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 |
3,656,518 |
T→C |
D915D (GAT→GAC) |
mdtF → |
multidrug efflux pump RND permease MdtF |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,656,518 | 0 | T | C | 100.0%
| 64.4
/ NA
| 22 | D915D (GAT→GAC) | mdtF | multidrug efflux pump RND permease MdtF |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (17/5); total (17/5) |
CGCACTCTATGAGAGCTGGTCAATTCCGTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGATCTGCGCGGCTTAAGTAATGACGTCTACTTCCAGGTTGGTTTGCTGACCACCATCGGGCTTTCCGCCAAAAACGCCATCCT > NZ_CP009273/3656434‑3656598
|
cgcACTCTATGAGAGCTGGTCAATTCCGTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTgcg < 2:315161/90‑1 (MQ=255)
gccggTCAATTCCGTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCt > 2:450633/4‑81 (MQ=255)
gccggTCAATTCCGTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCt < 1:450633/78‑1 (MQ=255)
gCTGGTCAATTCCGTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATg > 1:25472/1‑90 (MQ=255)
gCTGGTCAATTCCGTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATg > 1:78408/1‑90 (MQ=255)
tGGTCAATTCCGTTCTCGGTGGTGTTGGTTGTTCCGTTAGGCGTCGTAGGCGCATTACTGGCCCCCGACCTGCGCGGCTTAAGAAGTGAc > 2:421853/1‑90 (MQ=255)
tGGTCAATTCCGTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATGAc > 1:301140/1‑90 (MQ=255)
tGGTCAATTCCGTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATGAc > 2:316719/1‑90 (MQ=255)
ggTCAATTCCGTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATGAc < 1:256863/89‑1 (MQ=255)
ggTCAATTCCGTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATGAc > 2:256863/1‑89 (MQ=255)
cAATTCCGTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATGACGTCt < 2:78408/90‑1 (MQ=255)
gTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATGACGTCTACTTCCa > 2:120673/1‑90 (MQ=255)
gTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATGACGTCTACTTCCa > 2:113910/1‑90 (MQ=255)
ctcGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATGACGTCTACTTCCAggt < 2:60805/90‑1 (MQ=255)
cGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATGACGTCTACTTCCAggttg > 2:123949/1‑90 (MQ=255)
cGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATGACGTCTACTTCCAggttg > 1:349693/1‑90 (MQ=255)
cGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATGACGTCTACTTCCAggttg > 2:318518/1‑90 (MQ=255)
cGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATGACGTCTACTTCCAggttg > 1:253933/1‑90 (MQ=255)
gTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATGACGTCTACTTCCAGGTTGGTTTGCTGACCACCATCgg > 1:270842/1‑90 (MQ=255)
gtcgtTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATGACGTCTACTTCCAGGTTGGTTTGCTGACCACCATCGGGCTTTcc > 2:173591/1‑90 (MQ=255)
tGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATGACGTCTACTTCCAGGTTGGTTTGCTGACCACCATCGGGCTTTCCGCCaa > 1:336628/1‑90 (MQ=255)
ggCCACCGACCTGCGCGGCTTAAGTAATGACGTCTACTTCCAGGTTGGTTTGCTGACCACCATCGGGCTTTCCGCCAAAAACGCCATCCt > 2:162562/1‑90 (MQ=255)
|
CGCACTCTATGAGAGCTGGTCAATTCCGTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGATCTGCGCGGCTTAAGTAATGACGTCTACTTCCAGGTTGGTTTGCTGACCACCATCGGGCTTTCCGCCAAAAACGCCATCCT > NZ_CP009273/3656434‑3656598
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ 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
CTCTATGAGAGCTGGTCAATTCCGTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGATCTGCGCGGCTTAAGTAATGACGTCTACTTCCAGGTTGGTTTGCTGACCACCATCGGGCTTTCCGCCAA > NZ_CP009273/3656438‑3656586
|
CTCTATGAGAGCTGGTCAATTCCGTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATG > SRR3722113.25687/1‑100 (MQ=60)
CTCTATGAGAGCTGGTCAATTCCGTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATG > SRR3722113.79094/1‑100 (MQ=60)
TCTATGAGAGCCGGTCAATTCCGTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATGA < SRR3722113.455399/100‑1 (MQ=60)
CTATGAGAGCTGGTCAATTCCGTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATGAC > SRR3722113.304006/1‑100 (MQ=60)
TGGTCAATTCCGTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATGACGTCTACTTCC < SRR3722113.259114/100‑1 (MQ=60)
ATTCCGTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATGACGTCTACTTCCAGGTTG > SRR3722113.256145/1‑100 (MQ=60)
ATTCCGTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATGACGTCTACTTCCAGGTTG > SRR3722113.353252/1‑100 (MQ=60)
TGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATGACGTCTACTTCCAGGTTGGTTTGCTGACCACCATCGG > SRR3722113.273232/1‑100 (MQ=60)
TAGGCGTCGTTGGCGCATTACTGGCCACCGACCTGCGCGGCTTAAGTAATGACGTCTACTTCCAGGTTGGTTTGCTGACCACCATCGGGCTTTCCGCCAA > SRR3722113.340045/1‑100 (MQ=60)
|
CTCTATGAGAGCTGGTCAATTCCGTTCTCGGTGATGTTGGTTGTTCCGTTAGGCGTCGTTGGCGCATTACTGGCCACCGATCTGCGCGGCTTAAGTAATGACGTCTACTTCCAGGTTGGTTTGCTGACCACCATCGGGCTTTCCGCCAA > NZ_CP009273/3656438‑3656586
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
