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 I211 R1
|
223 |
18.0 |
1007644 |
96.3% |
970361 |
85.7 |
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%
| 94.3
/ NA
| 29 | K330N (AAA→AAC) | glcA | glycolate permease GlcA |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (16/13); total (16/13) |
GCCGCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCTTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGCCCCAGAC > NZ_CP009273/3113563‑3113731
|
gCCGCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTa > 1:188350/1‑90 (MQ=255)
ccGCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTaa > 1:443516/1‑90 (MQ=255)
gCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAAc < 1:288794/90‑1 (MQ=255)
ttCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGc < 1:434340/90‑1 (MQ=255)
cacTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCAt < 2:443516/90‑1 (MQ=255)
cacTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCAt < 1:81942/90‑1 (MQ=255)
ttgATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCa < 1:1490/90‑1 (MQ=255)
aaaTGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTg > 2:477852/1‑90 (MQ=255)
cTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTc > 1:494208/1‑64 (MQ=255)
cTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTc < 2:494208/64‑1 (MQ=255)
cTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGt > 2:349024/1‑90 (MQ=255)
cTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGt > 1:172670/1‑90 (MQ=255)
ggAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTa > 2:398479/1‑90 (MQ=255)
aaTTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGa < 2:253203/90‑1 (MQ=255)
cACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTaaaaa > 1:24217/1‑90 (MQ=255)
gTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTg > 1:119157/1‑90 (MQ=255)
tAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCAc < 1:235070/90‑1 (MQ=255)
cgcgCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCa > 1:108828/1‑45 (MQ=255)
cgcgCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCa < 2:108828/45‑1 (MQ=255)
cgcgCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCg > 1:19721/1‑90 (MQ=255)
cgccgcCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGaa > 1:478491/1‑90 (MQ=255)
cgccgcCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGaa < 2:216869/90‑1 (MQ=255)
cgccgcCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGaa > 2:452456/1‑90 (MQ=255)
cgccgcCCGGAGCAAACAACGCGTTAAACGGCTTCAt > 1:239385/1‑37 (MQ=25)
cgccgcCCGGAGCAAACAACGCGTTAAACGGCTTCAt < 2:239385/37‑1 (MQ=25)
aGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGccc < 2:150954/90‑1 (MQ=255)
aaTAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGCCCCAGa > 2:412490/1‑90 (MQ=255)
aaTAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGCCCCAGa > 1:113211/1‑90 (MQ=255)
aTAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGCCCCAGAc < 2:488400/90‑1 (MQ=255)
|
GCCGCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCTTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGCCCCAGAC > NZ_CP009273/3113563‑3113731
|
| 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
GACAATGGGTGCCGCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCTTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGCCCCAGACTATATTCTGAAGGCA > NZ_CP009273/3113553‑3113746
|
GACAATGGGTGCCGCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTA > SRR3722094.190926/1‑100 (MQ=60)
ACAATGGGTGCCGCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAA > SRR3722094.451308/1‑100 (MQ=60)
AATGGGTGCCGCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAAC < SRR3722094.141230/100‑1 (MQ=60)
GCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGG < SRR3722094.293139/100‑1 (MQ=60)
TTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCC < SRR3722094.441914/100‑1 (MQ=60)
CACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATG < SRR3722094.83114/100‑1 (MQ=60)
TTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACC < SRR3722094.1510/100‑1 (MQ=60)
AATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGActgtctcttatacaca > SRR3722094.502924/1‑84 (MQ=60)
AATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGT > SRR3722094.175071/1‑100 (MQ=60)
GGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAA > SRR3722094.24577/1‑100 (MQ=60)
TTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTG > SRR3722094.120880/1‑100 (MQ=60)
GTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCctgtctcttatacacatctgacgctgccgacgacc > SRR3722094.110396/1‑65 (MQ=60)
GTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCG > SRR3722094.20007/1‑100 (MQ=60)
GAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAA > SRR3722094.486941/1‑100 (MQ=60)
GAATAAAACGCGCCGCCCGGAGCAAACAACGCGTTAAACGGCTTCATGGTCCAGATGctgtctcttatacacatctgacgctgccgacgaccatcttagt > SRR3722094.242789/1‑57 (MQ=60)
TAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGA < SRR3722094.238383/100‑1 (MQ=60)
GCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGCCCCAGA > SRR3722094.114846/1‑100 (MQ=60)
GCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGCCCCAGACTATATctgtctctta > SRR3722094.121887/1‑90 (MQ=60)
|
GACAATGGGTGCCGCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCTTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGCCCCAGACTATATTCTGAAGGCA > NZ_CP009273/3113553‑3113746
|
| 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: ‑ |
