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 |
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%
| 123.3
/ NA
| 34 | I449I (ATT→ATC) | torA | trimethylamine‑N‑oxide reductase TorA |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (24/10); total (24/10) |
GTTATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATTCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTG > NZ_CP009273/1055975‑1056142
|
gTTATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTg < 1:169241/91‑1 (MQ=255)
gTTATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTg > 2:428538/1‑91 (MQ=255)
ttATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGc < 1:1125151/91‑1 (MQ=255)
tATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGcc < 2:596803/91‑1 (MQ=255)
tATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGcc > 1:793574/1‑91 (MQ=255)
tGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGttt > 1:152245/1‑91 (MQ=255)
gAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGtttt > 1:931293/1‑91 (MQ=255)
gAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGtttt > 1:241680/1‑91 (MQ=255)
gTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGa > 1:792370/1‑91 (MQ=255)
gTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGa > 1:753970/1‑91 (MQ=255)
gTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGa > 2:437610/1‑91 (MQ=255)
gTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGa > 2:515314/1‑91 (MQ=255)
gCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCt > 1:316731/1‑91 (MQ=255)
aCGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAAc > 1:605424/1‑91 (MQ=255)
gATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCgggg > 1:279763/1‑91 (MQ=255)
gATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCgggg < 1:177223/91‑1 (MQ=255)
ttCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGaa < 1:133640/91‑1 (MQ=255)
gCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTg > 2:862237/1‑91 (MQ=255)
ccTGTTCACGACAACAGTGACTACAAAGGCTCCAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGa < 1:8461/91‑1 (MQ=255)
ccTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGa < 1:813941/91‑1 (MQ=255)
acaGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACgg > 1:28786/1‑91 (MQ=255)
gTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTaa > 1:855225/1‑91 (MQ=255)
tGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTaaa < 1:150945/91‑1 (MQ=255)
gACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAAt > 1:782606/1‑91 (MQ=255)
gACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAAt < 2:1042562/91‑1 (MQ=255)
aaGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTaaa > 2:840316/1‑91 (MQ=255)
ggCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAAc > 1:345446/1‑91 (MQ=255)
tACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTgc > 1:391871/1‑91 (MQ=255)
tACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTgc > 1:1011254/1‑91 (MQ=255)
gcaCTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCt > 2:103224/1‑91 (MQ=255)
gcaCTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCt > 2:434321/1‑91 (MQ=255)
gcaCTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCt > 2:782564/1‑91 (MQ=255)
gcaCTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGCGATCACCTGGAACGGTAAATCGGTAAAACTGCCGCCGCt > 1:858911/1‑91 (MQ=255)
caCTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTg < 1:1095028/91‑1 (MQ=255)
|
GTTATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATTCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTG > NZ_CP009273/1055975‑1056142
|
| 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
GCCGGGGCGTAAAGGCGTTATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATTCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTT > NZ_CP009273/1055959‑1056156
|
GCCGGGGCGTAAAGGCGTTATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCC < SRR3722125.561477/101‑1 (MQ=60)
GCCGGGGCGTAAAGGCGTTATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCC < SRR3722125.340483/101‑1 (MQ=60)
GTAAAGGCGTTATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCC > SRR3722125.810893/1‑101 (MQ=60)
GGCGTTATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTT > SRR3722125.155142/1‑101 (MQ=60)
GCGTTATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTT > SRR3722125.951972/1‑101 (MQ=60)
GCGTTATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTT > SRR3722125.246528/1‑101 (MQ=60)
GTTATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTAT < SRR3722125.172503/101‑1 (MQ=60)
TTATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATC < SRR3722125.1150573/101‑1 (MQ=60)
ATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGA > SRR3722125.770267/1‑101 (MQ=60)
ATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGA > SRR3722125.809659/1‑101 (MQ=60)
GGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCT > SRR3722125.323242/1‑101 (MQ=60)
CTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAAC > SRR3722125.618464/1‑101 (MQ=60)
GCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGG > SRR3722125.285429/1‑101 (MQ=60)
GATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCA < SRR3722125.180665/101‑1 (MQ=60)
TTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAAC < SRR3722125.136171/101‑1 (MQ=60)
CCTGTTCACGACAACAGTGACTACAAAGGCTCCAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAA < SRR3722125.8618/101‑1 (MQ=60)
CCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAA < SRR3722125.831762/101‑1 (MQ=60)
GTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGG > SRR3722125.29303/1‑101 (MQ=60)
CACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAA > SRR3722125.874067/1‑101 (MQ=60)
CGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAAT > SRR3722125.346725/1‑101 (MQ=60)
CGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAAT > SRR3722125.799651/1‑101 (MQ=60)
TGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAAC > SRR3722125.352629/1‑101 (MQ=60)
TGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAAC < SRR3722125.153818/101‑1 (MQ=60)
CTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGC > SRR3722125.400079/1‑101 (MQ=60)
CTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGC > SRR3722125.1033871/1‑101 (MQ=60)
GGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGCGATCACCTGGAACGGTAAATCGGTAAAACTGCCGCCGCT > SRR3722125.877841/1‑101 (MQ=60)
CAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAA > SRR3722125.659237/1‑101 (MQ=60)
CAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAA > SRR3722125.825091/1‑101 (MQ=60)
CAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAA > SRR3722125.336850/1‑101 (MQ=60)
GCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGT > SRR3722125.416326/1‑101 (MQ=60)
CACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTA < SRR3722125.1119674/101‑1 (MQ=60)
TATCCCGATTGCCGGTTTTATCAATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTT > SRR3722125.1074669/1‑101 (MQ=60)
ATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTT > SRR3722125.837007/1‑101 (MQ=60)
|
GCCGGGGCGTAAAGGCGTTATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATTCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGTATTTT > NZ_CP009273/1055959‑1056156
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
