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 I207 R1
|
218 |
45.0 |
2482936 |
97.1% |
2410930 |
86.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
554,427 |
A→G |
intergenic (+217/‑3) |
fimA → / → fimC |
type 1 fimbrial major subunit FimA/type 1 fimbria chaperone FimC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 554,427 | 0 | A | G | 100.0%
| 104.8
/ NA
| 31 | intergenic (+217/‑3) | fimA/fimC | type 1 fimbrial major subunit FimA/type 1 fimbria chaperone FimC |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (15/16); total (15/16) |
AAGGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAACTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCG > NZ_CP009273/554342‑554511
|
aaGGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTat > 1:646044/1‑90 (MQ=255)
ggAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTatgat > 2:759356/1‑90 (MQ=255)
gAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTatgatg < 1:1037983/90‑1 (MQ=255)
gAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTatgatg > 2:26477/1‑90 (MQ=255)
atgatgTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGAc < 2:793992/90‑1 (MQ=255)
atgatgTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGAc < 2:543976/90‑1 (MQ=255)
atgatgTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGAc < 2:196880/90‑1 (MQ=255)
tgttgtAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAAt > 1:114114/1‑90 (MQ=255)
tgttgtAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAAt > 2:534312/1‑90 (MQ=255)
tgtAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATaaa < 2:895606/90‑1 (MQ=255)
gtAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAg > 1:414113/1‑90 (MQ=255)
aaaCCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTAtt < 1:710502/90‑1 (MQ=255)
aCCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGa > 1:55608/1‑90 (MQ=255)
cAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATg < 2:981259/90‑1 (MQ=255)
cAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATg < 1:206530/90‑1 (MQ=255)
aaaGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGc < 2:185853/90‑1 (MQ=255)
aaaGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGc > 1:1044086/1‑90 (MQ=255)
aaaGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGc < 2:592889/90‑1 (MQ=255)
cAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCAt < 2:945655/90‑1 (MQ=255)
aTCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATta > 2:220656/1‑90 (MQ=255)
tatTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTaa > 1:1019772/1‑90 (MQ=255)
ttCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATc > 1:1033651/1‑90 (MQ=255)
ttATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCAttt > 1:72568/1‑90 (MQ=255)
aGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCAt < 2:490464/90‑1 (MQ=255)
aGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCAt < 2:753016/90‑1 (MQ=255)
aGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCAt < 1:813680/90‑1 (MQ=255)
aGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGc < 1:202812/41‑1 (MQ=255)
aGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGc > 2:202812/1‑41 (MQ=255)
gCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGa < 2:861356/90‑1 (MQ=255)
cGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGAt > 1:385351/1‑90 (MQ=255)
tATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCg > 2:941312/1‑90 (MQ=255)
|
AAGGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAACTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCG > NZ_CP009273/554342‑554511
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TTTATTAAATGAAAAGGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAACTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCGCATTAGGTG > NZ_CP009273/554329‑554520
|
TTTATTAAATGAAAAGGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGC < SRR3722089.818031/100‑1 (MQ=60)
TATTAAATGAAAAGGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTA < SRR3722089.222519/100‑1 (MQ=60)
ATTAAATGAAAAGGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTAT > SRR3722089.654311/1‑100 (MQ=60)
AAATGAAAAGGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGAT < SRR3722089.185184/100‑1 (MQ=60)
GGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAAT > SRR3722089.115514/1‑100 (MQ=60)
GAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAA < SRR3722089.1053524/100‑1 (MQ=60)
ATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAG > SRR3722089.419123/1‑100 (MQ=60)
GTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGA > SRR3722089.56295/1‑100 (MQ=60)
GTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGC > SRR3722089.1059724/1‑100 (MQ=60)
AAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATT < SRR3722089.719753/100‑1 (MQ=60)
CAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATAT < SRR3722089.209132/100‑1 (MQ=60)
agatggtcgtcggcagcgtcagatgtgtataagagacagGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATT < SRR3722089.205371/61‑1 (MQ=60)
CATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAA > SRR3722089.1034968/1‑100 (MQ=60)
TTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATC > SRR3722089.1049105/1‑100 (MQ=60)
TTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTT > SRR3722089.73448/1‑100 (MQ=60)
AGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAG < SRR3722089.825063/100‑1 (MQ=60)
ATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGAT > SRR3722089.390047/1‑100 (MQ=60)
GGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCGCATTAG > SRR3722089.535847/1‑100 (MQ=60)
GTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATActgtctcttatacacatctgacgctgccgacgaccatcttagtgtagatctcggt > SRR3722089.149475/1‑45 (MQ=60)
GTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCGCATTAGGTG > SRR3722089.276049/1‑100 (MQ=60)
GTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCGCATTAGGTG > SRR3722089.1006560/1‑100 (MQ=60)
|
TTTATTAAATGAAAAGGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAACTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCGCATTAGGTG > NZ_CP009273/554329‑554520
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
