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 I97 R1
|
275 |
44.0 |
1733530 |
96.5% |
1672856 |
122.0 |
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%
| 81.4
/ NA
| 24 | I449I (ATT→ATC) | torA | trimethylamine‑N‑oxide reductase TorA |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (13/11); total (13/11) |
CGCAGGCACGCCGGGGCGTAAAGGCGTTATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATTCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAACTAACCCATTCCATCGCCATCAG > NZ_CP009273/1055950‑1056187
|
cgcAGGCACGCCGGGGCGTAAAGGCGTTATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTc > 2:467605/1‑139 (MQ=255)
cgcAGGCACGCCGGGGCGTAAAGGCGTTATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTc > 1:72527/1‑139 (MQ=255)
ccGTGGCGTAAAGGCGTTATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACTACAACAGTGACTACAACGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGa < 1:578284/139‑1 (MQ=255)
gCGTAAAGGCGTTATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGt > 2:195760/1‑138 (MQ=255)
ttATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGac > 2:721549/1‑138 (MQ=255)
aTTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCt < 2:499765/110‑1 (MQ=255)
aTTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCt > 1:499765/1‑110 (MQ=255)
gAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTaaa > 1:306390/1‑139 (MQ=255)
aGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAAt > 2:323637/1‑139 (MQ=255)
aGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAAt < 2:511090/139‑1 (MQ=255)
ccTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTa > 2:667849/1‑139 (MQ=255)
aCGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGc < 1:692827/139‑1 (MQ=255)
aCGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGc < 1:599352/139‑1 (MQ=255)
cGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGcc < 1:667849/139‑1 (MQ=255)
acaGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAAc < 1:467605/139‑1 (MQ=255)
acaGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAAc < 1:183250/139‑1 (MQ=255)
tGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCg > 1:623057/1‑39 (MQ=255)
tGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCg > 1:8914/1‑39 (MQ=255)
tGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCg < 2:623057/39‑1 (MQ=255)
tGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCg < 2:8914/39‑1 (MQ=255)
aaGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAACTAACCCATTCCa < 1:428539/139‑1 (MQ=255)
aCAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAACTAACCCATTCCATCGCCa > 1:647195/1‑139 (MQ=255)
aCAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAACTAACCCATTCCATCGCCa > 2:355807/1‑139 (MQ=255)
caCTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAACTAACCCATTCCATCGCCATcag > 1:442423/1‑136 (MQ=255)
|
CGCAGGCACGCCGGGGCGTAAAGGCGTTATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATTCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAACTAACCCATTCCATCGCCATCAG > NZ_CP009273/1055950‑1056187
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ 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
CACTACAACGGCGCAGGCACGCCGGGGCGTAAAGGCGTTATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATTCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAACTAACCCATTCCATCGCCATCAGCAGATCAACCGCAT > NZ_CP009273/1055939‑1056201
|
CACTACAACGGCGCAGGCACGCCGGGGCGTAAAGGCGTTATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCG > SRR3722120.73487/1‑151 (MQ=60)
GCCGTGGCGTAAAGGCGTTATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACTACAACAGTGACTACAACGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAAC < SRR3722120.586330/151‑1 (MQ=60)
GTAAAGGCGTTATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGActgtctcttatacacatct > SRR3722120.506936/1‑132 (MQ=60)
GGCGTTATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAAT > SRR3722120.310796/1‑151 (MQ=60)
cgccttagtctcgtgggctcggagatgtgtataagagacagCAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTT < SRR3722120.196263/110‑1 (MQ=60)
CACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCtgtctcttatacacatctccgagcccacgagactaaggcgaatctcgtatgccgtcttctgcttgaaaaaaaaaaagagatctataaa > SRR3722120.631711/1‑62 (MQ=60)
CACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCtgtctcttatacaaatctccgagcccacgagactaaggcgaatatcgtatgccgtcttctgcttgaaaaaaaaaaagacagaagaacg > SRR3722120.9024/1‑62 (MQ=60)
CACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAACTAACC < SRR3722120.607681/151‑1 (MQ=60)
CACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAACTAACC < SRR3722120.702286/151‑1 (MQ=60)
gctcggagatgtgtataagagacagCAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGGTCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAACTAACCC < SRR3722120.526502/126‑1 (MQ=60)
ACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAACTAACCC < SRR3722120.677001/151‑1 (MQ=60)
AACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAACTAACCCATTCC < SRR3722120.474387/151‑1 (MQ=60)
AACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAACTAACCCATTCC < SRR3722120.185769/151‑1 (MQ=60)
CTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAACTAACCCATTCCATCGCCAT > SRR3722120.656122/1‑151 (MQ=60)
AAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAACTAACCCATTCCATCGCCATCAGC < SRR3722120.434800/151‑1 (MQ=60)
GGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAACTAACCCATTCCATCGCCATCAGC > SRR3722120.448891/1‑148 (MQ=60)
CAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAATGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAACTAACCCATTCCATCGCCATCAGCAGATCAAC > SRR3722120.408795/1‑151 (MQ=60)
CAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAACTAACCCATTCCATCGCCATCAGCAGATCAAC > SRR3722120.794860/1‑151 (MQ=60)
GCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAACTAACCCctgtctcttatacacatctccgagcccacg > SRR3722120.508193/1‑121 (MQ=60)
|
CACTACAACGGCGCAGGCACGCCGGGGCGTAAAGGCGTTATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATTCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTTTGCCGGAACTAACCCATTCCATCGCCATCAGCAGATCAACCGCAT > NZ_CP009273/1055939‑1056201
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
