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 I199 R1
|
220 |
57.5 |
3163680 |
97.0% |
3068769 |
86.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
991,969 |
T→G |
L144F (TTA→TTC) |
ssuA ← |
aliphatic sulfonate ABC transporter substrate‑binding protein SsuA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 991,969 | 0 | T | G | 100.0%
| 89.6
/ NA
| 28 | L144F (TTA→TTC) | ssuA | aliphatic sulfonate ABC transporter substrate‑binding protein SsuA |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (16/12); total (16/12) |
AACGCGGCGCGGGCATCAGCGGGCGTCAGGTAAGTGGGTTGGATATCGGTAAACTTAAGTCCGGCCTGACGCAGTGCACGCAGTAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATCGGCTACGGTTTTGATCGGGCTGTTTTCTGC > NZ_CP009273/991886‑992055
|
aaCGCGGCGCGGGCATCAGCGGGCGTCAGGTAAGTGGGTTGGATATCGGTAAACTTAAGTCCGGCCTGACGCAGTGCACGCAGGAAAAgg > 1:1121891/1‑90 (MQ=255)
gcgcggGCATCAGCGGGCGTCAGGTAAGTGGGTTGGATATCGGTAAACTTAAGTCCGGCCTGACGCAGTGCACGCAGGAAAAGGTtgtgt < 2:944608/90‑1 (MQ=255)
gcgcggGCATCAGCGGGCGTCAGGTAAGTGGGTTGGATATCGGTAAACTTAAGTCCGGCCTGACGCAGTGCACGCAGGAAAAGGTtgtgt < 1:730574/90‑1 (MQ=255)
gggCGTCAGGTAAGTGGGTTGGATATCGGTAAACTTAAGTCCGGCCTGACGCAGTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCttt > 2:877600/1‑90 (MQ=255)
aaGTGGGTTGGATATCGGTAAACTTAAGTCCGGCCTGACGCAGTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCaa < 2:682171/90‑1 (MQ=255)
gTGGGTTGGATATCGGTAAACTTAAGTCCGGCCTGACGCAGTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACt > 1:54736/1‑90 (MQ=255)
gTTGGATATCGGTAAACTTAAGTCCGGCCTGACGCAGTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTtgt > 1:588925/1‑90 (MQ=255)
ttGGATATCGGTAAACTTAAGTCCGGCCTGACGCAGTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTtgtg > 2:827925/1‑90 (MQ=255)
tGGATATCGGTAAACTTAAGTCCGGCCTGACGCAGTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGa < 1:1429396/90‑1 (MQ=255)
tCGGTAAACTTAAGTCCGGCCTGACGCAGTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTa > 2:474786/1‑90 (MQ=255)
ggTAAACTTAAGTCCGGCCTGACGCAGTGCACGCAGGAAAAGGTtgtgt > 1:1434428/1‑49 (MQ=255)
ggTAAACTTAAGTCCGGCCTGACGCAGTGCACGCAGGAAAAGGTtgtgt < 2:1434428/49‑1 (MQ=255)
aaaCTTAAGTCCGGCCTGACGCAGTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATc > 2:1187084/1‑90 (MQ=255)
aaaCTTAAGTCCGGCCTGACGCAGTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATc < 2:54736/90‑1 (MQ=255)
aaGTCCGGCCTGACGCAGTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATCGGCTAc < 2:251878/90‑1 (MQ=255)
aaGTCCGGCCTGACGCAGTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATCGGCTAc < 1:1104352/90‑1 (MQ=255)
ggCCTGACGCAGTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGAc < 2:325594/68‑1 (MQ=255)
ggCCTGACGCAGTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGAc > 1:325594/1‑68 (MQ=255)
ggCCTGACGCAGTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATCGGCTACGGtttt > 2:901283/1‑90 (MQ=255)
gCCTGACGCAGTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATCGGCTACGGTTTTg > 1:947508/1‑90 (MQ=255)
gCCTGACGCAGTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATCGGCTACGGTTTTg > 1:719600/1‑90 (MQ=255)
cTGACGCAGTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATCGGCTACGGTTTTGAt < 1:877600/90‑1 (MQ=255)
cAGTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATCGGCTACGGTTTTGATCGGGCt < 2:1121891/90‑1 (MQ=255)
gTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATCGGCTACGGTTTTGATCGGGCTGt > 2:273944/1‑90 (MQ=255)
gTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATCGGCTACGGTTTTGATCGGGCTGt > 2:41287/1‑90 (MQ=255)
gTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATCGGCTACGGTTTTGATCGGGCTGt > 2:920674/1‑90 (MQ=255)
cGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATCGGCTACGGTTTTGATCGGGCTGTTTTCt > 1:243866/1‑90 (MQ=255)
cAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATCGGCTGCGGTTTTGATCGGGCTGTTTTCTGc < 1:1252336/90‑1 (MQ=255)
|
AACGCGGCGCGGGCATCAGCGGGCGTCAGGTAAGTGGGTTGGATATCGGTAAACTTAAGTCCGGCCTGACGCAGTGCACGCAGTAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATCGGCTACGGTTTTGATCGGGCTGTTTTCTGC > NZ_CP009273/991886‑992055
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ 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
TACCTTGCTGGAACGCGGCGCGGGCATCAGCGGGCGTCAGGTAAGTGGGTTGGATATCGGTAAACTTAAGTCCGGCCTGACGCAGTGCACGCAGTAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATCGGCTACGGTTTTGATCGGGCTGTTTTCTGCCACCAGAATCAC > NZ_CP009273/991875‑992067
|
TACCTTGCTGGAACGCGGCGCGGGCATCAGCGGGCGTCAGGTAAGTGGGTTGGATATCGGTAAACTTAGGTCCGGCCTGACGCAGTGCACGCAGGAAAAG < SRR3722078.1382007/100‑1 (MQ=60)
ACCTTGCTGGAACGCGGCGCGGGCATCAGCGGGCGTCAGGTAAGTGGGTTGGATATCGGTAAACTTAAGTCCGGCCTGACGCAGTGCACGCAGGAAAAGG > SRR3722078.1139016/1‑100 (MQ=60)
CCTTGCTGGAACGCGGCGCGGGCATCAGCGGGCGTCAGGTAAGTGGGTTGGATATCGGTAAACTTAAGTCCGGCCTGACGCAGTGCACGCAGGAAAAGGT < SRR3722078.1410824/100‑1 (MQ=60)
CCTTGCTGGAACGCGGCGCGGGCATCAGCGGGCGTCAGGTAAGTGGGTTGGATATCGGTAAACTTAAGTCCGGCCTGACGCAGTGCACGCAGGAAAAGGT < SRR3722078.200112/100‑1 (MQ=60)
GCGCGGGCATCAGCGGGCGTCAGGTAAGTGGGTTGGATATCGGTAAACTTAAGTCCGGCCTGACGCAGTGCACGCAGGAAAAGGTTGTGTGAACTGGAAC < SRR3722078.739714/100‑1 (MQ=60)
CGTCAGGTAAGTGGGTTGGATATCGGTAAACTTAAGTCCGGCCTGACGCAGTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACT > SRR3722078.55389/1‑100 (MQ=60)
AGGTAAGTGGGTTGGATATCGGTAAACTTAAGTCCGGCCTGACGCAGTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGT > SRR3722078.595773/1‑100 (MQ=60)
GTTGGATATCGGTAAACTTAAGTCCGGCCTGACGCAGTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCTgtctcttatacacatctgacgctgccgac > SRR3722078.1457768/1‑71 (MQ=60)
TGGATATCGGTAAACTTAAGTCCGGCCTGACGCAGTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGAT < SRR3722078.1452634/100‑1 (MQ=60)
ACTTAAGTCCGGCCTGACGCAGTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATCctgtctcttata > SRR3722078.329588/1‑88 (MQ=60)
CTTAAGTCCGGCCTGACGCAGTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATCGGCTACGGTTTTG > SRR3722078.960770/1‑100 (MQ=60)
CTTAAGTCCGGCCTGACGCAGTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATCGGCTACGGTTTTG > SRR3722078.728502/1‑100 (MQ=60)
AAGTCCGGCCTGACGCAGTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATCGGCTACGGTTTTGATC < SRR3722078.1121186/100‑1 (MQ=60)
CTGACGCAGTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATCGGCTACGGTTTTGATCGGGCTGTTT < SRR3722078.889389/100‑1 (MQ=60)
ACGCAGTGCACGCAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATCGGCTACGGTTTTGATCGGGCTGTTTTCT > SRR3722078.246851/1‑100 (MQ=60)
CAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATCGGCTGCGGTTTTGATCGGGCTGTTTTCTGCCACCAGAATC < SRR3722078.1272161/100‑1 (MQ=60)
CAGGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATCGGCTACGGTTTTGATCGGGCTGTTTTCTGCCACCAGAATC > SRR3722078.968142/1‑100 (MQ=60)
GGAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATCGGCTACGGTTTTGATCGGGCTGTTTTCTGCCACCAGAATCAC > SRR3722078.1380267/1‑100 (MQ=60)
|
TACCTTGCTGGAACGCGGCGCGGGCATCAGCGGGCGTCAGGTAAGTGGGTTGGATATCGGTAAACTTAAGTCCGGCCTGACGCAGTGCACGCAGTAAAAGGTTGTGTGAACTGGAACCTTTCTGAAAGGCAACTTTGTGACCTTTAAGATCGGCTACGGTTTTGATCGGGCTGTTTTCTGCCACCAGAATCAC > NZ_CP009273/991875‑992067
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
