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 F2 I225 R1
|
227 |
21.4 |
1179702 |
97.1% |
1145490 |
86.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,579,168 |
T→C |
E339G (GAA→GGA) |
ggt ← |
gamma‑glutamyltransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,579,168 | 0 | T | C | 96.4%
| 80.7
/ ‑3.5
| 28 | E339G (GAA→GGA) | ggt | gamma‑glutamyltransferase |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base C (19/8); total (19/9) |
| Fisher's exact test for biased strand distribution p-value = 3.21e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.85e-01 |
ATTTGATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATTCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATTTCT > NZ_CP009273/3579084‑3579246
|
aTTTGATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAg > 2:522890/1‑90 (MQ=255)
aTTTGATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAg > 2:101716/1‑90 (MQ=255)
tttGATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGc < 1:238146/90‑1 (MQ=255)
aTCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATTCCGAGCGGTc < 1:416391/90‑1 (MQ=255)
aTCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTc < 2:501393/90‑1 (MQ=255)
aTCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTc < 2:322480/90‑1 (MQ=255)
aTCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTc < 2:504896/90‑1 (MQ=255)
aTCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTc < 2:179138/90‑1 (MQ=255)
tGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTAtt > 1:472361/1‑90 (MQ=255)
tGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTAtt > 1:302937/1‑90 (MQ=255)
tGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTAtt > 1:131854/1‑90 (MQ=255)
tGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTAtt > 2:3028/1‑90 (MQ=255)
tAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTcc > 2:9987/1‑90 (MQ=255)
aGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCg > 1:114669/1‑90 (MQ=255)
ggTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCAt > 2:542792/1‑90 (MQ=255)
gTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATg > 2:278245/1‑90 (MQ=255)
tCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGa > 1:487172/1‑90 (MQ=255)
cAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGAt > 1:250810/1‑90 (MQ=255)
tGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTgcatc > 2:434584/1‑90 (MQ=255)
tGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTgcatc > 2:487658/1‑90 (MQ=255)
aCTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGgcg < 2:487172/90‑1 (MQ=255)
cTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGgcgc < 2:250810/90‑1 (MQ=255)
ttGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTg > 1:120890/1‑90 (MQ=255)
aaaaTCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCaaa > 1:478698/1‑90 (MQ=255)
aattcGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGc > 1:332368/5‑90 (MQ=255)
aaTCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGc > 2:489597/1‑90 (MQ=255)
ccGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGt < 2:120890/90‑1 (MQ=255)
cGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATttct > 2:199280/1‑90 (MQ=255)
|
ATTTGATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATTCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATTTCT > NZ_CP009273/3579084‑3579246
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ 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
CTTTATTGATATCAATTTGATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATTCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGC > NZ_CP009273/3579070‑3579237
|
CTTTATTGATATCAATTTGATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCC < SRR3722109.104438/100‑1 (MQ=60)
CTTTATTGATATCAATTTGATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCC < SRR3722109.429870/100‑1 (MQ=60)
TTTGATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTA < SRR3722109.240955/100‑1 (MQ=60)
ATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATTCCGAGCGGTCGGCGTAGGCG < SRR3722109.422478/100‑1 (MQ=60)
GCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATT > SRR3722109.133469/1‑100 (MQ=60)
GCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATT > SRR3722109.306874/1‑100 (MQ=60)
GCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATT > SRR3722109.479478/1‑100 (MQ=60)
GATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCG > SRR3722109.116090/1‑100 (MQ=60)
GGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCctgtctcttatacacatctgacgctgccgacgaat > SRR3722109.247447/1‑65 (MQ=60)
GCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGCCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGA > SRR3722109.494519/1‑100 (MQ=60)
CTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGAT > SRR3722109.253767/1‑100 (MQ=60)
CCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTG > SRR3722109.122382/1‑100 (MQ=60)
GTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAA > SRR3722109.485913/1‑100 (MQ=60)
ACTTTGACAAAATTCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGC > SRR3722109.336767/1‑100 (MQ=60)
|
CTTTATTGATATCAATTTGATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATTCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGC > NZ_CP009273/3579070‑3579237
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
