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 F4 I88 R1
|
217 |
30.5 |
1742422 |
95.9% |
1670982 |
87.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
592,602 |
C→T |
Q6* (CAA→TAA) |
cusF → |
Cu(+)/Ag(+) efflux RND transporter periplasmic metallochaperone CusF |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 592,602 | 0 | C | T | 100.0%
| 75.8
/ NA
| 22 | Q6* (CAA→TAA) | cusF | Cu(+)/Ag(+) efflux RND transporter periplasmic metallochaperone CusF |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (9/13); total (9/13) |
GGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGCAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGCGAAGCAC > NZ_CP009273/592514‑592686
|
ggATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTaa < 1:861297/91‑1 (MQ=255)
cTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCaa < 2:721629/91‑1 (MQ=255)
cGCTTGTAACCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATg > 2:747756/1‑91 (MQ=255)
cTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTAc < 1:82579/91‑1 (MQ=255)
cTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTAc < 2:205759/91‑1 (MQ=255)
tGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTAcc < 1:733752/91‑1 (MQ=255)
tttAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTaa > 1:61923/1‑91 (MQ=255)
tttAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTaa < 1:837451/91‑1 (MQ=255)
tttAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTaa < 2:211199/91‑1 (MQ=255)
tttAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTaa < 2:488611/91‑1 (MQ=255)
gagTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGcc > 2:166651/1‑91 (MQ=255)
agTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGccc < 1:348398/91‑1 (MQ=255)
agTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGccc < 2:832273/91‑1 (MQ=255)
tGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGc < 1:443608/91‑1 (MQ=255)
tGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGc > 2:216709/1‑91 (MQ=255)
cAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTAc < 1:413809/54‑1 (MQ=255)
cAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTAc > 2:413809/1‑54 (MQ=255)
gagaATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGa > 2:169655/1‑91 (MQ=255)
gaATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATAATGaaa > 2:79662/1‑91 (MQ=255)
aaTGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATg > 2:151742/1‑91 (MQ=255)
aaaaaGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGCGa > 2:425572/1‑91 (MQ=255)
gCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGCGAAGcac < 1:740402/91‑1 (MQ=255)
|
GGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGCAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGCGAAGCAC > NZ_CP009273/592514‑592686
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 30 ≤ 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
CTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGCAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGCGAAGCACAACCACAGGTTATTAG > NZ_CP009273/592507‑592702
|
CTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTC < SRR3722118.309524/101‑1 (MQ=60)
TCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCG < SRR3722118.593272/101‑1 (MQ=60)
GGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGT < SRR3722118.880455/101‑1 (MQ=60)
gggctcggagatgtgtataagagacagCTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGC < SRR3722118.422515/74‑1 (MQ=60)
CTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGC < SRR3722118.84115/101‑1 (MQ=60)
TGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCT < SRR3722118.749874/101‑1 (MQ=60)
ACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAA > SRR3722118.63067/1‑101 (MQ=60)
TTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCT < SRR3722118.855932/101‑1 (MQ=60)
AGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGA < SRR3722118.355619/101‑1 (MQ=60)
TGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACAT < SRR3722118.452962/101‑1 (MQ=60)
GCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGCGAAGCACAACCACAGGT < SRR3722118.756685/101‑1 (MQ=60)
GCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGCGAAGCACAACCACAGGT > SRR3722118.863892/1‑101 (MQ=60)
CTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGActgtctcttatacacatctccgagcccacgagacggactcct > SRR3722118.663745/1‑59 (MQ=60)
TGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGCGAAGCACAACCACAGGTTATT < SRR3722118.50754/101‑1 (MQ=60)
TAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGCGAAGCACAACCACAGGTTATTAG < SRR3722118.306908/101‑1 (MQ=60)
|
CTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGCAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGCGAAGCACAACCACAGGTTATTAG > NZ_CP009273/592507‑592702
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
