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 I194 R1
|
197 |
32.2 |
1845014 |
95.2% |
1756453 |
85.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,220,044 |
A→G |
S236P (TCG→CCG) |
yohF ← |
SDR family oxidoreductase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,220,044 | 0 | A | G | 100.0%
| 61.9
/ NA
| 19 | S236P (TCG→CCG) | yohF | SDR family oxidoreductase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (15/4); total (15/4) |
ACCCAATGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGACTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGTTGCGCCAAAACGCCGC > NZ_CP009273/2219957‑2220126
|
aCCCAATGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCt > 1:788992/1‑90 (MQ=255)
aaTGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGccc < 2:368212/90‑1 (MQ=255)
aTGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGGGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCg > 1:322285/1‑90 (MQ=255)
tGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCgg < 1:815256/90‑1 (MQ=255)
aaaTATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCggtg > 1:396616/1‑90 (MQ=255)
cACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAAt > 1:387379/1‑90 (MQ=255)
gcTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAAc < 2:397634/90‑1 (MQ=255)
gAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTgcg > 1:153658/1‑67 (MQ=255)
gAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTgcg < 2:153658/67‑1 (MQ=255)
gAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCAcaccac > 1:571410/1‑90 (MQ=255)
gAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCAcaccac > 1:77881/1‑90 (MQ=255)
gAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCAcaccac > 1:122229/1‑90 (MQ=255)
gAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCAcaccac > 1:438878/1‑90 (MQ=255)
gAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCAcaccac > 1:288860/1‑90 (MQ=255)
gAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCAcaccac > 1:13767/1‑90 (MQ=255)
gtgGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGc > 2:281494/1‑90 (MQ=255)
gccATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGTTGCGcc > 2:78341/1‑90 (MQ=255)
gccATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGTTGCGcc > 1:575056/1‑90 (MQ=255)
aTCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGTTGCGCCAAAAcgccgc > 1:880173/1‑90 (MQ=255)
|
ACCCAATGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGACTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGTTGCGCCAAAACGCCGC > NZ_CP009273/2219957‑2220126
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 30 ≤ 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
CCAAAATATTACCCAATGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGACTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGTTGCGCCAAAACGCCGCAAGGGAATCG > NZ_CP009273/2219947‑2220136
|
CCAAAATATTACCCAATGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCT > SRR3722072.802809/1‑100 (MQ=60)
ATATTACCCAATGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGGGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCG > SRR3722072.327923/1‑100 (MQ=60)
TTACCCAATGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTG > SRR3722072.403774/1‑100 (MQ=60)
ATGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAAT > SRR3722072.394318/1‑100 (MQ=60)
TGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATT < SRR3722072.829460/100‑1 (MQ=60)
AATATCCACGCACCTTACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGC > SRR3722072.338933/1‑100 (MQ=60)
ATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACctgtctcttatac > SRR3722072.156355/1‑87 (MQ=60)
ATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCAC > SRR3722072.14032/1‑100 (MQ=60)
ATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCAC > SRR3722072.79327/1‑100 (MQ=60)
ATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCAC > SRR3722072.581618/1‑100 (MQ=60)
ATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCAC > SRR3722072.446889/1‑100 (MQ=60)
ATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCAC > SRR3722072.293850/1‑100 (MQ=60)
ATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCAC > SRR3722072.124455/1‑100 (MQ=60)
ACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGTTGCGCC > SRR3722072.585333/1‑100 (MQ=60)
gtgtataagagacagATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGTTGCGCCAAAAC < SRR3722072.835589/85‑1 (MQ=60)
GCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGTTGCGCCAAAACGCCGC > SRR3722072.895320/1‑100 (MQ=60)
CTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGTTGCGCCAAAACGCCGCAAGGGAAT > SRR3722072.851795/1‑100 (MQ=60)
ATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGTTGCGCCAAAACGCCGCAAGGGAATCG > SRR3722072.359078/1‑100 (MQ=60)
|
CCAAAATATTACCCAATGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGACTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGTTGCGCCAAAACGCCGCAAGGGAATCG > NZ_CP009273/2219947‑2220136
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
