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 |
|
A2 F5 I184 R1
|
278 |
29.6 |
1166432 |
97.3% |
1134938 |
124.1 |
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%
| 122.9
/ NA
| 35 | 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 (16/19); total (16/19) |
AATAATTAAAGCACTGAACTTGTTACATAGTGCGGGTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGAGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGGCGCTGATCTGGAGTTCGTTCGATGAGAATATAGAAGCTTCAGCCGGA > NZ_CP009273/771661‑771926
|
aataatTAAAGCACTGAACTTGTTACATAGTGCGGGTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGgt > 1:55531/1‑139 (MQ=255)
aaaGCACTGAACTTGTTACATAGTGCGGGTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCaaa < 1:224730/138‑1 (MQ=255)
cACTGAACTTGTTACATAGTGCGGGTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCaa < 2:404931/139‑1 (MQ=255)
aaCTTGTTACATAGTGCGGGTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGaa > 1:400784/1‑139 (MQ=255)
gTTACATAGTGCGGGTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACaa < 2:400784/137‑1 (MQ=255)
aCATAGTGCGGGTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACg < 2:419542/138‑1 (MQ=255)
cATAGTGCGGGTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGAc < 2:532429/139‑1 (MQ=255)
tGCGGGTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCt > 2:361157/1‑139 (MQ=255)
aaaTCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCg > 2:181815/1‑139 (MQ=255)
ggttggttTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAat > 2:186192/1‑139 (MQ=255)
aaTGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTcag < 2:573467/138‑1 (MQ=255)
aaTGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTcag < 2:286325/138‑1 (MQ=255)
cAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCaa < 1:393666/89‑1 (MQ=255)
cAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCaa > 2:393666/1‑89 (MQ=255)
cAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATa > 1:202190/1‑121 (MQ=255)
cAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATa < 2:202190/121‑1 (MQ=255)
cAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGtgctg > 2:151066/1‑139 (MQ=255)
cAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGtgctg > 2:180469/1‑139 (MQ=255)
aGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGtgctgc < 2:99347/139‑1 (MQ=255)
tCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGt < 2:319415/137‑1 (MQ=255)
cTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTg > 1:365884/1‑139 (MQ=255)
tGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTgc > 2:429716/1‑139 (MQ=255)
gagagCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGGCGCTGATCTGGAgttcgt < 2:50069/139‑1 (MQ=255)
agCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGGCGCTGATCTGGAgttcgttc > 1:537588/1‑138 (MQ=255)
cGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATa > 1:79977/1‑79 (MQ=255)
cGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATa < 2:79977/79‑1 (MQ=255)
cGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGGCGCTGATCTGGAGTTCGTTCGAt < 1:361157/139‑1 (MQ=255)
cGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGGCGCTGATCTGGAGTTCGTTCGAt < 2:12840/139‑1 (MQ=255)
gAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTcag > 1:66739/1‑77 (MQ=255)
gAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTcag < 2:66739/77‑1 (MQ=255)
aaCAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTgcggcg > 2:253795/1‑105 (MQ=255)
aaCAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTgcggcg < 1:253795/105‑1 (MQ=255)
gAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGGCGCTGATCTGGAGTTCGTTCGATGAGAATATAGAAGCTTCAGCCGGa < 1:180469/139‑1 (MQ=255)
ccGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTgcgg < 1:472364/88‑1 (MQ=255)
ccGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTgcgg > 2:472364/1‑88 (MQ=255)
|
AATAATTAAAGCACTGAACTTGTTACATAGTGCGGGTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGAGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGGCGCTGATCTGGAGTTCGTTCGATGAGAATATAGAAGCTTCAGCCGGA > NZ_CP009273/771661‑771926
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CCTTACGATGAAATAATTAAAGCACTGAACTTGTTACATAGTGCGGGTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGAGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGGCGCTGATCTGGAGTTCGTTCGATGAGAATATAGAAGCTTCAGCCGGAGGCGGCGGTGGT > NZ_CP009273/771650‑771938
|
CCTTACGATGAAATAATTAAAGCACTGAACTTGTTACATAGTGCGGGTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTG > SRR3722139.56172/1‑151 (MQ=60)
TTAAAGCACTGAACTTGTTACATAGTGCGGGTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAAC > SRR3722139.405535/1‑151 (MQ=60)
TAAAGCACTGAACTTGTTACATAGTGCGGGTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAAC < SRR3722139.227482/150‑1 (MQ=60)
agtacggtctcgtgggctcggagatgtgtataagagacaGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAAC < SRR3722139.398350/112‑1 (MQ=60)
GTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCctgtctct > SRR3722139.204686/1‑143 (MQ=60)
TATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGC > SRR3722139.370278/1‑151 (MQ=60)
agtacggtctcgtgggctcggagatgtgtataagagacagGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGGCGCTGATCTGG < SRR3722139.477868/110‑1 (MQ=60)
cggagatgtgtataagagacaGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGGCGCTGATCTGGAG < SRR3722139.256995/128‑1 (MQ=60)
GCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGGCGCTGATCTGGAGTTCGTTCG > SRR3722139.543758/1‑150 (MQ=60)
TTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCctgtctcttatacacatctccgagcccacgagaccgtactagatctcgt > SRR3722139.80902/1‑101 (MQ=60)
gctcggagatgtgtataagagacaGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGGCGCTGATCTGGAGTTCGTTCGATGAGAATATAGC < SRR3722139.437860/127‑1 (MQ=60)
GCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGGCGCTGATCTGGAGTTCGTTCGATGAGAATATAGA < SRR3722139.365504/151‑1 (MQ=60)
GGGTAACAGGCGAACAGTTTTTGGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATctgtctcttatacacatctccgagcccacgagaccgtactagatctcgtatg > SRR3722139.67532/1‑99 (MQ=60)
GGAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGGCGCTGATCTGGAGTTCGTTCGATGAGAATATAGAAGCTTCAGCCGGAGGCGGCGGTGG < SRR3722139.182707/151‑1 (MQ=60)
GAAACCGAGGGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGGCGCTGATCTGGAGTTCGTTCGATGAGAATATAGAAGCTTCAGCCGGAGGCGGCGGTGGT > SRR3722139.538999/1‑151 (MQ=60)
|
CCTTACGATGAAATAATTAAAGCACTGAACTTGTTACATAGTGCGGGTGTGAAATCGGTTGGTTTAATGACGCAGCCTATCTAAACATCTGCGTTTCCCTTGCTTGAAAGAGAGCGGGTAACAGGCGAACAGTTTTTGGAAACCGAGAGTGTCAAAGGCAACCGAACAAAACGACAAGCTCAAGCGGGCGATAATTATTTCAGCAGTGCTGCATGTCATCTTATTTGCGGCGCTGATCTGGAGTTCGTTCGATGAGAATATAGAAGCTTCAGCCGGAGGCGGCGGTGGT > NZ_CP009273/771650‑771938
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
