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 I231 R1
|
218 |
12.8 |
703680 |
97.2% |
683976 |
86.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,771,044 |
A→G |
K96E (AAA→GAA) |
lldP → |
L‑lactate permease |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,771,044 | 0 | A | G | 100.0%
| 61.5
/ NA
| 19 | K96E (AAA→GAA) | lldP | L‑lactate permease |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (10/9); total (10/9) |
TGGTTTATGGTTTCTTCTACGGGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGAAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCAAATGC > NZ_CP009273/3770964‑3771113
|
tggtTTATGGTTTCTTCTACGGGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGc < 1:19491/90‑1 (MQ=255)
tggtTTATGGTTTCTTCTACGGGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGc < 2:49838/90‑1 (MQ=255)
tATGGTTTCTTCTACGGGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGttt < 2:200165/90‑1 (MQ=255)
ttcttcTACGGGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCCATTTAAcaaa > 1:141091/1‑88 (MQ=255)
ttcttcTACGGGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGAcatc > 1:104329/1‑90 (MQ=255)
tACGGGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGc < 1:164350/90‑1 (MQ=255)
tgtgGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTa < 1:221551/90‑1 (MQ=255)
aTCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGc > 2:64016/1‑58 (MQ=255)
aTCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGc < 1:64016/58‑1 (MQ=255)
aTCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCg > 2:130614/1‑90 (MQ=255)
gcgTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATa < 2:4775/90‑1 (MQ=255)
gTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAAc < 1:345144/90‑1 (MQ=255)
tCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTg > 2:42262/1‑90 (MQ=255)
ttattGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATa > 1:4282/1‑80 (MQ=255)
ttattGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATa < 2:4282/80‑1 (MQ=255)
gCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGt > 2:332850/1‑90 (MQ=255)
aGCGGTGATCGTCTATAAGATCTCGGTGGACGCCGGATAATTTAAAAAAAATCGCTCGGCTAATCTTTCGATAACCCCTGACCAGCGTCt > 1:172340/1‑90 (MQ=255)
ggTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCa > 2:146596/1‑90 (MQ=255)
tCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCAAATGc > 2:162952/1‑90 (MQ=255)
|
TGGTTTATGGTTTCTTCTACGGGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGAAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCAAATGC > NZ_CP009273/3770964‑3771113
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ 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
CTGGCCTCGGTGGTTTATGGTTTCTTCTACGGGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGAAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCAAATGCTGATCGTCGGTTTCTGTTTCGGCGC > NZ_CP009273/3770954‑3771138
|
CTGGCCTCGGTGGTTTATGGTTTCTTCTACGGGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGC < SRR3722116.347820/100‑1 (MQ=60)
gtcagatgtgtataagagacaGGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACAT < SRR3722116.64811/79‑1 (MQ=60)
TGGTTTATGGTTTCTTCTACGGGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACAT < SRR3722116.19752/100‑1 (MQ=60)
GGTTTATGGTTTCTTCTACGGGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCcatttaacaaa > SRR3722116.142729/1‑89 (MQ=60)
GGTTTATGGTTTCTTCTACGGGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATC > SRR3722116.105608/1‑100 (MQ=60)
TACGGGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTC < SRR3722116.166238/100‑1 (MQ=60)
TGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGAT < SRR3722116.224473/100‑1 (MQ=60)
GCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACC > SRR3722116.4339/1‑100 (MQ=60)
GTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAG < SRR3722116.350289/100‑1 (MQ=60)
TCATTATTGCAGCGGTGATCGTCTATAAGATCTCGGTGGACGCCGGATAATTTAAAAAAAATCGCTCGGCTAATCTTTCGATAACCCCTGACCAGCGTCT > SRR3722116.174403/1‑100 (MQ=20)
CGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCAAATGCTGATCGTCGGTTTCTGTTTCGGCGC > SRR3722116.153398/1‑100 (MQ=60)
|
CTGGCCTCGGTGGTTTATGGTTTCTTCTACGGGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGAAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCAAATGCTGATCGTCGGTTTCTGTTTCGGCGC > NZ_CP009273/3770954‑3771138
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
