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 I230 R1
|
226 |
18.8 |
1048726 |
96.7% |
1014118 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,113,649 |
T→G |
K330N (AAA→AAC) |
glcA ← |
glycolate permease GlcA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,113,649 | 0 | T | G | 100.0%
| 72.3
/ NA
| 23 | K330N (AAA→AAC) | glcA | glycolate permease GlcA |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (10/13); total (10/13) |
CCGCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCTTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGCCC > NZ_CP009273/3113564‑3113726
|
ccGCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTaa > 2:70703/1‑90 (MQ=255)
ccGCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTaa > 1:369062/1‑90 (MQ=255)
cacTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCAt < 2:361712/90‑1 (MQ=255)
cTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATgg > 1:477857/1‑90 (MQ=255)
cTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATgg > 2:300607/1‑90 (MQ=255)
gttgATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTcc < 2:477857/90‑1 (MQ=255)
ttgATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCa < 2:113502/90‑1 (MQ=255)
gCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATgg < 2:211279/90‑1 (MQ=255)
gggATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGAt < 2:489049/80‑1 (MQ=255)
gggATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGAt > 1:489049/1‑80 (MQ=255)
ggATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCa < 2:221959/90‑1 (MQ=255)
ggAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTa > 1:46818/1‑90 (MQ=255)
tAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTa > 2:102312/1‑90 (MQ=255)
tCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTaaaa < 1:237351/90‑1 (MQ=255)
cAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACgg < 2:42772/90‑1 (MQ=255)
gTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTg > 1:30092/1‑90 (MQ=255)
tGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCa > 2:170832/1‑54 (MQ=255)
tGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCa < 1:170832/54‑1 (MQ=255)
aaaCGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGc > 1:444917/1‑90 (MQ=255)
cgccgcCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGaa < 2:335772/90‑1 (MQ=255)
cgccgcCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGaa < 2:46818/90‑1 (MQ=255)
aGCAAATACCGCGTTAAACGGCTTCATGGTCCAGATGGTTACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGccc < 2:158631/90‑1 (MQ=255)
aGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGccc < 2:67474/90‑1 (MQ=255)
|
CCGCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCTTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGCCC > NZ_CP009273/3113564‑3113726
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ 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
ACAATGGGTGCCGCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCTTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGC > NZ_CP009273/3113554‑3113711
|
ACAATGGGTGCCGCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAA > SRR3722114.373462/1‑100 (MQ=60)
GCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGG > SRR3722114.483844/1‑100 (MQ=60)
ggctcggagatgtgtataagagacagTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACC < SRR3722114.172530/74‑1 (MQ=60)
ATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGC > SRR3722114.495169/1‑100 (MQ=60)
TGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTA > SRR3722114.47277/1‑100 (MQ=60)
TTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTG > SRR3722114.30383/1‑100 (MQ=60)
TCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCA < SRR3722114.239601/100‑1 (MQ=60)
CCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGC > SRR3722114.450429/1‑100 (MQ=60)
|
ACAATGGGTGCCGCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCTTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGC > NZ_CP009273/3113554‑3113711
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
