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 F5 I102 R1
|
278 |
39.1 |
2251254 |
95.8% |
2156701 |
87.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
481,730 |
Δ1 bp |
coding (514/648 nt) |
acrR → |
multidrug efflux transporter transcriptional repressor AcrR |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 481,728 | 0 | T | . | 100.0%
| 167.9
/ NA
| 38 | coding (512/648 nt) | acrR | multidrug efflux transporter transcriptional repressor AcrR |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base . (21/17); total (21/17) |
ACAAACGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATATTTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACT > NZ_CP009273/481642‑481812
|
aCAAACGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATAttccg > 1:148252/1‑88 (MQ=255)
aCAAACGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATAttccg > 2:949913/1‑88 (MQ=255)
aCAAACGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATAttccg > 1:1043627/1‑88 (MQ=255)
aaCGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGcc > 1:1055589/1‑91 (MQ=255)
aaCGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGcc > 2:26534/1‑91 (MQ=255)
aaCGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGcc > 1:628754/1‑91 (MQ=255)
aaCGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGcc > 1:366638/1‑91 (MQ=255)
aaCGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGcc > 1:326240/1‑91 (MQ=255)
aaCGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGcc > 1:263020/1‑91 (MQ=255)
cGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTg > 1:3975/1‑91 (MQ=255)
ttGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACt > 2:362251/1‑91 (MQ=255)
gAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCtt < 2:592058/91‑1 (MQ=255)
gAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCtt > 1:636680/1‑91 (MQ=255)
gCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGc < 2:1055589/91‑1 (MQ=255)
gAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTg > 2:758082/1‑88 (MQ=255)
gAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTg < 1:758082/88‑1 (MQ=255)
gAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGccc > 2:816343/1‑91 (MQ=255)
gAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGccc > 2:38943/1‑91 (MQ=255)
gAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGccc > 2:343189/1‑91 (MQ=255)
aaTGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGc < 1:614154/91‑1 (MQ=255)
aaTGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGc < 1:237162/91‑1 (MQ=255)
tGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCt > 2:1071427/1‑91 (MQ=255)
cTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCtttt > 2:960724/1‑91 (MQ=255)
ttAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTaa < 1:618461/91‑1 (MQ=255)
aCGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAaaga > 1:384600/1‑91 (MQ=255)
cgTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGc < 2:94164/91‑1 (MQ=255)
tCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGccc < 2:326240/91‑1 (MQ=255)
tCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGACTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGccc < 2:347622/91‑1 (MQ=255)
gcaATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTa > 2:288470/1‑91 (MQ=255)
attattATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGt > 1:494801/1‑91 (MQ=255)
tattatGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTg > 2:781591/1‑91 (MQ=255)
attatGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGc < 2:1096699/91‑1 (MQ=255)
attatGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGc < 2:263020/91‑1 (MQ=255)
ttatGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGcc < 1:343189/91‑1 (MQ=255)
ttatGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGcc < 2:30470/91‑1 (MQ=255)
tatGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCa < 1:80171/91‑1 (MQ=255)
tGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCaa > 1:794173/1‑49 (MQ=255)
tGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCaa < 2:794173/49‑1 (MQ=255)
gcgcGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCt > 2:635452/1‑91 (MQ=255)
gcgcGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCt > 2:376292/1‑91 (MQ=255)
cgcgGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCtt < 1:529121/91‑1 (MQ=255)
ggCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACt < 2:158955/91‑1 (MQ=255)
|
ACAAACGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATATTTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACT > NZ_CP009273/481642‑481812
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 31 ≤ 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
TGACCGTATAGAACAAACGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATATTTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACTGGAGATGTATCTCCTG > NZ_CP009273/481630‑481828
|
TGACCGTATAGAACAAACGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATATTC < SRR3722125.19626/101‑1 (MQ=60)
TGACCGTATAGAACAAACGTTAAAACATTGTATTGAAGCGAAAATGTTGCCCGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATATTN < SRR3722125.235423/101‑1 (MQ=60)
ACCGTATAGAACAAACGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCG > SRR3722125.1067049/1‑101 (MQ=60)
ACCGTATAGAACAAACGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCG > SRR3722125.151070/1‑101 (MQ=60)
GTATAGAACAAACGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCC > SRR3722125.1079335/1‑101 (MQ=60)
GTATAGAACAAACGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCC > SRR3722125.642302/1‑101 (MQ=60)
GTATAGAACAAACGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCC > SRR3722125.374327/1‑101 (MQ=60)
GTATAGAACAAACGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCC > SRR3722125.268326/1‑101 (MQ=60)
GTATAGAACAAACGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCC > SRR3722125.332968/1‑101 (MQ=60)
ATAGAACAAACGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTG > SRR3722125.4061/1‑101 (MQ=60)
ACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTT > SRR3722125.650408/1‑101 (MQ=60)
AGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATC < SRR3722125.774486/101‑1 (MQ=60)
AATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGA < SRR3722125.241905/101‑1 (MQ=60)
AATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGA < SRR3722125.627401/101‑1 (MQ=60)
GGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGA > SRR3722125.392663/1‑101 (MQ=60)
TTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCC < SRR3722125.631796/101‑1 (MQ=60)
TCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGT > SRR3722125.505265/1‑101 (MQ=60)
GCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCctgtctcttatacacatctccgagcccacgag > SRR3722125.811509/1‑69 (MQ=60)
TTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACTGG < SRR3722125.350322/101‑1 (MQ=60)
TATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACTGGA < SRR3722125.81669/101‑1 (MQ=60)
CGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACTGGAGATG < SRR3722125.540383/101‑1 (MQ=60)
CGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACTGGAGATGTA > SRR3722125.594035/1‑101 (MQ=60)
GCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACTGGAGATGTATC > SRR3722125.18944/1‑101 (MQ=60)
GCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACTGGAGATGTATC > SRR3722125.1032405/1‑101 (MQ=60)
ATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACTGGAGATGTATCTCC > SRR3722125.55606/1‑101 (MQ=60)
ATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACTGGAGATGTATCTCC > SRR3722125.52931/1‑101 (MQ=60)
ATTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACTGGAGATGTATCTCCct > SRR3722125.674092/1‑99 (MQ=60)
|
TGACCGTATAGAACAAACGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATATTTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACTGGAGATGTATCTCCTG > NZ_CP009273/481630‑481828
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
