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 I96 R1
|
227 |
23.3 |
882352 |
98.0% |
864704 |
126.9 |
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 | . | 95.0%
| 77.1
/ ‑2.9
| 20 | intergenic (‑30/+142) | maa/hha | maltose O‑acetyltransferase/HHA domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base A (0/0); major base . (8/11); minor base G (0/1); total (8/12) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.95e-01 |
ATTGTATCGGTGAATAAGCTGACGAGCGCGCAGGCGATCGCGAGATAACGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGCAACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGTATGTCTTCATGGCGAAAAAGTATAAAATTCTTAATAAACAGCC > NZ_CP009273/475267‑475517
|
aTTGTATCGGTGAATAAGCTGACGAGCGCGCAGGCGATCGCGAGATAACGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGCac < 2:229867/139‑2 (MQ=255)
gTATCGGTGAATAAGCTGACGAGCGCGCAGGCGATCGCGAGATAACGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGCaca > 1:120171/1‑135 (MQ=255)
gCTGACGAGCGCGCAGGCGATCGCGAGATAACGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGG‑GACACAGTAAGACGAAAAGt < 1:85134/139‑1 (MQ=255)
aCGAGCGCGCAGGCGATCGCGAGATAACGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCa < 2:255011/137‑1 (MQ=255)
cgcAGGCGATCGCGAGATAACGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAagag > 2:258144/1‑138 (MQ=255)
gCGATCGCGAGATAACGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGtt < 2:170042/139‑1 (MQ=255)
tCGCGAGATAACGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCa < 2:429829/139‑1 (MQ=255)
gTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCtgtgt > 1:95368/1‑139 (MQ=255)
tctcATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCtgtgtg < 1:264417/139‑1 (MQ=255)
tGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATa > 2:335296/1‑135 (MQ=255)
ccGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAg < 2:228268/136‑1 (MQ=255)
ccGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGa < 1:367166/137‑1 (MQ=255)
aGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATcaca < 2:120171/139‑1 (MQ=255)
cACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGTATGTCt > 2:236524/1‑139 (MQ=255)
aCCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGTATGTCtt > 1:246000/1‑139 (MQ=255)
tctGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGTATGTCTTCATGGCGAAAAAGTATAAAAt < 2:333955/138‑1 (MQ=255)
ctGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCAt < 1:96613/79‑1 (MQ=255)
ctGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCAt > 2:96613/1‑79 (MQ=255)
cTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGTATGTCTTCATGGCGAAAAAGTATAAAATTCTTAATAAACAg < 1:35977/138‑1 (MQ=255)
tGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGTATGTCTTCATGGCGAAAAAGTATAAAATTCTTAATAAACAGcc > 1:437888/1‑139 (MQ=255)
aCCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGtt < 2:125360/59‑1 (MQ=255)
aCCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGtt > 1:125360/1‑59 (MQ=255)
|
ATTGTATCGGTGAATAAGCTGACGAGCGCGCAGGCGATCGCGAGATAACGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGCAACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGTATGTCTTCATGGCGAAAAAGTATAAAATTCTTAATAAACAGCC > NZ_CP009273/475267‑475517
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 35 ≤ 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
GGGAATGATTGTATCGGTGAATAAGCTGACGAGCGCGCAGGCGATCGCGAGATAACGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGCAACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGTATGTCTTCATGGCGAAAAAGTATAAAATTCTTAATAAACAGCCGGTTATAGCTCCGAAAGCGAATTATTTATTAGCGA > NZ_CP009273/475260‑475552
|
GGGAATGATTGTATCGGTGAATAAGCTGACGAGCGCGCAGGCGATCGCGAGATAACGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGT < SRR3722119.90742/151‑1 (MQ=60)
AGCTGACGAGCGCGCAGGCGATCGCGAGATAACGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGG‑GACACAGTAAGACGAAAAGTCAGTGAAGAGA < SRR3722119.85958/151‑1 (MQ=60)
acgagattcgccttagtctcgtgggctcggagatgtgtataagagacagCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGT < SRR3722119.97560/101‑1 (MQ=60)
CGCGAGATAACGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTG > SRR3722119.96302/1‑151 (MQ=60)
GTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCAC < SRR3722119.267146/151‑1 (MQ=60)
GCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGT < SRR3722119.370876/149‑1 (MQ=60)
CGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGTATGTCTTC > SRR3722119.248555/1‑151 (MQ=60)
GTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGTATGTCTTCATGGCGAAAAAGTATAAAATTCTTAATAAACAGCCG > SRR3722119.442270/1‑151 (MQ=60)
GCTCATTACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCctgtctcttatacacatctccgagcccacgagactaaggcgaatctcgtatgccgtcttctgcttgaaa > SRR3722119.126608/1‑81 (MQ=60)
ACTGACCTCCGGTTGCTGAAAATGCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGTATGTCTTCATGGCGAAAAAGTATAAAATTCTTAATAAACAGCCGGTTATAGC < SRR3722119.36295/150‑1 (MQ=60)
GCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGctgtctcttatacacatctccgagcccacgagactaaggcgaatctcgtatgccgtcttctgcttgaaaaaaaaaa > SRR3722119.290320/1‑74 (MQ=60)
GCGGC‑ACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGTATGTCTTCATGGCGAAAAAGTATAAAATTCTTAATAAACAGCCGGTTATAGCTCCGAAAGCGAATTATTTATTAG < SRR3722119.289174/150‑1 (MQ=60)
gcACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGTATGTCTTCATGGCGAAAAAGTATAAAATTCTTAATAAACAGCCGGTTATAGCTCCGAAAGCGAATTATTTATTAGCGA > SRR3722119.129134/3‑150 (MQ=60)
|
GGGAATGATTGTATCGGTGAATAAGCTGACGAGCGCGCAGGCGATCGCGAGATAACGTCTCATCTGCCGAGCGATACAACTCACCAGCAATCATCTTTTCTTTTTCTGTGCTCATTACTGACCTCCGGTTGCTGAAAATGCGGCAACACAGTAAGACGAAAAGTCAGTGAAGAGAACGTTCCCATTACATCTGTGTGATAAAGATCACATAGGGTATGTCTTCATGGCGAAAAAGTATAAAATTCTTAATAAACAGCCGGTTATAGCTCCGAAAGCGAATTATTTATTAGCGA > NZ_CP009273/475260‑475552
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
