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 I206 R1
|
206 |
23.7 |
1314362 |
96.8% |
1272302 |
86.2 |
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%
| 38.0
/ NA
| 13 | 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 (5/8); total (5/8) |
GGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAACTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGC > NZ_CP009273/554344‑554497
|
gggAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTatga < 2:446836/90‑1 (MQ=255)
gAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTatgatg < 1:95216/90‑1 (MQ=255)
atgatgTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGAc < 2:617547/90‑1 (MQ=255)
tgttgtAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAAt > 1:228966/1‑90 (MQ=255)
gttgtAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATa < 1:552838/90‑1 (MQ=255)
gtAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAg > 1:37404/1‑90 (MQ=255)
aaaGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGc < 1:276107/90‑1 (MQ=255)
aTCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATta < 1:636148/90‑1 (MQ=255)
aTCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATta > 2:612766/1‑90 (MQ=255)
ttATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCAttt < 1:152077/90‑1 (MQ=255)
cAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCa > 1:198541/1‑90 (MQ=255)
cAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCa > 2:113845/1‑90 (MQ=255)
gAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCAtgc < 2:379425/90‑1 (MQ=255)
|
GGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAACTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGC > NZ_CP009273/554344‑554497
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ 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
CTTTATTAAATGAAAAGGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAACTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCGCATTAGG > NZ_CP009273/554328‑554518
|
CTTTATTAAATGAAAAGGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAG < SRR3722088.251809/100‑1 (MQ=60)
CTTTATTAAATGAAAAGGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAG < SRR3722088.442270/100‑1 (MQ=60)
TTATTAAATGAAAAGGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTCCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCT < SRR3722088.105339/100‑1 (MQ=60)
GGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAAT > SRR3722088.231247/1‑100 (MQ=60)
GAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAA < SRR3722088.96180/100‑1 (MQ=60)
ATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAG > SRR3722088.37798/1‑100 (MQ=60)
GTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGA < SRR3722088.559603/100‑1 (MQ=60)
AAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATT < SRR3722088.278769/100‑1 (MQ=60)
ATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTT < SRR3722088.644014/100‑1 (MQ=60)
TTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGC < SRR3722088.153620/100‑1 (MQ=60)
TTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCA > SRR3722088.200517/1‑100 (MQ=60)
GCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATctgtctcttatacacatctccgagcccacgagaccgtactagatctc > SRR3722088.258844/1‑53 (MQ=60)
|
CTTTATTAAATGAAAAGGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAACTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCGCATTAGG > NZ_CP009273/554328‑554518
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
