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 F5 I102 R1
|
278 |
39.1 |
2251254 |
95.8% |
2156701 |
87.1 |
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%
| 194.2
/ NA
| 51 | 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 (30/21); total (30/21) |
GGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGCAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGCGAAGCAC > NZ_CP009273/592514‑592686
|
ggAGTCAGTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTaa < 2:913445/91‑1 (MQ=255)
ttCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTc > 2:457872/1‑91 (MQ=255)
ttCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTc > 1:24441/1‑91 (MQ=255)
cACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGc > 2:928272/1‑91 (MQ=255)
ttGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTc > 1:33814/1‑91 (MQ=255)
gTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAg > 2:316392/1‑91 (MQ=255)
gTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAg > 2:751755/1‑91 (MQ=255)
cGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTc < 2:696368/91‑1 (MQ=255)
cTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGt > 2:74608/1‑91 (MQ=255)
tCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGttt > 1:749100/1‑91 (MQ=255)
tCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGttt > 2:687138/1‑91 (MQ=255)
tCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGttt > 1:902653/1‑91 (MQ=255)
gCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCg < 2:599081/91‑1 (MQ=255)
gAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTgg > 2:324567/1‑91 (MQ=255)
aaTTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGc < 1:316392/91‑1 (MQ=255)
aaTTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGc < 2:336904/91‑1 (MQ=255)
tttAGAGTATGACTTTTAACTCCTGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTaa < 1:189585/91‑1 (MQ=255)
tttAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTaa < 2:390912/91‑1 (MQ=255)
tttAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTaa < 1:751755/91‑1 (MQ=255)
gagTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGcc < 1:125064/91‑1 (MQ=255)
agTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTc < 2:633378/64‑1 (MQ=255)
agTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTc > 1:633378/1‑64 (MQ=255)
agTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGccc < 2:24441/91‑1 (MQ=255)
tGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTc < 2:710723/60‑1 (MQ=255)
tGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTc > 1:710723/1‑60 (MQ=255)
tGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGc > 1:912245/1‑91 (MQ=255)
tGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGc > 2:638668/1‑91 (MQ=255)
tGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGc > 2:587027/1‑91 (MQ=255)
tGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGc > 2:897370/1‑91 (MQ=255)
tttAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGc < 1:1097110/72‑1 (MQ=255)
tttAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGc > 2:1097110/1‑72 (MQ=255)
tttAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACg > 1:8439/1‑91 (MQ=255)
tttAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACg > 1:754395/1‑91 (MQ=255)
ttAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGa < 1:687138/91‑1 (MQ=255)
tAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTAtt > 1:800165/1‑67 (MQ=255)
tAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTAtt < 2:800165/67‑1 (MQ=255)
tAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGaa > 1:160184/1‑91 (MQ=255)
tCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAAcatc > 2:301503/1‑91 (MQ=255)
tCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAAcatc > 1:370389/1‑91 (MQ=255)
cAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAAcatcat < 2:315978/91‑1 (MQ=255)
cAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAAcatcat > 1:577880/1‑91 (MQ=255)
cAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAAcatcat > 2:791845/1‑91 (MQ=255)
gagaATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGa < 1:457872/91‑1 (MQ=255)
gagaATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGa < 1:1120778/91‑1 (MQ=255)
gaATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTATCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGaaa > 1:1119153/1‑91 (MQ=255)
aaTGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATg > 2:27722/1‑91 (MQ=255)
aaTGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATg > 1:874403/1‑91 (MQ=255)
gAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGc < 2:50813/91‑1 (MQ=255)
gAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGc < 2:370389/91‑1 (MQ=255)
aaaaaGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGCGa > 1:600000/1‑91 (MQ=255)
aaaaGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGCGaa < 2:387704/91‑1 (MQ=255)
gCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGCGAAGcac < 2:29076/91‑1 (MQ=255)
|
GGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGCAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGCGAAGCAC > NZ_CP009273/592514‑592686
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ 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 > SRR3722125.24869/1‑101 (MQ=60)
ATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTC > SRR3722125.34410/1‑101 (MQ=60)
CTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTT > SRR3722125.922657/1‑101 (MQ=60)
CTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTT > SRR3722125.765272/1‑101 (MQ=60)
aagagacagGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCC < SRR3722125.1121825/92‑1 (MQ=60)
AATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTctgtctcttatacacat > SRR3722125.647022/1‑84 (MQ=60)
AATTATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCC < SRR3722125.322894/101‑1 (MQ=60)
ATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTctgtctcttatacacatctcc > SRR3722125.726049/1‑80 (MQ=60)
ATTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGC > SRR3722125.932455/1‑101 (MQ=60)
TTTAGAGTATGACTTTTAACTCCTGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCT < SRR3722125.193290/101‑1 (MQ=60)
TTTAGAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCT < SRR3722125.767994/101‑1 (MQ=60)
GAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACG > SRR3722125.8595/1‑101 (MQ=60)
GAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACG < SRR3722125.127414/101‑1 (MQ=60)
GAGTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACG > SRR3722125.770701/1‑101 (MQ=60)
GTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCtgtctcttataca > SRR3722125.817636/1‑88 (MQ=60)
GTATGACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAA > SRR3722125.163251/1‑101 (MQ=60)
GACTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATC > SRR3722125.378149/1‑101 (MQ=60)
CTTTTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCAT > SRR3722125.590266/1‑101 (MQ=60)
TTAACTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCAT < SRR3722125.701958/101‑1 (MQ=60)
CTCCAGGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTATCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAA > SRR3722125.1144415/1‑101 (MQ=60)
GGAGAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATG > SRR3722125.893750/1‑101 (MQ=60)
tataagagacagAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGC < SRR3722125.711370/89‑1 (MQ=60)
GAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGC < SRR3722125.1146081/101‑1 (MQ=60)
GAGAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGC < SRR3722125.467541/101‑1 (MQ=60)
GAATAAATGAAAAAAGCACTGTAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGCGA > SRR3722125.612912/1‑101 (MQ=60)
TAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGCGAAGCACAACCACAGGTTATTAG < SRR3722125.652441/101‑1 (MQ=60)
TAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGCGAAGCACAACCACAGGTTATTAG < SRR3722125.494084/101‑1 (MQ=60)
TAAGTCGCAATGTTCAGTCTGTTTACCGTTATTGGCTTTAATGCCCAGGCTAACGAACATCATCATGAAACCATGAGCGAAGCACAACCACAGGTTATTAG < SRR3722125.1072467/101‑1 (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: ‑ |
