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 |
771,797 |
A→G |
intergenic (+64/‑1) |
tolR → / → tolA |
colicin uptake protein TolR/cell envelope integrity protein TolA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 771,797 | 0 | A | G | 100.0%
| 103.6
/ NA
| 28 | intergenic (+64/‑1) | tolR/tolA | colicin uptake protein TolR/cell envelope integrity protein TolA |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (13/15); total (13/15) |
CGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGAGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGGCGC > NZ_CP009273/771720‑771882
|
cGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCaa > 2:600818/1‑91 (MQ=255)
aGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCg < 2:53771/91‑1 (MQ=255)
aaCATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGa < 2:568828/91‑1 (MQ=255)
aaCATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGa < 1:600818/91‑1 (MQ=255)
cATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACa < 1:388389/91‑1 (MQ=255)
tCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACAGAACAAAACGACAAg > 2:546156/1‑91 (MQ=255)
cTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGc > 1:22591/1‑91 (MQ=255)
cTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGc > 2:321616/1‑91 (MQ=255)
cTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGc > 1:404149/1‑91 (MQ=255)
cTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGc > 1:329350/1‑91 (MQ=255)
ttCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGc < 2:472084/91‑1 (MQ=255)
tgcttgAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGa < 1:356945/91‑1 (MQ=255)
tgcttgAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGa > 2:580176/1‑91 (MQ=255)
tgcttgAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGa < 2:490435/91‑1 (MQ=255)
agagagCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAattatt < 2:329350/91‑1 (MQ=255)
agCGGGTAACCGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTcag > 2:764587/1‑91 (MQ=255)
agCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTcag > 1:12889/1‑91 (MQ=255)
gCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTcagc < 2:462962/91‑1 (MQ=255)
gCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTcagc < 1:833187/91‑1 (MQ=255)
cGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTcagca < 1:303722/91‑1 (MQ=255)
gggTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTcagcag < 2:404149/91‑1 (MQ=255)
ggTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGt > 2:225971/1‑91 (MQ=255)
ggTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGt > 1:714880/1‑91 (MQ=255)
ggTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGt < 1:504768/91‑1 (MQ=255)
gAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTc > 2:69651/1‑91 (MQ=255)
ggAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTgc < 2:494328/91‑1 (MQ=255)
aCCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTgcggcg > 1:243634/1‑91 (MQ=255)
ccGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGgcgc < 1:321616/91‑1 (MQ=255)
|
CGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGAGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGGCGC > NZ_CP009273/771720‑771882
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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
GTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGAGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGGCGCTGATCTGGAG > NZ_CP009273/771698‑771892
|
GTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGG < SRR3722118.211871/101‑1 (MQ=60)
GTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGG < SRR3722118.439019/101‑1 (MQ=60)
TTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGC < SRR3722118.826014/101‑1 (MQ=60)
ATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGC > SRR3722118.23008/1‑101 (MQ=60)
ATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGC > SRR3722118.412624/1‑101 (MQ=60)
ATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGC > SRR3722118.336117/1‑101 (MQ=60)
AACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAG < SRR3722118.613630/101‑1 (MQ=60)
CATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCG < SRR3722118.396530/101‑1 (MQ=60)
TGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTC < SRR3722118.364373/101‑1 (MQ=60)
CTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAG > SRR3722118.13136/1‑101 (MQ=60)
AATGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGT > SRR3722118.730565/1‑101 (MQ=60)
GCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCAT < SRR3722118.851549/101‑1 (MQ=60)
CGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATG < SRR3722118.309963/101‑1 (MQ=60)
GGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTC < SRR3722118.515465/101‑1 (MQ=60)
GTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGGCG > SRR3722118.248572/1‑101 (MQ=60)
TTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTACTGCATGTCATCTTATTTGCGGCGCTG > SRR3722118.107888/1‑101 (MQ=60)
CCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGGCGCTGATCTGGAG < SRR3722118.328220/101‑1 (MQ=60)
|
GTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGAGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGGCGCTGATCTGGAG > NZ_CP009273/771698‑771892
|
| 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: ‑ |
