGCCTTTTTCCACA > NZ_CP009273/2358363‑2358545
|
TTTCAGGACTACGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATG > SRR3722112.646127/1‑100 (MQ=60)
ATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAGATTGAAAATTTAGTGG < SRR3722112.400902/100‑1 (MQ=60)
GATTTGAGTGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAGATTGAAAATTTAGTGGTTAAC > SRR3722112.303103/1‑100 (MQ=60)
TGTCGCCACCCGAAAAACGTTACGTTTG‑AAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAGATTGAAAATTTAGTGGTTAACGAATTCCC < SRR3722112.183311/100‑1 (MQ=60)
AACCGTTACGTTTG‑AAGGTCTTCTGTAAAAATGATGACAGCCATTACTGGCTGTCAGATTGAAAATTTAGTGGTTAACGAATTCCCCATCCAGATAAACT < SRR3722112.392310/100‑1 (MQ=60)
CGTTTG‑AAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAGATTGAAAATTTAGTGGTTAACGAATTCCCCATCCAGATAAACTTTGCCTTT > SRR3722112.457174/1‑100 (MQ=60)
AGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAGATTGAAAATTTAGTGGTTAACGAATTCCCCATCCAGATAAACTTTGCCTTTTTCCACA < SRR3722112.506823/100‑1 (MQ=60)
|
TTTCAGGACTACGCGTGGGTAAAACCTGAAGATCTGGTGCATTATGATTTGAATGTCGCCACCCGAAAAACGTTACGTTTGAAAGGTCTTCTGTAACAATGATGACAGCCATTACTGGCTGTCAGATTGAAAATTTAGTGGTTAACGAATTCCCCATCCAGATAAACTTTGCCTTTTTCCACA > NZ_CP009273/2358363‑2358545
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
