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 I194 R1
|
197 |
32.2 |
1845014 |
95.2% |
1756453 |
85.4 |
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%
| 87.2
/ NA
| 25 | 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 (15/10); total (15/10) |
AATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAACTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCGC > NZ_CP009273/554347‑554512
|
aaTGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTAtgatga > 1:419663/1‑90 (MQ=255)
atgatgTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGAc < 1:553355/90‑1 (MQ=255)
aCCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGa < 2:919190/90‑1 (MQ=255)
aCCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGa < 1:289639/90‑1 (MQ=255)
aCCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGa > 1:512994/1‑90 (MQ=255)
aCCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGa > 1:199465/1‑90 (MQ=255)
aCCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGa > 2:358804/1‑90 (MQ=255)
cAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATg < 1:262332/90‑1 (MQ=255)
cAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATg < 2:728122/90‑1 (MQ=255)
ccaGCAATCATTTCTTTATATTCCTTATTTTTTCCGTCAGCAATCCACAATGCGTATTAGCTATAATGACTAAAATAAAGTTATTGATGc < 2:512994/88‑1 (MQ=255)
aaaGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGc > 2:785016/1‑90 (MQ=255)
aaaGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGc < 2:663609/90‑1 (MQ=255)
aaaGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGc < 1:785016/90‑1 (MQ=255)
aaGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCt < 1:582523/90‑1 (MQ=255)
tttCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTAtatt < 1:809193/90‑1 (MQ=255)
ttCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATc > 2:269929/1‑90 (MQ=255)
tATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTc > 1:859400/1‑90 (MQ=255)
caAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGa > 1:92197/1‑90 (MQ=255)
caAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGa > 1:549828/1‑90 (MQ=255)
aaGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAg > 1:314904/1‑90 (MQ=255)
aGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAgg > 1:817087/1‑90 (MQ=255)
aGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAgg > 1:206786/1‑90 (MQ=255)
tATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCg > 1:689869/1‑90 (MQ=255)
tATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCg > 2:850091/1‑90 (MQ=255)
aTTAGCTATGATGGCTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCGc > 1:890479/1‑90 (MQ=255)
|
AATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAACTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCGC > NZ_CP009273/554347‑554512
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 33 ≤ 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
TTATTAAATGAAAAGGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAACTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCGCATTAGGTGCCACG > NZ_CP009273/554330‑554525
|
TTATTAAATGAAAAGGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCT < SRR3722072.618550/100‑1 (MQ=60)
GATGAAAAGGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATG < SRR3722072.844643/100‑1 (MQ=60)
AATGAAAAGGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATG < SRR3722072.39715/100‑1 (MQ=60)
ATGAAAAGGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGA > SRR3722072.427267/1‑100 (MQ=60)
GGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGActgtctctta > SRR3722072.415668/1‑90 (MQ=60)
ATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAG < SRR3722072.563294/100‑1 (MQ=60)
GTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGA > SRR3722072.202908/1‑100 (MQ=60)
GTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGA > SRR3722072.522227/1‑100 (MQ=60)
ACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTAT < SRR3722072.294641/100‑1 (MQ=60)
CAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATAT < SRR3722072.266788/100‑1 (MQ=60)
AAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATT < SRR3722072.798768/100‑1 (MQ=60)
AAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTT < SRR3722072.592921/100‑1 (MQ=60)
TTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATC < SRR3722072.823297/100‑1 (MQ=60)
TTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTC > SRR3722072.874235/1‑100 (MQ=60)
CAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGA > SRR3722072.93893/1‑100 (MQ=60)
CAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGA > SRR3722072.559713/1‑100 (MQ=60)
GGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAG > SRR3722072.320403/1‑100 (MQ=60)
GGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGG > SRR3722072.831320/1‑100 (MQ=60)
GGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGG > SRR3722072.210323/1‑100 (MQ=60)
ACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCG > SRR3722072.702207/1‑100 (MQ=60)
CACAAGGCGTATTAGCTATGATGGCTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCGC > SRR3722072.905814/1‑100 (MQ=60)
TATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCGCATTAGGTGC > SRR3722072.228541/1‑100 (MQ=60)
AGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCGCATTAGGTGCCACG > SRR3722072.11602/1‑100 (MQ=60)
|
TTATTAAATGAAAAGGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAACTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCGCATTAGGTGCCACG > NZ_CP009273/554330‑554525
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑ |
