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 I210 R1
|
226 |
19.6 |
1130256 |
95.4% |
1078264 |
84.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,174,665 |
T→G |
L206W (TTG→TGG) |
nagK → |
N‑acetylglucosamine kinase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,174,665 | 0 | T | G | 100.0%
| 42.3
/ NA
| 14 | L206W (TTG→TGG) | nagK | N‑acetylglucosamine kinase |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (8/6); total (8/6) |
GGTCAGCATGGCTGCATTGAAAATTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTTGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATC > NZ_CP009273/1174586‑1174736
|
ggTCAGCATGGCTGCATTGAAAATTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGCTccc > 2:287676/1‑90 (MQ=255)
gCATTGAAAATTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTgcgc < 1:54774/90‑1 (MQ=255)
gtctgGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGa < 2:239566/90‑1 (MQ=255)
ttGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAggg > 1:82682/1‑90 (MQ=255)
tGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGgc > 2:203476/1‑90 (MQ=255)
aaCACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGtt > 2:348868/1‑90 (MQ=255)
cacTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTAt > 1:418358/1‑90 (MQ=255)
acTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATc < 1:122633/90‑1 (MQ=255)
tattatCATCAACCGTGGCAGGCTCCCGAAATTATTgc < 1:469879/38‑1 (MQ=38)
tattatCATCAACCGTGGCAGGCTCCCGAAATTATTgc > 2:469879/1‑38 (MQ=255)
catcaACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATc < 1:73593/82‑1 (MQ=255)
catcaACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATc > 2:73593/1‑82 (MQ=255)
aCCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTg < 1:327233/68‑1 (MQ=255)
aCCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTg > 2:327233/1‑68 (MQ=255)
|
GGTCAGCATGGCTGCATTGAAAATTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTTGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATC > NZ_CP009273/1174586‑1174736
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CTGCATTGAAAATTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTTGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTGGATTTATTAGCGGTTTGTCTG > NZ_CP009273/1174597‑1174759
|
ctaagatggtcgtcggcagcgtcagatgtgtataagagacagGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGAT < SRR3722092.479202/58‑1 (MQ=60)
GCATTGAAAATTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCA < SRR3722092.55682/100‑1 (MQ=60)
GGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGG > SRR3722092.84095/1‑100 (MQ=60)
GCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTAT > SRR3722092.426449/1‑100 (MQ=60)
tataagagacagATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCT < SRR3722092.333041/88‑1 (MQ=60)
ACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTGGATTTATT < SRR3722092.124712/100‑1 (MQ=60)
ACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTGGATTTATT < SRR3722092.74837/100‑1 (MQ=60)
ATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTGGATTTATTAGCGGT > SRR3722092.256885/1‑100 (MQ=60)
ACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCtgtctcttatacacatctgacgctgccga > SRR3722092.444920/1‑71 (MQ=60)
|
CTGCATTGAAAATTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTTGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTGGATTTATTAGCGGTTTGTCTG > NZ_CP009273/1174597‑1174759
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
