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 I200 R1
|
216 |
30.8 |
1683622 |
97.2% |
1636480 |
87.0 |
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 | 90.0%
| 55.9
/ ‑0.1
| 20 | L206W (TTG→TGG) | nagK | N‑acetylglucosamine kinase |
| Reads supporting (aligned to +/- strand): ref base T (1/1); new base G (9/9); total (10/10) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.57e-01 |
CTGTGGTCAGCATGGCTGCATTGAAAATTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTTGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTGGATTTATTAGCGGTT > NZ_CP009273/1174582‑1174753
|
cTGTGGTCAGCATGGCTGCATTGAAAATTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGc < 2:316833/90‑1 (MQ=255)
cAGCATGGCTGCATTGAAAATTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGaa > 1:205010/1‑90 (MQ=255)
cAGCATGGCTGCATTGAAAATTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGaa < 2:281241/90‑1 (MQ=255)
tGGCTGCATTGAAAATTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAattat < 1:113142/90‑1 (MQ=255)
aTTGAAAATTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTTGCAGGCTCCCGAAATTATTGCGCtt > 1:592225/1‑90 (MQ=255)
gCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGt < 1:733590/90‑1 (MQ=255)
cacTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTg < 1:350894/82‑1 (MQ=255)
cacTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTg > 2:350894/1‑82 (MQ=255)
acTATTATCATCAACCGTTGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATc < 2:54008/90‑1 (MQ=255)
tattatCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGa < 1:250258/56‑1 (MQ=255)
tattatCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGa > 2:250258/1‑56 (MQ=255)
tattatCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTg > 2:623188/1‑90 (MQ=255)
tatCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTGGAt < 1:242914/90‑1 (MQ=255)
catcaACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTGGATtta > 1:529482/1‑90 (MQ=255)
atcaACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCaa > 1:553740/1‑60 (MQ=255)
atcaACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCaa < 2:553740/60‑1 (MQ=255)
caACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGt > 1:453227/1‑75 (MQ=255)
caACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGt < 2:453227/75‑1 (MQ=255)
caACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTGGATttatta > 1:727536/1‑90 (MQ=255)
aCCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTGGATTTATTAGc > 1:20881/1‑90 (MQ=255)
ttGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTGGATTTATTAGCGGtt < 2:578672/90‑1 (MQ=255)
|
CTGTGGTCAGCATGGCTGCATTGAAAATTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTTGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTGGATTTATTAGCGGTT > NZ_CP009273/1174582‑1174753
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CCGCTGCGGCTGTGGTCAGCATGGCTGCATTGAAAATTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTTGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTGGATTTATTAGCGGTTTGTCTGGGAA > NZ_CP009273/1174573‑1174763
|
tcgtgggctcggagatgtgtataagagacagGAAAATTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGCT < SRR3722079.299610/69‑1 (MQ=60)
CGGCTGTGGTCAGCATGGCTGCATTGAAAATTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAA > SRR3722079.206779/1‑100 (MQ=60)
GCATGGCTGCATTGAAAATTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTTGCAGGCTCCCGAAATTATTGCGCTT > SRR3722079.598148/1‑100 (MQ=60)
TGGCTGCATTGAAAATTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTAT < SRR3722079.114065/100‑1 (MQ=60)
ctcggagatgtgtataagagacagGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCA < SRR3722079.252354/76‑1 (MQ=60)
tgggctcggagatgtgtataagagacagACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCG < SRR3722079.843841/72‑1 (MQ=60)
GCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTAT < SRR3722079.741437/100‑1 (MQ=60)
TGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCT < SRR3722079.353657/100‑1 (MQ=60)
ACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTGGATTTA > SRR3722079.534412/1‑100 (MQ=60)
CACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTctgtctcttatacacatctc > SRR3722079.559059/1‑80 (MQ=60)
CTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTGGATTctgtc > SRR3722079.457195/1‑95 (MQ=60)
CTATTATCACCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTGGATTTATTA > SRR3722079.735317/1‑100 (MQ=60)
ATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTGGATTTATTAGC > SRR3722079.21026/1‑100 (MQ=60)
TATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTGGATTTATTAGCGG < SRR3722079.244957/100‑1 (MQ=60)
ATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTGGATTTATTAGCGGT > SRR3722079.5587/1‑100 (MQ=60)
TGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTGGATTTATTAGCGGTTTGTCTGGGAA < SRR3722079.34171/100‑1 (MQ=60)
|
CCGCTGCGGCTGTGGTCAGCATGGCTGCATTGAAAATTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTTGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTGGATTTATTAGCGGTTTGTCTGGGAA > NZ_CP009273/1174573‑1174763
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
