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 I208 R1
|
222 |
13.1 |
731276 |
96.6% |
706412 |
85.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,494,539 |
T→C |
F222S (TTC→TCC) |
nanX → |
MFS transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,494,539 | 0 | T | C | 100.0%
| 108.0
/ NA
| 30 | F222S (TTC→TCC) | nanX | MFS transporter |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (16/14); total (16/14) |
GGAGTGGATTGAAGATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTTCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATACA > NZ_CP009273/4494453‑4494624
|
ggAGTGGATTGAAGATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCt < 1:146166/90‑1 (MQ=255)
ggATTGAAGATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCt > 1:364572/1‑90 (MQ=255)
gAAGATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGtttt > 1:82741/1‑90 (MQ=255)
tAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCt > 1:175606/1‑90 (MQ=255)
atatAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTAtt < 1:211533/90‑1 (MQ=255)
aaaTCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAAc > 2:262336/1‑90 (MQ=255)
aaaTCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAAc > 1:337505/1‑90 (MQ=255)
aaTCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACt > 2:3981/1‑90 (MQ=255)
aCATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCg > 2:97970/1‑90 (MQ=255)
aCATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCg > 1:223850/1‑90 (MQ=255)
cATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGa < 2:211745/90‑1 (MQ=255)
tttttGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATa < 2:82741/90‑1 (MQ=255)
gtctgtctTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACgg < 2:184069/90‑1 (MQ=255)
ctgtctTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGac > 1:332487/1‑90 (MQ=255)
aaaCCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACttccttcc < 2:228770/90‑1 (MQ=255)
aaCCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTtccttcct > 1:35976/1‑90 (MQ=255)
aaCCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTtccttcct > 1:230461/1‑90 (MQ=255)
cacaTCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTAcc < 1:250767/90‑1 (MQ=255)
acaTCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCt > 1:146199/1‑90 (MQ=255)
aTCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTgg < 1:262336/90‑1 (MQ=255)
tctcTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATg < 1:132362/90‑1 (MQ=255)
tctcTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATg < 2:364572/90‑1 (MQ=255)
tctcTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATg < 2:337505/90‑1 (MQ=255)
tctcTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATg < 2:223850/90‑1 (MQ=255)
tctATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGa < 2:111206/90‑1 (MQ=255)
ctATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAg > 2:322790/1‑90 (MQ=255)
ctATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAg > 2:360940/1‑90 (MQ=255)
gATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTaa < 2:100347/90‑1 (MQ=255)
gTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATACa > 2:217247/1‑90 (MQ=255)
gTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATACa > 1:346310/1‑90 (MQ=255)
|
GGAGTGGATTGAAGATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTTCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATACA > NZ_CP009273/4494453‑4494624
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 32 ≤ 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
GAAAGTCAGGAGTGGATTGAAGATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTTCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATACAGT > NZ_CP009273/4494445‑4494626
|
GAAAGTCAGGAGTGGATTGAAGATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTTCCTCG < SRR3722090.226649/100‑1 (MQ=60)
AGTCAGGAGTGGATTGAAGATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCT > SRR3722090.369334/1‑100 (MQ=60)
GGAGTGGATTGAAGATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTT < SRR3722090.147676/100‑1 (MQ=60)
GGAGTGGATTGAAGATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTT > SRR3722090.83653/1‑100 (MQ=60)
GGATTGAAGATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCT > SRR3722090.177462/1‑100 (MQ=60)
cacatctttcaatctctatgatcgtttccctcgtctgtttttgtctatttCCAACCAATTCCTTTTTTCCAAAATTCCTTCCTTAATTGGAATTCCGGTTTTTTCCCCCCTTCCGGTTCCTTGGTTTTTTTTTTGGTTCCTTAATTTTTT < SRR3722090.270933/0‑1 (MQ=60)
ATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAAC < SRR3722090.213893/100‑1 (MQ=60)
ATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAAC > SRR3722090.341904/1‑100 (MQ=60)
GGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCG > SRR3722090.226398/1‑100 (MQ=60)
ACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGAC > SRR3722090.336816/1‑100 (MQ=60)
GTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCT > SRR3722090.233126/1‑100 (MQ=60)
GTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCT > SRR3722090.36348/1‑100 (MQ=60)
TCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCT > SRR3722090.147709/1‑100 (MQ=60)
CACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAA < SRR3722090.253806/100‑1 (MQ=60)
ATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGG < SRR3722090.265562/100‑1 (MQ=60)
TCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATAC < SRR3722090.133762/100‑1 (MQ=60)
CTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATACA > SRR3722090.350814/1‑100 (MQ=60)
CTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGtctcttatacacatctccgagcc > SRR3722090.258405/1‑77 (MQ=60)
CTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATACAGT > SRR3722090.356351/1‑100 (MQ=60)
|
GAAAGTCAGGAGTGGATTGAAGATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTTCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATACAGT > NZ_CP009273/4494445‑4494626
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
