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 I181 R1
|
159 |
32.7 |
1279082 |
96.9% |
1239430 |
121.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
420,401 |
A→G |
intergenic (‑27/‑66) |
acpH ← / → queA |
ACP phosphodiesterase/tRNA preQ1(34) S‑adenosylmethionine ribosyltransferase‑isomerase QueA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 420,401 | 0 | A | G | 100.0%
| 52.9
/ NA
| 17 | intergenic (‑27/‑66) | acpH/queA | ACP phosphodiesterase/tRNA preQ1(34) S‑adenosylmethionine ribosyltransferase‑isomerase QueA |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (7/10); total (7/10) |
GGCGGAAAACTTTCTTCAGGATTTCCGCGTACGAAATCAGCCAGTAAATTGCCGGAAAGCGAGCTTTCCGCGAGATGGGCTAAATGCAGGTGAGCTAAAAAATTCATCGATTATATTCTATCCAAAAGGGGGTAAAGGTTGCAGGGAGAGCGCCCCGGCACTAGACTACCCGCCTCTTATTTTAGTCTGAGTCAGTGTCATGCGCGTTACCGATTTCTCCTTTGAATTGCCCGAATCCCTGATTGCCCACTATCCCATG > NZ_CP009273/420268‑420526
|
ggCGGAAAACTTTCTTCAGGATTTCCGCGTACGAAATCAGCCAGTAAATTGCCGGAAAGCGAGCTTTCCGCGAGATGGGCTAAATGCAGGTGAGCTAAAAAATTCATCGATTATATTCTATCCAAAAGGGGGTGAAGGt > 2:617731/1‑139 (MQ=255)
tcttcAGGATTTCCGCGTACGAAATCAGCCAGTAAATTGCCGGAAAGCGAGCTTTCCGCGAGATGGGCTAAATGCAGGTGAGCTAAAAAATTCATCGATTATATTCTATCCAAAAGGGGGTGAAGGTTGCAGGGagag < 2:256121/138‑1 (MQ=255)
cGAAATCAGCCAGTAAATTGCCGGAAAGCGAGCTTTCCGCGAGATGGGCTAAATGCAGGTGAGCTAAAAAATTCATCGATTATATTCTATCCAAAAGGGGGTGAAGGTTGCAGGGAGAGCGCCCCGGCACTAGACTAcc < 2:193893/139‑1 (MQ=255)
aTTGCCGGAAAGCGAGTTTTCCGCGAGATGGGCTAAATGCAGGTGAGCTAAAAAATTCATCGATTATATTCTATCCAAAAGGGGGTGAAGGTTGCAGGGAGAGCGCCCCGGCACTAGACTACCCGCCTCTTATTTTAGt < 2:244810/139‑1 (MQ=255)
ttGCCGGAAAGCGAGCTTTCCGCGAGATGGGCTAAATGCAGGTGAGCTAAAAAATTCATCGATTATATTCTATCCAAAAGGGGGTGAAGGTTGCAGGGAGAGCGCCCCGGCACTAGACTACCCGCCTCTTATTTTAGTc < 2:287420/139‑1 (MQ=255)
ggTGAGCTAAAAAATTCATCGATTATATTCTATCCAAAAGGGGGTGAAGGTTGCAGGGAGAGCGCCCCGGCACTAGACTACCCGCCTCTTATTTTAGTCTGAGt > 2:149819/1‑104 (MQ=255)
ggTGAGCTAAAAAATTCATCGATTATATTCTATCCAAAAGGGGGTGAAGGTTGCAGGGAGAGCGCCCCGGCACTAGACTACCCGCCTCTTATTTTAGTCTGAGt < 1:149819/104‑1 (MQ=255)
aGCTAAAAAATTCATCGATTATATTCTATCCAAAAGGGGGTGAAGGTTGCAGGGAGAGCGCCCCGGCACTAGACTACCCGCCTCTTATTTTAGTc > 1:337816/1‑95 (MQ=255)
aGCTAAAAAATTAATCGATTATATTCTATCCAAAAGGGGGTGAAGGTTGAAGGGAGAGCGCCCCGGCACTAGACTACCCGCCTCTTATTTTAGTc < 2:337816/95‑1 (MQ=255)
cTAAAAAATTCATCGATTATATTCTATCCAAAAGGGGGTGAAGGTTGCAGGGAGAGCGCCCCGGCACTAGACTACCCGCCTCTTATTTTAGTCTGAGTCAGTGTCATGCGCGTTACCGATTTCTCCTTTGAATTGccc > 2:602867/1‑138 (MQ=255)
atatTCTATCCAAAAGGGGGTGAAGGTTGCAGGGAGAGCGCCCCGGCACTAGACTACCCGCCTCTTATTTTAGTCTGAGTCAGTGTCATGCGCGTTACCGATTTCTCCTTTGAATTGCCCGAATCCCTGATTGCCCAc < 1:560799/138‑1 (MQ=255)
atatTCTATCCAAAAGGGGGTGAAGGTTGCAGGGAGAGCGCCCCGGCACTAGACTACCCGCCTCTTATTTTAGTCTGAGTCAGTGTCATGCGCGTTACCGATTTCTCCTTTGAATTGCCCGAATCCCTGATTGCCCAc < 1:617731/138‑1 (MQ=255)
tCCAAAAGGGGGTGAAGGTTGCAGGGAGAGCGCCCCGGCACTAGACTACCCGCctc < 2:269040/56‑1 (MQ=255)
tCCAAAAGGGGGTGAAGGTTGCAGGGAGAGCGCCCCGGCACTAGACTACCCGCctc > 1:269040/1‑56 (MQ=255)
tCCAAAAGGGGGTGAAGGTTGCAGGGAGAGCGCCCCGGCACTAGACTACCCGCCTCTTATTTTAGTCTGAGTCAGTGTCATGCGCGTTACCGATTTCTCCTTTGAATTGCCCGAATCCCTGATTGCCCACTATCCCATg > 1:364385/1‑139 (MQ=255)
aaGGGGGTGAAGGTTGCAGGGAGAGCGCCCCGGCACTAGACTACCCGCCTCTTATTTTAGTCTGAGTCAGTGTCATGCGCGTTACCGATTTCTCCTTTGAATTGCCCGAATCCCTGATTGCCCAc > 1:588701/1‑125 (MQ=255)
aaGGGGGTGAAGGTTGCAGGGAGAGCGCCCCGGCACTAGACTACCCGCCTCTTATTTTAGTCTGAGTCAGTGTCATGCGCGTTACCGATTTCTCCTTTGAATTGCCCGAATCCCTGATTGCCCAc < 2:588701/125‑1 (MQ=255)
|
GGCGGAAAACTTTCTTCAGGATTTCCGCGTACGAAATCAGCCAGTAAATTGCCGGAAAGCGAGCTTTCCGCGAGATGGGCTAAATGCAGGTGAGCTAAAAAATTCATCGATTATATTCTATCCAAAAGGGGGTAAAGGTTGCAGGGAGAGCGCCCCGGCACTAGACTACCCGCCTCTTATTTTAGTCTGAGTCAGTGTCATGCGCGTTACCGATTTCTCCTTTGAATTGCCCGAATCCCTGATTGCCCACTATCCCATG > NZ_CP009273/420268‑420526
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
AGCCACGACGTCGGGCGGAAAACTTTCTTCAGGATTTCCGCGTACGAAATCAGCCAGTAAATTGCCGGAAAGCGAGCTTTCCGCGAGATGGGCTAAATGCAGGTGAGCTAAAAAATTCATCGATTATATTCTATCCAAAAGGGGGTAAAGGTTGCAGGGAGAGCGCCCCGGCACTAGACTACCCGCCTCTTATTTTAGTCTGAGTCAGTGTCATGCGCGTTACCGATTTCTCCTTTGAATTGCCCGAATCCCTGATTGCCCACTATCCCATGCCTGAACGCAGTAGCTGTC > NZ_CP009273/420255‑420545
|
gcatggcacatctttcttttttttttttcaagcagaagacggcatacgagatctagtacggtctcgtgggctcggagatgtgtataagagacagAAATGCAGGTGAGCTAAAAAATTCATCGATTATATTCTATCCAAAAGGGGGTGAAGG < SRR3722135.72469/57‑1 (MQ=60)
GACGTCGGGCGGAAAACTTTCTTCAGGATTTCCGCGTACGAAATCAGCCAGTAAATTGCCGGAAAGAGAGCTTTCCGCGAGATGGGCTAAATGCAGGTGAGCTAAAAAATTCATCGATTATATTCTATCCAAAAGGGGGTGAAGGTTGCAG < SRR3722135.613508/151‑1 (MQ=60)
CGTCGGGCGGAAAACTTTCTTCAGGATTTCCGCGTACGAAATCAGCCAGTAAATTGCCGGAAAGCGAGCTTTCCGCGAGATGGGCTAAATGCAGGTGAGCTAAAAAATTCATCGATTATATTCTATCCAAAAGGGGGTGAAGGTTGCAGGG < SRR3722135.8806/151‑1 (MQ=60)
gctcggagatgtgtataagagacaGGGCTAAATGCAGGTGAGCTAAAAAATTCATCGATTATATTCTATCCAAAAGGGGGTGAAGGTTGCAGGGAGAGCGCCCCGGCACTAGACTACCCGCCTCTTATTTTAGTCTGAGTCAGTGTCATGC < SRR3722135.151898/127‑1 (MQ=60)
AAATGCAGGTGAGCTAAAAAATTCATCGATTATATTCTATCCAAAAGGGGGTGAAGGTTGCAGGGAGAGCGCCCCGGCACTAGACTACCCGCCTCTTATTTTAGTCTGAGTCAGTGTCtgtctcttatacacatctccgagcccacgagac > SRR3722135.342611/1‑118 (MQ=60)
ATTATATTCTATCCAAAAGGGGGTGAAGGTTGCAGGGAGAGCGCCCCGGCACTAGACTACCCGCCTCTTATTTTAGTCctgtctcttatacacatctccgagcccacgagaccgtactagatctcgtatgccgtcttctgcttgaaaaaa > SRR3722135.272870/1‑78 (MQ=60)
ATTATATTCTATCCAAAAGGGGGTGAAGGTTGCAGGGAGAGCGCCCCGGCACTAGACTACCCGCCTCTTATTTTAGTCTGAGTCAGTGTCATGCGCGTTACCGATTTCTCCTTTGAATTGCCCGAATCCCTGATTGCCCACTATCCCATGC > SRR3722135.369529/1‑151 (MQ=60)
TATATTCTATCCAAAAGGGGGTGAAGGTTGCAGGGAGAGCGCCCCGGCACTAGACTACCCGCCTCTTATTTTAGTCTGAGTCAGTGTCATGCGCGTTACCGATTTCTCCTTTGAATTGCCCGAATCCCTGATTGCCCACTATCCCATGCC < SRR3722135.568205/150‑1 (MQ=60)
TATATTCTATCCAAAAGGGGGTGAAGGTTGCAGGGAGAGCGCCCCGGCACTAGACTACCCGCCTCTTATTTTAGTCTGAGTCAGTGTCATGCGCGTTACCGATTTCTCCTTTGAATTGCCCGAATCCCTGATTGCCCACTATCCCATGCC < SRR3722135.625795/150‑1 (MQ=60)
ATTCTATCCAAAAGGGGGTGAAGGTTGCAGGGAGAGCGCCCCGGCACTAGACTACCCGCCTCTTATTTTAGTCTGAGTCAGTGTCATGCGCGTTACCGATTTCTCCTTTGAATTGCCCGAATCCCTGATTGCCCACTATCCCATGCCctgt > SRR3722135.596409/1‑147 (MQ=60)
GGGGGTGAAGGTTGCAGGGAGAGCGCCCCGGCACTAGACTACCCGCCTCTTATTTTAGTCTGAGTCAGTGTCATGCGCGTTACCGATTTCTCCTTTGAATTGCCCGAATCCCTGATTGCCCACTATCCCATGCCTGAACGCAGTAGCTGTC > SRR3722135.279874/1‑151 (MQ=60)
|
AGCCACGACGTCGGGCGGAAAACTTTCTTCAGGATTTCCGCGTACGAAATCAGCCAGTAAATTGCCGGAAAGCGAGCTTTCCGCGAGATGGGCTAAATGCAGGTGAGCTAAAAAATTCATCGATTATATTCTATCCAAAAGGGGGTAAAGGTTGCAGGGAGAGCGCCCCGGCACTAGACTACCCGCCTCTTATTTTAGTCTGAGTCAGTGTCATGCGCGTTACCGATTTCTCCTTTGAATTGCCCGAATCCCTGATTGCCCACTATCCCATGCCTGAACGCAGTAGCTGTC > NZ_CP009273/420255‑420545
|
| 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: ‑ |
