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 F3 I96 R1
|
172 |
34.7 |
2005794 |
96.2% |
1929573 |
85.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,632,437 |
(T)7→6 |
intergenic (‑71/+8) |
BW25113_RS08135 ← / ← BW25113_RS25620 |
hypothetical protein/hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,632,431 | 0 | T | . | 100.0%
| 139.2
/ NA
| 33 | intergenic (‑65/+14) | BW25113_RS08135/BW25113_RS25620 | hypothetical protein/hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base . (13/20); total (13/20) |
ATTTGGATATTCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGAATAGACACCAAGCAAAAAAGCTCCCGAAGGAGCCTTCATTTTCA > NZ_CP009273/1632349‑1632515
|
aTTTGGATATTCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGAttttttca < 2:504823/90‑3 (MQ=255)
ggATATTCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCatgat < 2:422684/90‑1 (MQ=255)
ggATATTCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCatgat < 1:699890/90‑1 (MQ=255)
atTCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTa > 2:901406/1‑90 (MQ=255)
tCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTAcc < 2:964365/90‑1 (MQ=255)
tCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTAcc < 2:355755/90‑1 (MQ=255)
aCGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCgt < 1:671878/90‑1 (MQ=255)
aCGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCgt < 2:435514/90‑1 (MQ=255)
aCGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCgt < 1:253414/90‑1 (MQ=255)
atgatgGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCgtagta < 2:525796/90‑1 (MQ=255)
tAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTATc < 2:540237/90‑1 (MQ=255)
tAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTATc < 1:882627/90‑1 (MQ=255)
aaCTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCatgat > 1:770399/1‑67 (MQ=255)
aaCTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCatgat < 2:770399/67‑1 (MQ=255)
aCTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTATCCa < 2:676056/90‑1 (MQ=255)
tCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATc < 1:649223/90‑1 (MQ=255)
tCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATc < 1:777058/90‑1 (MQ=255)
cAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTAcc > 1:192332/1‑68 (MQ=255)
cAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTAcc < 2:192332/68‑1 (MQ=255)
cAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGa > 2:264473/1‑90 (MQ=255)
cAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGa > 1:926816/1‑90 (MQ=255)
gTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGAAt > 2:414127/1‑90 (MQ=255)
tACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCgt > 2:23003/1‑54 (MQ=255)
tACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCgt < 1:23003/54‑1 (MQ=255)
tACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGAATAGACACCAAGCaaa > 1:121867/1‑90 (MQ=255)
ctgctgGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCgt > 2:404868/1‑49 (MQ=39)
ctgctgGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCgt < 1:404868/49‑1 (MQ=39)
ctgctgGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGAATAGACACCAAGCAAAAAAGc < 1:982058/90‑1 (MQ=255)
gctgGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGAATAGACACCAAGCAAAAAAGCTc > 2:720625/1‑90 (MQ=255)
ctgGTTCAGAGTTAAAAAAACTAAGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGAATAGACACCAAGCAAAAAAGCTcc < 2:655303/90‑1 (MQ=255)
tgGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGAATAGACACCAAGCAAAAAAGCTccc > 1:817217/1‑90 (MQ=255)
aaCTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTATc > 2:671985/1‑42 (MQ=38)
aaCTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTATc < 1:671985/42‑1 (MQ=38)
cTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGAATAGACACCAAGCAAAAAAGCTCCCGAAGGAGCCTTCATTTTCa > 1:927964/1‑90 (MQ=255)
|
ATTTGGATATTCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGAATAGACACCAAGCAAAAAAGCTCCCGAAGGAGCCTTCATTTTCA > NZ_CP009273/1632349‑1632515
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TTGGATATTCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGAATAGACACCAAGCAAAAAAGCTCCCGAAGGAGCCTTCATTTTCA > NZ_CP009273/1632351‑1632515
|
agatgtgtataagagacagGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGT < SRR3722236.610049/81‑1 (MQ=60)
GGATATTCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAG < SRR3722236.711704/100‑1 (MQ=60)
gtcggcagcgtcagatgtgtataagagacagGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAG < SRR3722236.410535/69‑1 (MQ=60)
cagcgtcagatgtgtataagagacagTCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAG < SRR3722236.23345/74‑1 (MQ=60)
ACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAG < SRR3722236.257156/100‑1 (MQ=60)
ACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAG < SRR3722236.683066/100‑1 (MQ=60)
TGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGctgtctcttatac > SRR3722236.783650/1‑87 (MQ=60)
GTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGctgtctcttata > SRR3722236.195183/1‑88 (MQ=60)
GTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGA > SRR3722236.943184/1‑100 (MQ=60)
agccttcgtcggcagcgtcagatgtgtataagagacagGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGAATAG < SRR3722236.683174/62‑1 (MQ=60)
TAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGAATAG < SRR3722236.898148/100‑1 (MQ=60)
TCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGAATAGACAC < SRR3722236.790450/100‑1 (MQ=60)
TCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGAATAGACAC < SRR3722236.659938/100‑1 (MQ=60)
TCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGAATAGACACCAAGCAAA > SRR3722236.123580/1‑100 (MQ=60)
CTACCACTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGAATAGACACCAAGCAAAAAAGCTCCC > SRR3722236.831458/1‑100 (MQ=60)
CTGCTGGTTCAGAGTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGAATAGACACCAAGCAAAAAAGCTCCCGAAGGA < SRR3722236.999364/100‑1 (MQ=60)
GTTAAAAAAACTATGA‑TTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGAATAGACACCAAGCAAAAAAGCTCCCGAAGGAGCCTTCATTTTCA > SRR3722236.944353/1‑100 (MQ=60)
|
TTGGATATTCACGCATGATGGTGTTAACTCCAGTCATCGCTGGCACTACCACTGCTGGTTCAGAGTTAAAAAAACTATGATTTTTTTCATGATGTTACCGTAGTATGTGAGTATCCATCGAATAGACACCAAGCAAAAAAGCTCCCGAAGGAGCCTTCATTTTCA > NZ_CP009273/1632351‑1632515
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
