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 |
475,405 |
Δ1 bp |
intergenic (‑31/+141) |
maa ← / ← hha |
maltose O‑acetyltransferase/HHA domain‑containing protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 475,404 | 0 | A | . | 100.0%
| 156.9
/ NA
| 35 | intergenic (‑30/+142) | maa/hha | maltose O‑acetyltransferase/HHA domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base . (16/19); total (16/19) |
CGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGCAACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGTATGTCTTCAT > NZ_CP009273/475315‑475484
|
cGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGCac > 2:529623/1‑90 (MQ=255)
cGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGCac < 1:529623/91‑2 (MQ=255)
tctcATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGCacac < 2:161867/91‑4 (MQ=255)
tcATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAg > 2:53525/1‑91 (MQ=255)
aTCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTa < 1:30183/91‑1 (MQ=255)
gAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGaa > 2:81360/1‑91 (MQ=255)
gAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGaa > 2:378901/1‑91 (MQ=255)
gAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGaa > 1:180194/1‑91 (MQ=255)
gCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGaaaa > 2:796722/1‑91 (MQ=255)
cACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAaga > 1:123073/1‑91 (MQ=255)
ccAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAgaga > 2:705915/1‑91 (MQ=255)
cAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGaa < 2:326698/91‑1 (MQ=255)
gCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGCacac < 2:6193/62‑4 (MQ=255)
gCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGCacac > 1:6193/1‑59 (MQ=255)
atcatcTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTc < 1:484847/91‑1 (MQ=255)
cttttcttttTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCAtt < 1:865787/91‑1 (MQ=255)
tttcctttttcgTTGCTCATTACTGACCTCCGGTTGTTGAAAATGCGGC‑ACACAGTAAAACGAAAAGTCATTGAAGAGAAC‑TTTCCATTAc < 2:487268/91‑1 (MQ=255)
ctttttctGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATc < 1:313216/91‑1 (MQ=255)
ctttttctGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATc < 2:51867/91‑1 (MQ=255)
ttctGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCtgtg < 1:833118/91‑1 (MQ=255)
gtgCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGAt > 1:155858/1‑91 (MQ=255)
tgCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATa < 1:770409/91‑1 (MQ=255)
tgCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATa < 1:214794/91‑1 (MQ=255)
cATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGa < 2:867444/91‑1 (MQ=255)
aTTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGAt < 1:155478/91‑1 (MQ=255)
ttACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCtg > 2:250040/1‑78 (MQ=255)
ttACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCtg < 1:250040/78‑1 (MQ=255)
ttACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGaac < 1:460108/91‑3 (MQ=255)
ttACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATc < 2:28303/91‑1 (MQ=255)
tACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATca < 2:178906/91‑1 (MQ=255)
tGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACAt < 1:81360/91‑1 (MQ=255)
gACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATa > 1:94610/1‑91 (MQ=255)
gACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATa > 1:57647/1‑91 (MQ=255)
ccTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAgg < 2:180194/91‑1 (MQ=255)
cTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAggg > 1:844536/1‑91 (MQ=255)
ccGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGTa > 2:309929/1‑91 (MQ=255)
ccGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGTa > 2:404567/1‑91 (MQ=255)
ggTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGTATg > 1:105353/1‑91 (MQ=255)
cTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGTATGTCTTc > 1:702846/1‑91 (MQ=255)
gAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGTATGTCTTCAt < 2:510033/91‑1 (MQ=255)
|
CGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGCAACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGTATGTCTTCAT > NZ_CP009273/475315‑475484
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ 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
GATAACGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGCAACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGTATGTCTTC > NZ_CP009273/475310‑475482
|
GATAACGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGT < SRR3722118.476038/101‑1 (MQ=60)
CGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGAC < SRR3722118.540856/101‑1 (MQ=60)
CTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAA > SRR3722118.183747/1‑101 (MQ=60)
ATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAG < SRR3722118.30735/101‑1 (MQ=60)
CGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGA > SRR3722118.125377/1‑101 (MQ=60)
CAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGActgtctcttatacacatct > SRR3722118.6325/1‑82 (MQ=60)
CAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATT < SRR3722118.867495/101‑1 (MQ=60)
ATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATN < SRR3722118.469215/101‑1 (MQ=60)
ATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATC < SRR3722118.495100/101‑1 (MQ=60)
CTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGT < SRR3722118.885066/101‑1 (MQ=60)
TTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGAT > SRR3722118.158879/1‑101 (MQ=60)
CTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAA < SRR3722118.319659/101‑1 (MQ=60)
cagTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAG < SRR3722118.255125/98‑1 (MQ=60)
TTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGAT < SRR3722118.851477/101‑1 (MQ=60)
TGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACAT < SRR3722118.219104/101‑1 (MQ=60)
TGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACAT < SRR3722118.787335/101‑1 (MQ=60)
GCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATA > SRR3722118.58719/1‑101 (MQ=60)
GCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATA > SRR3722118.96342/1‑101 (MQ=60)
CATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGG > SRR3722118.863204/1‑101 (MQ=60)
ATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGT < SRR3722118.158490/101‑1 (MQ=60)
TTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGAACACATAGGGTA < SRR3722118.469813/101‑1 (MQ=60)
ACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGTATG > SRR3722118.107291/1‑101 (MQ=60)
TGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGTATGTC < SRR3722118.82880/101‑1 (MQ=60)
CCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGTATGTCTTC > SRR3722118.718191/1‑101 (MQ=60)
|
GATAACGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGCAACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGTATGTCTTC > NZ_CP009273/475310‑475482
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
