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 I229 R1
|
214 |
17.4 |
943020 |
97.5% |
919444 |
87.1 |
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%
| 48.5
/ NA
| 17 | F257C (TTT→TGT) | emrD | multidrug efflux MFS transporter EmrD |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (10/7); total (10/7) |
CTGCTCCGGCGTGCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTTTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATCTGCTGCCTGCTGGCTGG > NZ_CP009273/3847965‑3848135
|
cTGCTCCGGCGTGCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGtgttt > 1:107032/1‑90 (MQ=255)
gCTCCGGCGTGCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTg > 1:248741/1‑90 (MQ=255)
ccGGCGTGCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGgcg > 2:145605/1‑90 (MQ=255)
cGTGCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATCCCGGCAGCGTGTTTTGGCGCATg < 2:420111/90‑1 (MQ=255)
tGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCg > 1:467315/1‑90 (MQ=255)
tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCTTACGTCCCAATAAACGCt > 2:28613/1‑90 (MQ=255)
tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt > 1:189129/1‑90 (MQ=255)
tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt > 2:329715/1‑90 (MQ=255)
tGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCt > 2:234015/1‑90 (MQ=255)
gTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCa > 1:115841/1‑90 (MQ=255)
gTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAAtg < 2:467315/90‑1 (MQ=255)
cAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAAtgtg > 2:195310/1‑90 (MQ=255)
gTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGc > 2:16126/1‑90 (MQ=255)
tATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCa < 1:145605/90‑1 (MQ=255)
aTTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAg < 1:112881/90‑1 (MQ=255)
tttGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTc < 2:189129/90‑1 (MQ=255)
ggCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATCTGCTGCCTgctggc < 1:368693/90‑1 (MQ=255)
aGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATCTGCTGCCTGctggctgg < 2:357875/90‑1 (MQ=255)
|
CTGCTCCGGCGTGCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTTTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATCTGCTGCCTGCTGGCTGG > NZ_CP009273/3847965‑3848135
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ 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
CCTTTGAAGCCTGCTCCGGCGTGCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTTTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATCTGCTGCCTGCTGGCTGGCTTGCTG > NZ_CP009273/3847955‑3848142
|
CCTTTGAAGCCTGCTCCGGCGTGCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTT > SRR3722113.107980/1‑100 (MQ=60)
TTTGAAGCCTGCTCCGGCGTGCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTG > SRR3722113.250892/1‑100 (MQ=60)
GGCGTGCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCG > SRR3722113.472266/1‑100 (MQ=60)
GTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCT > SRR3722113.190610/1‑100 (MQ=60)
GGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCA > SRR3722113.116844/1‑100 (MQ=60)
TATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATC < SRR3722113.146807/100‑1 (MQ=60)
ATTTTGTTTATTCTGCCGATTCCGGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATCT < SRR3722113.113867/100‑1 (MQ=60)
GGCAGCGTGTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATCTGCTGCCTGCTGGCTGGCTTGCTG < SRR3722113.372517/100‑1 (MQ=60)
|
CCTTTGAAGCCTGCTCCGGCGTGCTGATGGGCGCGGTGTTAGGGCTGAGCAGTATGACGGTCAGTATTTTGTTTATTCTGCCGATTCCGGCAGCGTTTTTTGGCGCATGGTTTGCCGGACGTCCCAATAAACGCTTCTCCACGTTAATGTGGCAGTCGGTTATCTGCTGCCTGCTGGCTGGCTTGCTG > NZ_CP009273/3847955‑3848142
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑ |
