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 I200 R1
|
216 |
30.8 |
1683622 |
97.2% |
1636480 |
87.0 |
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 | 84.2%
| 37.2
/ 2.3
| 19 | intergenic (+217/‑3) | fimA/fimC | type 1 fimbrial major subunit FimA/type 1 fimbria chaperone FimC |
| Reads supporting (aligned to +/- strand): ref base A (2/1); new base G (7/9); total (9/10) |
| Fisher's exact test for biased strand distribution p-value = 5.82e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.91e-01 |
GGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAACTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCGCATTA > NZ_CP009273/554344‑554516
|
gggAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTatga < 2:621375/90‑1 (MQ=255)
atgatgTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGAc < 2:193635/90‑1 (MQ=255)
gttgtAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATa < 2:123822/90‑1 (MQ=255)
gttgtAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAACTATGATGACTAAAATa > 1:168960/1‑90 (MQ=255)
ttgtAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATaa > 2:381125/1‑90 (MQ=255)
aaGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGtt > 1:467763/1‑90 (MQ=255)
aaaCCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTAtt > 2:319570/1‑90 (MQ=255)
cAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATg < 2:301459/90‑1 (MQ=255)
aaaGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGc < 1:617142/90‑1 (MQ=255)
aaGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCt < 1:410976/90‑1 (MQ=255)
ttATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCAttt > 2:221458/1‑90 (MQ=255)
tATTTTTGCCGTCAGGAATACACAAGGCGTATTAACTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTc > 1:147328/1‑90 (MQ=255)
tttGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGcc > 2:141158/1‑90 (MQ=255)
gTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGcc > 1:296371/1‑90 (MQ=255)
aGGAATACACAAGGCGTATTAACTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCAt < 2:360097/90‑1 (MQ=255)
gAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCAtgc < 1:80715/90‑1 (MQ=255)
gAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCAtgc < 2:507020/90‑1 (MQ=255)
cacaAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCg > 1:320459/1‑90 (MQ=255)
gCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGa < 2:320459/90‑1 (MQ=255)
aCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCGCATTa < 2:168960/90‑1 (MQ=255)
|
GGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAACTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCGCATTA > NZ_CP009273/554344‑554516
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CTTTATTAAATGAAAAGGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAACTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCGCATTAGGTGCCAC > NZ_CP009273/554328‑554524
|
CTTTATTAAATGAAAAGGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAA < SRR3722079.502967/100‑1 (MQ=60)
TTTATTAAATGAAAAGGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGC < SRR3722079.511127/100‑1 (MQ=60)
TTATTAAATGAAAAGGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCT < SRR3722079.175616/100‑1 (MQ=60)
TTATTAAATGAAAAGGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCT < SRR3722079.225597/100‑1 (MQ=60)
TTATTAAATGAAAAGGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCT < SRR3722079.336365/100‑1 (MQ=60)
AAATGAAAAGGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGAT < SRR3722079.491373/100‑1 (MQ=60)
GGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAACTATGATGACTAAAATA > SRR3722079.170432/1‑100 (MQ=60)
GATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTT > SRR3722079.471856/1‑100 (MQ=60)
AAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATT < SRR3722079.623412/100‑1 (MQ=60)
AAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTT < SRR3722079.414491/100‑1 (MQ=60)
TTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAACTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTC > SRR3722079.148599/1‑100 (MQ=60)
TATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCC > SRR3722079.298803/1‑100 (MQ=60)
GTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCG > SRR3722079.323033/1‑100 (MQ=60)
GAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGG < SRR3722079.81371/100‑1 (MQ=60)
TAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCGCATTAGGTGCCAC > SRR3722079.546656/1‑100 (MQ=60)
|
CTTTATTAAATGAAAAGGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAACTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCGCATTAGGTGCCAC > NZ_CP009273/554328‑554524
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
