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 F4 I88 R1
|
217 |
30.5 |
1742422 |
95.9% |
1670982 |
87.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
928,200 |
T→C |
R50R (CGT→CGC) |
lrp → |
leucine‑responsive transcriptional regulator Lrp |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 928,200 | 0 | T | C | 100.0%
| 140.1
/ NA
| 38 | R50R (CGT→CGC) | lrp | leucine‑responsive transcriptional regulator Lrp |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (15/23); total (15/23) |
GTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGTCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTG > NZ_CP009273/928116‑928285
|
gTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTg > 1:243117/1‑91 (MQ=255)
gTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTg < 2:243747/91‑1 (MQ=255)
ggATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACaa < 1:848748/91‑1 (MQ=255)
ggCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGtt < 2:291819/91‑1 (MQ=255)
ggCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGtt < 1:798320/91‑1 (MQ=255)
tATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTAtt > 1:265111/1‑91 (MQ=255)
aTTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTc < 2:476779/91‑1 (MQ=255)
aTTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTc < 2:46943/91‑1 (MQ=255)
aTTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTc > 1:493991/1‑91 (MQ=255)
ttCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAg < 1:853433/91‑1 (MQ=255)
ttCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAg < 1:355705/91‑1 (MQ=255)
ttCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAg < 2:265111/91‑1 (MQ=255)
ttCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAg < 2:103404/91‑1 (MQ=255)
aaCGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACaa > 1:378520/1‑75 (MQ=255)
aaCGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACaa < 2:378520/75‑1 (MQ=255)
cGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACaa > 1:858383/1‑70 (MQ=255)
cGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACaa < 2:858383/70‑1 (MQ=255)
gAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACgg > 1:164695/1‑91 (MQ=255)
aGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGgc < 2:705404/91‑1 (MQ=255)
cTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGgcgc < 2:836116/91‑1 (MQ=255)
cTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTACACGgcgc < 1:809274/91‑1 (MQ=255)
aCGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAAc < 1:281850/91‑1 (MQ=255)
aCGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAAc < 2:338332/91‑1 (MQ=255)
gtgGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAAccccc > 1:769262/1‑91 (MQ=255)
gtgGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAAccccc > 2:737011/1‑91 (MQ=255)
gtgGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAAccccc > 1:367050/1‑91 (MQ=255)
gggACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCAt < 1:144353/91‑1 (MQ=255)
tttCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCt > 1:765289/1‑91 (MQ=255)
cGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATc < 2:295734/91‑1 (MQ=255)
cGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATc < 1:433831/91‑1 (MQ=255)
cGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATc < 2:790517/91‑1 (MQ=255)
gTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACtt > 2:210336/1‑91 (MQ=255)
gTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACtt > 2:193902/1‑91 (MQ=255)
gtgtGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGgcgc > 1:202413/1‑48 (MQ=255)
gtgtGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGgcgc < 2:202413/48‑1 (MQ=255)
gtgCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATc < 2:290098/74‑1 (MQ=255)
gtgCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATc > 1:290098/1‑74 (MQ=255)
gtgCGCCGCCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTg > 2:860180/1‑91 (MQ=255)
|
GTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGTCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTG > NZ_CP009273/928116‑928285
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 31 ≤ 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
GTAACATTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGTCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTGAGATTACTCTGAAT > NZ_CP009273/928100‑928299
|
GTAACATTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGC > SRR3722118.698247/1‑101 (MQ=60)
TTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTG > SRR3722118.248047/1‑101 (MQ=60)
AGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATT > SRR3722118.270510/1‑101 (MQ=60)
GGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTC < SRR3722118.867548/101‑1 (MQ=60)
GGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTC > SRR3722118.504470/1‑101 (MQ=60)
GGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGC < SRR3722118.815860/101‑1 (MQ=60)
GCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCctgtct > SRR3722118.386430/1‑95 (MQ=60)
TTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCctgcctcttag > SRR3722118.877439/1‑90 (MQ=60)
TTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGG > SRR3722118.167915/1‑101 (MQ=60)
TTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGG < SRR3722118.872370/101‑1 (MQ=60)
TTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGG < SRR3722118.363100/101‑1 (MQ=60)
CGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAActgtctcttatacacatctccgagcccacgaga > SRR3722118.260354/1‑68 (MQ=60)
CTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTACACGGCGCTGCTTAACCC < SRR3722118.827062/101‑1 (MQ=60)
TTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCC > SRR3722118.374694/1‑101 (MQ=60)
TTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCC > SRR3722118.786162/1‑101 (MQ=60)
ACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATC < SRR3722118.287647/101‑1 (MQ=60)
CGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCT > SRR3722118.782093/1‑101 (MQ=60)
GGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATG < SRR3722118.147118/101‑1 (MQ=60)
CGCCGTGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTA < SRR3722118.442985/101‑1 (MQ=60)
TGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTctgtctcttatacacatctccgagcccacgagacggactcctatatcgtatgccgtcttctgct > SRR3722118.517314/1‑37 (MQ=60)
TGCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCtgtctcttatacacatctccgagcccacgaga > SRR3722118.206452/1‑69 (MQ=60)
GCCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACctgtctcttatacacatctccgagcccacgagacggactcctatctcgt > SRR3722118.544313/1‑52 (MQ=60)
CCTTGAGCGTGTGCGCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTActgtctc > SRR3722118.296045/1‑94 (MQ=60)
GCCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTGAGATTACTCTGAAT < SRR3722118.381721/101‑1 (MQ=60)
|
GTAACATTCTTAATGAGTTGCAAAAGGATGGGCGTATTTCTAACGTCGAGCTTTCTAAACGTGTGGGACTTTCCCCAACGCCGTGCCTTGAGCGTGTGCGTCGGCTGGAAAGACAAGGGTTTATTCAGGGCTATACGGCGCTGCTTAACCCCCATTATCTGGATGCATCACTTCTGGTATTCGTTGAGATTACTCTGAAT > NZ_CP009273/928100‑928299
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
