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 I195 R1
|
222 |
27.1 |
1551108 |
96.0% |
1489063 |
86.0 |
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%
| 49.8
/ NA
| 16 | S236P (TCG→CCG) | yohF | SDR family oxidoreductase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (10/6); total (10/6) |
ACCCAATGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGACTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGTTGCGCCAAAACGCCGCA > NZ_CP009273/2219957‑2220127
|
aCCCAATGAAAGATCCACGCACCTCACTGCGCTATTCTGGGGTGTACTGTGGATGCGCCAAGATAAAGCCGCCATCCACTATCAACGGCt > 1:149500/1‑90 (MQ=255)
tGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCgg < 1:302473/90‑1 (MQ=255)
tGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCgg < 1:64816/90‑1 (MQ=255)
cGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAAttt > 2:166020/1‑90 (MQ=255)
aCCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTgcg > 2:676283/1‑90 (MQ=255)
ccTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTgcgc > 1:642029/1‑90 (MQ=255)
gcTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAAc < 1:740500/90‑1 (MQ=255)
gggTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCcac > 2:39124/1‑90 (MQ=255)
gAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCAcaccac > 1:235916/1‑90 (MQ=255)
gAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCAcaccac > 2:164699/1‑90 (MQ=255)
aCTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACAccacca > 2:558690/1‑90 (MQ=255)
tgGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCt > 1:645021/1‑90 (MQ=255)
tCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCaa < 2:645021/90‑1 (MQ=255)
cGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACaaa < 1:766985/68‑1 (MQ=255)
cGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACaaa > 2:766985/1‑68 (MQ=255)
tCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGTTGCGCCAAAACGCCGCa < 1:166020/90‑1 (MQ=255)
|
ACCCAATGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGACTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGTTGCGCCAAAACGCCGCA > NZ_CP009273/2219957‑2220127
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 29 ≤ 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
GACCAAAATATTACCCAATGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGACTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGTTGCGCCAAAACGCCGCAAGGGAATCGAAGGC > NZ_CP009273/2219945‑2220141
|
GACCAAAATATTACCCAATGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGG > SRR3722073.274711/1‑100 (MQ=60)
CCAAAATATTACCCAATGAAAGATCCACGCACCTCACTGCGCTATTCTGGGGTGTACTGTGGATGCGCCAAGATAAAGCCGCCATCCACTATCAACGGCT > SRR3722073.152564/1‑100 (MQ=60)
gagacagtacccgcgctccacaatgcggTATTCTGGGTTTATCTGGGGCTTCGCCAACAAAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAA < SRR3722073.193024/72‑1 (MQ=48)
TGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATT < SRR3722073.308865/100‑1 (MQ=60)
TGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATT < SRR3722073.66332/100‑1 (MQ=60)
TATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGC > SRR3722073.655276/1‑100 (MQ=60)
GCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACAC < SRR3722073.755505/100‑1 (MQ=60)
tataagagacagACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCAC < SRR3722073.782467/88‑1 (MQ=60)
ATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCAC > SRR3722073.240850/1‑100 (MQ=60)
GGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCT > SRR3722073.658312/1‑100 (MQ=60)
ATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGTTGCGCCAAAACGCCGCAAGGGAATCG > SRR3722073.298334/1‑100 (MQ=60)
ATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGTTGCGCCAAAACGCCGCAAGGGAATCG > SRR3722073.413928/1‑100 (MQ=60)
TCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGTTGCGCCAAAACGCCGCAAGGGAATCGA < SRR3722073.169313/100‑1 (MQ=60)
CGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGTTGCGCCAAAACGCCGCAAGGGAATCGAAGGC < SRR3722073.570353/100‑1 (MQ=60)
|
GACCAAAATATTACCCAATGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGACTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGTTGCGCCAAAACGCCGCAAGGGAATCGAAGGC > NZ_CP009273/2219945‑2220141
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
