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 I207 R1
|
218 |
45.0 |
2482936 |
97.1% |
2410930 |
86.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,848,051 |
T→G |
F257C (TTT→TGT) |
emrD → |
multidrug efflux MFS transporter EmrD |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,848,051 | 0 | T | G | 100.0%
| 115.8
/ NA
| 35 | F257C (TTT→TGT) | emrD | multidrug efflux MFS transporter EmrD |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (31/4); total (31/4) |
CTGCTCCGGCGTGCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTTTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTAT > NZ_CP009273/3847965‑3848117
|
cTGCTCCGGCGTGCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGtgttt > 2:316236/1‑90 (MQ=255)
cTGCTCCGGCGTGCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGtgttt > 2:1137107/1‑90 (MQ=255)
cTGCTCCGGCGTGCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGtgttt > 1:636871/1‑90 (MQ=255)
gATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGc > 1:1097597/1‑90 (MQ=255)
gcgcGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGAc > 2:457737/1‑90 (MQ=255)
tAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATa > 2:919247/1‑90 (MQ=255)
tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCAt > 2:918487/1‑63 (MQ=255)
tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCAt < 1:918487/63‑1 (MQ=255)
tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt > 1:1030424/1‑90 (MQ=255)
tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt > 2:678665/1‑90 (MQ=255)
tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt > 2:492865/1‑90 (MQ=255)
tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt > 2:164986/1‑90 (MQ=255)
tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt > 2:1149835/1‑90 (MQ=255)
tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt > 1:934328/1‑90 (MQ=255)
tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt > 1:833821/1‑90 (MQ=255)
tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt > 1:347061/1‑90 (MQ=255)
tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt > 1:768503/1‑90 (MQ=255)
tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt > 1:711429/1‑90 (MQ=255)
tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt > 1:303401/1‑90 (MQ=255)
tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt > 1:407030/1‑90 (MQ=255)
tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt > 1:54693/1‑90 (MQ=255)
tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt > 1:488970/1‑90 (MQ=255)
tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACCCt > 1:837561/1‑90 (MQ=255)
cAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGTGCATGGTTTGCCGGACGTCCCAATAAACGCTtctc < 1:869218/90‑1 (MQ=255)
gTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCa > 1:797673/1‑90 (MQ=255)
aCGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTc < 1:32679/67‑1 (MQ=255)
aCGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTc > 2:32679/1‑67 (MQ=255)
ggTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAAt > 1:91373/1‑90 (MQ=255)
cAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAAtgtg > 1:822717/1‑90 (MQ=255)
cAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAAtgtg > 2:867183/1‑90 (MQ=255)
cAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAAtgtg > 2:461913/1‑90 (MQ=255)
cAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAAtgtg > 1:211681/1‑90 (MQ=255)
cAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAAtgtg > 1:253805/1‑90 (MQ=255)
cAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAAtgtg > 1:772819/1‑90 (MQ=255)
cAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAAtgtg > 1:826589/1‑90 (MQ=255)
ttATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTa < 2:833821/90‑1 (MQ=255)
tATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTAt > 1:1135258/1‑90 (MQ=255)
tATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTAt > 2:117380/1‑90 (MQ=255)
|
CTGCTCCGGCGTGCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTTTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTAT > NZ_CP009273/3847965‑3848117
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ 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
CCTTTGAAGCCTGCTCCGGCGTGCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTTTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATCTGCTGCCTGCTGGCTGGCTTGCTGATGTGG > NZ_CP009273/3847955‑3848148
|
CCTTTGAAGCCTGCTCCGGCGTGCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTT > SRR3722089.644988/1‑100 (MQ=60)
CCGGCGTGCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGC > SRR3722089.1114171/1‑100 (MQ=60)
atgtgtataagagacaGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGG < SRR3722089.931882/84‑1 (MQ=60)
gtataagagacagGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACG < SRR3722089.33073/87‑1 (MQ=60)
GTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCT > SRR3722089.720689/1‑100 (MQ=60)
GTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCT > SRR3722089.948001/1‑100 (MQ=60)
GTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCT > SRR3722089.845604/1‑100 (MQ=60)
GTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCT > SRR3722089.778858/1‑100 (MQ=60)
GTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCT > SRR3722089.1045819/1‑100 (MQ=60)
GTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCT > SRR3722089.55370/1‑100 (MQ=60)
GTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCT > SRR3722089.411958/1‑100 (MQ=60)
GTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCT > SRR3722089.351375/1‑100 (MQ=60)
GTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCT > SRR3722089.494770/1‑100 (MQ=60)
GTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCT > SRR3722089.307255/1‑100 (MQ=60)
GTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACCCT > SRR3722089.849417/1‑100 (MQ=60)
GGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCA > SRR3722089.808689/1‑100 (MQ=60)
GCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAAT > SRR3722089.92503/1‑100 (MQ=60)
CAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGTGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATG < SRR3722089.881682/100‑1 (MQ=60)
GTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTG > SRR3722089.783278/1‑100 (MQ=60)
GTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTG > SRR3722089.834299/1‑100 (MQ=60)
GTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTG > SRR3722089.838245/1‑100 (MQ=60)
GTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTG > SRR3722089.257059/1‑100 (MQ=60)
GTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTG > SRR3722089.214351/1‑100 (MQ=60)
GTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTAT > SRR3722089.1152526/1‑100 (MQ=60)
GTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATCTGCTGCCTGCTGGCTGGCTTGCTGATGTGG > SRR3722089.774695/1‑100 (MQ=60)
GTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATCTGCTGCCTGCTGGCTGGCTTGCTGATGTGG > SRR3722089.263833/1‑100 (MQ=60)
GTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATCTGCTGCCTGCTGGCTGGCTTGCTGATGTGC > SRR3722089.592637/1‑100 (MQ=60)
|
CCTTTGAAGCCTGCTCCGGCGTGCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTTTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATCTGCTGCCTGCTGGCTGGCTTGCTGATGTGG > NZ_CP009273/3847955‑3848148
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑ |
