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 I206 R1
|
206 |
23.7 |
1314362 |
96.8% |
1272302 |
86.2 |
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%
| 73.0
/ NA
| 23 | S236P (TCG→CCG) | yohF | SDR family oxidoreductase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (13/10); total (13/10) |
CAATGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGACTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGTTGCGCCAAAACGCCGCAAG > NZ_CP009273/2219960‑2220129
|
cAATGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGcc > 1:294872/1‑90 (MQ=255)
aaTGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCGACGGCTGccc < 1:409875/90‑1 (MQ=255)
aaTGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGccc < 2:503385/90‑1 (MQ=255)
aTGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGccc > 1:316004/1‑89 (MQ=255)
aTGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGccc < 2:316004/89‑1 (MQ=255)
aCTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTc < 1:592376/90‑1 (MQ=255)
aCTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTc < 2:319717/90‑1 (MQ=255)
cTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCgg > 1:433936/1‑65 (MQ=255)
cTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCgg < 2:433936/65‑1 (MQ=255)
cTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACa > 1:361092/1‑90 (MQ=255)
gggTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCcac > 2:585073/1‑90 (MQ=255)
gAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCAcaccac > 1:403292/1‑90 (MQ=255)
gAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCAcaccac > 1:556857/1‑90 (MQ=255)
gAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCAcaccac > 1:194184/1‑90 (MQ=255)
gAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCAcaccac > 2:6086/1‑90 (MQ=255)
aCTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACAccacca < 2:294872/90‑1 (MQ=255)
ttCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCa > 2:533546/1‑90 (MQ=255)
tCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCaa < 1:472684/90‑1 (MQ=255)
tCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCaa < 1:328677/90‑1 (MQ=255)
cgccATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGTTgcgc > 1:339215/1‑90 (MQ=255)
gccATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGTTGCGcc > 2:17512/1‑90 (MQ=255)
gccATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGTTGCGcc > 2:461766/1‑90 (MQ=255)
aaCGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGTTGCGCCAAAACGCCGCAAg < 2:607757/90‑1 (MQ=255)
|
CAATGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGACTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGTTGCGCCAAAACGCCGCAAG > NZ_CP009273/2219960‑2220129
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ 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
ACCAAAATATTACCCAATGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGACTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGTTGCGCCAAAACGCCGCAAGGGAATCG > NZ_CP009273/2219946‑2220136
|
ACCAAAATATTACCCAATGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGC < SRR3722088.272880/100‑1 (MQ=60)
ACCAAAATATTACCCAATGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGC < SRR3722088.485668/100‑1 (MQ=60)
AAATATTACCCAATGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCC > SRR3722088.297710/1‑100 (MQ=60)
ATATTACCCAATGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCG > SRR3722088.319196/1‑100 (MQ=60)
AATGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCGACGGCTGCCCGGTGGTGTAA < SRR3722088.414391/100‑1 (MQ=60)
CCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTctgtctcttatacac > SRR3722088.438894/1‑85 (MQ=60)
CCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACA > SRR3722088.364919/1‑100 (MQ=60)
ACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGC < SRR3722088.599653/100‑1 (MQ=60)
ATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCAC > SRR3722088.196117/1‑100 (MQ=60)
ATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCAC > SRR3722088.407699/1‑100 (MQ=60)
ATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCAC > SRR3722088.563677/1‑100 (MQ=60)
TCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGT < SRR3722088.332069/100‑1 (MQ=60)
TCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGT < SRR3722088.478274/100‑1 (MQ=60)
AACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGTTGCGC > SRR3722088.342769/1‑100 (MQ=60)
ATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGTTGCGCCAAAACGCCGCAAGGGAATCG > SRR3722088.395865/1‑100 (MQ=60)
ATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGTTGCGCCAAAACGCCGCAAGGGAATCG > SRR3722088.591752/1‑100 (MQ=60)
|
ACCAAAATATTACCCAATGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGACTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGTTGCGCCAAAACGCCGCAAGGGAATCG > NZ_CP009273/2219946‑2220136
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
