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 F4 I88 R1
|
217 |
30.5 |
1742422 |
95.9% |
1670982 |
87.3 |
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%
| 131.7
/ NA
| 30 | coding (512/648 nt) | acrR | multidrug efflux transporter transcriptional repressor AcrR |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base . (16/14); total (16/14) |
AACGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATATTTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTAC > NZ_CP009273/481645‑481811
|
aaCGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGcc > 2:608967/1‑91 (MQ=255)
aaCGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGcc > 2:401852/1‑91 (MQ=255)
aaCGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGcc > 2:498963/1‑91 (MQ=255)
aCGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCt < 2:126191/91‑1 (MQ=255)
gTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTgg > 1:534268/1‑91 (MQ=255)
gAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTg < 2:270335/88‑1 (MQ=255)
gAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTg > 1:270335/1‑88 (MQ=255)
gAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGccc > 2:537958/1‑91 (MQ=255)
gAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGccc < 2:600548/91‑1 (MQ=255)
aaTGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGc < 2:423377/91‑1 (MQ=255)
aaTGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGc < 1:368329/91‑1 (MQ=255)
aaTGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGc < 2:744435/91‑1 (MQ=255)
aaTGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGc < 2:205145/91‑1 (MQ=255)
tGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCaa < 1:792469/91‑1 (MQ=255)
ttGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGACACCTGGCTCTTTGCCCCGccctc > 1:160847/1‑87 (MQ=255)
tGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCt > 1:106800/1‑91 (MQ=255)
cgcgTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAGAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAaagaa > 1:814238/1‑91 (MQ=255)
tCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGccc < 2:498361/91‑1 (MQ=255)
tCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGccc < 1:344151/91‑1 (MQ=255)
tCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGccc < 1:216550/91‑1 (MQ=255)
attattATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGt > 1:790451/1‑91 (MQ=255)
atGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCAt < 1:537958/91‑1 (MQ=255)
tGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATc > 1:854613/1‑91 (MQ=255)
tGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATc > 2:820779/1‑91 (MQ=255)
gcgcGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCt > 1:768327/1‑91 (MQ=255)
gcgcGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCt < 2:51986/91‑1 (MQ=255)
gcgcGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCt > 1:467673/1‑91 (MQ=255)
gcgGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTa > 1:803737/1‑91 (MQ=255)
cgGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTAc > 1:788763/1‑91 (MQ=255)
cgGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTAc < 1:700640/91‑1 (MQ=255)
|
AACGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATATTTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTAC > NZ_CP009273/481645‑481811
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 32 ≤ 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
|
gacagGTATAGAACAAACGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATATTC < SRR3722118.107434/96‑1 (MQ=60)
agatgtgtataagagacaGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATATTC < SRR3722118.155787/83‑1 (MQ=60)
gaagacggcatacgagataggagtccgtctcgtgggctcggagatgtgtataagagacagGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAAC < SRR3722118.412612/41‑1 (MQ=60)
TTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGG > SRR3722118.545606/1‑101 (MQ=60)
GTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATATTT‑CGGCCTGATGGAAAACTGGCTCTTTGCCC > SRR3722118.275864/1‑101 (MQ=60)
AGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGACACCTGGCTCTTTGCCCCGCcctc > SRR3722118.163980/1‑97 (MQ=60)
GCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCT > SRR3722118.108767/1‑101 (MQ=60)
AATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGA < SRR3722118.375990/101‑1 (MQ=60)
TGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATC < SRR3722118.809887/101‑1 (MQ=60)
GATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAGAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAA > SRR3722118.832152/1‑101 (MQ=60)
TCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGT < SRR3722118.351285/101‑1 (MQ=60)
TCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGT < SRR3722118.220898/101‑1 (MQ=60)
TCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGT > SRR3722118.807814/1‑101 (MQ=60)
GCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATC > SRR3722118.873579/1‑101 (MQ=60)
CAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCT > SRR3722118.477541/1‑101 (MQ=60)
CAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCT > SRR3722118.785202/1‑101 (MQ=60)
ATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTA > SRR3722118.821390/1‑101 (MQ=60)
TTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTAC > SRR3722118.806086/1‑101 (MQ=60)
ATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACTGGAG < SRR3722118.549371/101‑1 (MQ=60)
CGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACTGGAGATGTA < SRR3722118.715921/101‑1 (MQ=60)
NTTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACTGGAGATGTATCTCCTG > SRR3722118.509611/1‑101 (MQ=60)
ATTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACTGGAGATGTATCTCCct > SRR3722118.874531/1‑99 (MQ=60)
|
TGACCGTATAGAACAAACGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATATTTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACTGGAGATGTATCTCCTG > NZ_CP009273/481630‑481828
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
