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 |
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%
| 99.6
/ NA
| 23 | intergenic (‑30/+142) | maa/hha | maltose O‑acetyltransferase/HHA domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base . (9/14); total (9/14) |
GTATCGGTGAATAAGCTGACGAGCGCGCAGGCGATCGCGAGATAACGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGCAACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGTATGTCTTCATGGCGAAAAAGTATAAAATTCTTAATAAACAGCCGG > NZ_CP009273/475270‑475519
|
gTATCGGTGAATAAGCTGACGAGCGCGCAGGCGATCGCGAGATAACGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGAACTCCGGTTGCTGAAAATGCGGCaca > 1:542266/1‑135 (MQ=255)
aaTAAGCTGACGAGCGCGCAGGCGATCGCGAGATAACGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGa < 2:273427/139‑1 (MQ=255)
aaTAAGCTGACGAGCGCGCAGGCGATCGCGAGATAACGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGa < 2:61791/139‑1 (MQ=255)
cTGACGAGCGCGCAGGCGATCGCGAGATAACGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTc < 2:182240/139‑1 (MQ=255)
cGAGCGCGCAGGCGATCGCGAGATAACGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGt > 1:267680/1‑138 (MQ=255)
cgcgcAGGCGATCGCGAGATAACGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGaa > 1:54964/1‑137 (MQ=255)
aGGCGATCGCGAGATAACGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGCaca < 2:555647/109‑3 (MQ=255)
aGGCGATCGCGAGATAACGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGCaca > 1:555647/1‑107 (MQ=255)
aTCGCGAGATAACGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTcc > 1:332955/1‑138 (MQ=255)
gaTAACGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACAt < 2:54964/139‑1 (MQ=255)
gaTAACGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACAt < 2:111710/139‑1 (MQ=255)
ctcATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGa > 2:321910/1‑139 (MQ=255)
aTCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGAt < 1:471535/137‑1 (MQ=255)
aTCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATa > 1:413751/1‑138 (MQ=255)
aTCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATa > 2:313406/1‑138 (MQ=255)
ccGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGAC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAg < 1:56898/136‑1 (MQ=255)
aGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATcaca < 2:259870/139‑1 (MQ=255)
aGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATcaca < 1:422463/139‑1 (MQ=255)
gATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAg < 2:578413/139‑1 (MQ=255)
gATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAAAACGTTCCCATTACATCTGTGTGATAAAGATCACATAg < 2:267680/139‑1 (MQ=255)
cAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGCa > 2:327617/1‑61 (MQ=255)
cAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGCa < 1:327617/61‑1 (MQ=255)
cAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGTATGTCTTCa > 2:516876/1‑139 (MQ=255)
atcTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGTATGTCTTCATGGCGaaa < 1:516876/139‑1 (MQ=255)
atcTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGTATGTCTTCATGGCGaaa < 2:413751/139‑1 (MQ=255)
aCCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGCACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGTATGTCTTCATGGCGAAAAAGTATAAAATTCTTAATAAACAGCCgg > 2:324940/1‑139 (MQ=255)
cGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAg > 2:312463/1‑86 (MQ=255)
cGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAg < 1:312463/86‑1 (MQ=255)
|
GTATCGGTGAATAAGCTGACGAGCGCGCAGGCGATCGCGAGATAACGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGCAACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGTATGTCTTCATGGCGAAAAAGTATAAAATTCTTAATAAACAGCCGG > NZ_CP009273/475270‑475519
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ 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
AGGGAATGATTGTATCGGTGAATAAGCTGACGAGCGCGCAGGCGATCGCGAGATAACGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGCAACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGTATGTCTTCATGGCGAAAAAGTATAAAAT > NZ_CP009273/475259‑475502
|
AGGGAATGATTGTATCGGTGAATAAGCTGACGAGCGCGCAGGCGATCGCGAGATAACGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGAACTCCGGTTGCTGAAAATGCGGC‑ACAC > SRR3722139.548518/1‑149 (MQ=60)
tcaagcagaagacggcatacgagatctagtacggtctcgtgggctcggagatgtgtataagagacaGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGAC < SRR3722139.331635/84‑1 (MQ=60)
GAATAAGCTGACGAGCGCGCAGGCGATCGCGAGATAACGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTG > SRR3722139.271086/1‑150 (MQ=60)
AAGCTGACGAGCGCGCAGGCGATCGCGAGATAACGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAG > SRR3722139.55601/1‑149 (MQ=60)
GACGAGCGCGCAGGCGATCGCGAGATAACGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGActgtctcttatacacatctc > SRR3722139.562021/1‑131 (MQ=60)
GCGCGCAGGCGATCGCGAGATAACGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCC > SRR3722139.337034/1‑150 (MQ=60)
GATAACGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAA > SRR3722139.418664/1‑150 (MQ=60)
CATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACAT < SRR3722139.477033/149‑1 (MQ=60)
GCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGAC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGG < SRR3722139.57546/148‑1 (MQ=60)
GAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGTATGTC < SRR3722139.427442/151‑1 (MQ=60)
agtacggtctcgtgggctcggagatgtgtataagagacagTTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGTATGTCTTC < SRR3722139.316328/108‑1 (MQ=60)
CATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGTATGTCTTCATGGCGAAAAAGTATAAAAT < SRR3722139.522813/151‑1 (MQ=60)
|
AGGGAATGATTGTATCGGTGAATAAGCTGACGAGCGCGCAGGCGATCGCGAGATAACGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGCAACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGTATGTCTTCATGGCGAAAAAGTATAAAAT > NZ_CP009273/475259‑475502
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
