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 I197 R1
|
189 |
12.7 |
697584 |
97.1% |
677354 |
86.2 |
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%
| 50.9
/ NA
| 17 | F222S (TTC→TCC) | nanX | MFS transporter |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (6/11); total (6/11) |
TGGATTGAAGATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTTCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATA > NZ_CP009273/4494457‑4494622
|
tGGATTGAAGATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTc < 1:38445/90‑1 (MQ=255)
ggATTGAAGATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCt > 1:168534/1‑90 (MQ=255)
tGAAGATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGttt < 2:156497/90‑1 (MQ=255)
aGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTg > 1:229337/1‑90 (MQ=255)
aaaTCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATTGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAAc < 2:291504/90‑1 (MQ=255)
aaaTCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAAc > 1:98999/1‑90 (MQ=255)
tttttGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATa < 2:306177/90‑1 (MQ=255)
ctgtctTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGac < 2:229337/90‑1 (MQ=255)
tgtctTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGact < 2:214265/90‑1 (MQ=255)
gtctTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGacta > 1:311332/1‑90 (MQ=255)
aTCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTgg < 1:35571/90‑1 (MQ=255)
cTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCa < 2:28391/90‑1 (MQ=255)
tctcTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATg < 2:63931/90‑1 (MQ=255)
tctATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGa < 1:80472/90‑1 (MQ=255)
tCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATa > 1:193458/1‑90 (MQ=255)
gTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATg < 2:238097/79‑1 (MQ=255)
gTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATg > 1:238097/1‑79 (MQ=255)
|
TGGATTGAAGATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTTCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATA > NZ_CP009273/4494457‑4494622
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ 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
AGTCAGGAGTGGATTGAAGATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTTCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATACAG > NZ_CP009273/4494448‑4494625
|
AGTCAGGAGTGGATTGAAGATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCT > SRR3722076.170616/1‑100 (MQ=60)
TGGATTGAAGATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTC < SRR3722076.38899/100‑1 (MQ=60)
GATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTG > SRR3722076.232488/1‑100 (MQ=60)
ATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAAC > SRR3722076.100203/1‑100 (MQ=60)
GGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGctgtctcttatacacatctgacgctgccgacg > SRR3722076.115222/1‑68 (MQ=60)
ATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTA > SRR3722076.316043/1‑100 (MQ=60)
ATCTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGG < SRR3722076.35986/100‑1 (MQ=60)
CTTTCAATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCctgtctcttatacacatctgacgctgccgacgatggcggtcgtgtagatc > SRR3722076.48246/1‑50 (MQ=60)
ATCTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATA > SRR3722076.195938/1‑100 (MQ=60)
CTCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATACC > SRR3722076.241431/1‑100 (MQ=60)
TCTATGATCGTTTCCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATACAG < SRR3722076.81482/100‑1 (MQ=60)
|
AGTCAGGAGTGGATTGAAGATAAATATAAGGATAAATCAACATTTTTGTCTGTCTTCAGAAAACCACATCTTTCAATCTCTATGATCGTTTTCCTCGTCTGTTTTTGTCTATTTGGTGCAAACTGGCCGATAAACGGACTACTTCCTTCCTACCTGGCAGATAATGGAGTTAATACAG > NZ_CP009273/4494448‑4494625
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
