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 |
|
A2 F5 I184 R1
|
278 |
29.6 |
1166432 |
97.3% |
1134938 |
124.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,056,058 |
T→C |
I449I (ATT→ATC) |
torA → |
trimethylamine‑N‑oxide reductase TorA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,056,058 | 0 | T | C | 100.0%
| 38.2
/ NA
| 12 | I449I (ATT→ATC) | torA | trimethylamine‑N‑oxide reductase TorA |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (6/6); total (6/6) |
CAACGGCGCAGGCACGCCGGGGCGTAAAGGCGTTATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATTCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAACTAACCCATTCCATCGCCATCAG > NZ_CP009273/1055944‑1056187
|
cAACGGCGCAGGCACGCCGGGGCGTAAAGGCGTTATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCg < 1:204955/139‑1 (MQ=255)
cAGGCACGCCGGGGCGTAAAGGCGTTATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCg > 2:354824/1‑138 (MQ=255)
gAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTaaa > 1:373096/1‑139 (MQ=255)
aCGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGc < 1:529150/139‑1 (MQ=255)
cGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCTTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGTTAAATCTGCCGCCGCTGAAAATGTGTATTTTTGcc < 2:310334/139‑1 (MQ=255)
cGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGcc < 1:135170/139‑1 (MQ=255)
aacaGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGaa < 1:310217/139‑1 (MQ=255)
caGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAAc > 1:295010/1‑138 (MQ=255)
aCAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAACTAACCCATTCCATCGCCa > 1:62822/1‑139 (MQ=255)
cagcaCTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAACTAACCCATTCCATCGCCATcag < 1:76018/139‑1 (MQ=255)
caCTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAACTAACCCATTCCATCGCCATcag > 1:335930/1‑136 (MQ=255)
caCTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAACTAACCCATTCCATCGCCATcag > 2:566945/1‑136 (MQ=255)
|
CAACGGCGCAGGCACGCCGGGGCGTAAAGGCGTTATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATTCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAACTAACCCATTCCATCGCCATCAG > NZ_CP009273/1055944‑1056187
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
AGGTGGTGGTTTTGGTTTTGGCTGGCACTACAACGGCGCAGGCACGCCGGGGCGTAAAGGCGTTATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATTCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAACTAACCCATTCCATCGCCATCAGCAGATCAACCGCATTATTG > NZ_CP009273/1055914‑1056206
|
AGGTGGTGGTTTTGGTTTTGGCTGGCACTACAACGGCGCAGGCACGCCGGGGCGTAAAGGCGTTATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATT < SRR3722139.502735/151‑1 (MQ=60)
attggcttgcgtctagttttttttttttttttcaagcagaagacggcatacgagatctagtacggtctcgtgggctcggagatgtgtataagagacagGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACC < SRR3722139.97344/53‑1 (MQ=60)
ACAACGGCGCAGGCACGCCGGGGCGTAAAGGCGTTATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACC < SRR3722139.207491/151‑1 (MQ=60)
GGCGTTATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAAT > SRR3722139.377570/1‑151 (MQ=60)
GTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAACT > SRR3722139.298712/1‑150 (MQ=60)
ggctcggagatgtgtataagagacagCAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAACTAACC < SRR3722139.52628/125‑1 (MQ=60)
CACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAACTAACC < SRR3722139.535242/151‑1 (MQ=60)
ACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAACTAACCC < SRR3722139.136806/151‑1 (MQ=60)
CAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAACTAACCCATTC < SRR3722139.314059/151‑1 (MQ=60)
CTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAACTAACCCATTCCATCGCCAT > SRR3722139.63546/1‑151 (MQ=60)
GGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAACTAACCCATTCCATCGCCATCAGC > SRR3722139.340033/1‑148 (MQ=60)
GCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAACTAACCCATTCCATCGCCATCAGCAGATCAACCG < SRR3722139.76900/151‑1 (MQ=60)
ATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAACTAACCCATTCCATCGCCATCAGCAGATCAACCGCATTATTG < SRR3722139.541444/151‑1 (MQ=60)
|
AGGTGGTGGTTTTGGTTTTGGCTGGCACTACAACGGCGCAGGCACGCCGGGGCGTAAAGGCGTTATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATTCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAACTAACCCATTCCATCGCCATCAGCAGATCAACCGCATTATTG > NZ_CP009273/1055914‑1056206
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
