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 I207 R1
|
218 |
45.0 |
2482936 |
97.1% |
2410930 |
86.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,336,062 |
A→G |
intergenic (+78/‑116) |
lapB → / → pyrF |
lipopolysaccharide assembly protein LapB/orotidine‑5'‑phosphate decarboxylase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,336,062 | 0 | A | G | 100.0%
| 98.5
/ NA
| 29 | intergenic (+78/‑116) | lapB/pyrF | lipopolysaccharide assembly protein LapB/orotidine‑5'‑phosphate decarboxylase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (15/14); total (15/14) |
GGCCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCGCGCC > NZ_CP009273/1335976‑1336144
|
ggCCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGgaaa < 1:495400/90‑1 (MQ=255)
cTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGc < 2:499291/90‑1 (MQ=255)
tGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGcc > 1:105597/1‑90 (MQ=255)
aaaaaaaTCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGgag < 2:241215/90‑1 (MQ=255)
aaaaaaaTCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGgag < 1:572357/90‑1 (MQ=255)
aaaaaaaGCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGgag < 1:764976/90‑1 (MQ=255)
tACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGgag > 1:517798/1‑64 (MQ=255)
tACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGgag < 2:517798/64‑1 (MQ=255)
tACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTAttt > 1:899292/1‑90 (MQ=255)
aCTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAAt > 2:723562/1‑80 (MQ=255)
aCTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAAt < 1:723562/80‑1 (MQ=255)
aaTTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCAc < 1:597226/90‑1 (MQ=255)
aaTTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCAc < 2:901539/90‑1 (MQ=255)
aaTTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCAc > 1:1060797/1‑90 (MQ=255)
tattaATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACggg > 1:382726/1‑90 (MQ=255)
ttaATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTa > 1:669368/1‑90 (MQ=255)
ttaATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTa > 1:445818/1‑90 (MQ=255)
gTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATg > 1:777214/1‑90 (MQ=255)
tCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACg < 2:498981/79‑1 (MQ=255)
tCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACg > 1:498981/1‑79 (MQ=255)
ccATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTc < 1:606539/90‑1 (MQ=255)
aTTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGc > 2:666236/1‑90 (MQ=255)
ccGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGt > 1:979775/1‑85 (MQ=255)
ccGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGt < 2:979775/85‑1 (MQ=255)
ccGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTAcc > 2:876569/1‑90 (MQ=255)
aaCGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACg > 2:1180189/1‑63 (MQ=255)
aaCGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACg < 1:1180189/63‑1 (MQ=255)
ggCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCGCGcc < 2:1163398/90‑1 (MQ=255)
gcgcAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCAc > 1:605347/1‑55 (MQ=255)
gcgcAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCAc < 2:605347/55‑1 (MQ=255)
|
GGCCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCGCGCC > NZ_CP009273/1335976‑1336144
|
| 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
CTTGATGGCCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCGCGCCA > NZ_CP009273/1335970‑1336145
|
CTTGATGGCCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCC > SRR3722089.106898/1‑100 (MQ=60)
GGCCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAG < SRR3722089.501271/100‑1 (MQ=60)
AAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAAC < SRR3722089.579138/100‑1 (MQ=60)
AAAAAAAGCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAAC < SRR3722089.775250/100‑1 (MQ=60)
AGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACctgtctcttatacaca > SRR3722089.523881/1‑84 (MQ=60)
AGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTT > SRR3722089.912335/1‑100 (MQ=60)
GTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTC < SRR3722089.732979/100‑1 (MQ=60)
ACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCAC > SRR3722089.1076715/1‑100 (MQ=60)
ACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGG > SRR3722089.387390/1‑100 (MQ=60)
ATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTA > SRR3722089.451165/1‑100 (MQ=60)
ATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTA > SRR3722089.678028/1‑100 (MQ=60)
AATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATG < SRR3722089.604536/100‑1 (MQ=60)
AATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATG > SRR3722089.787774/1‑100 (MQ=60)
atgtgtataagagacagGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGC < SRR3722089.1198169/83‑1 (MQ=60)
TTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCC > SRR3722089.504888/1‑100 (MQ=60)
CCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACC < SRR3722089.614061/100‑1 (MQ=60)
CCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACC > SRR3722089.994273/1‑100 (MQ=60)
GGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTgtctcttatacacatctgacgct > SRR3722089.612836/1‑77 (MQ=60)
|
CTTGATGGCCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGTTTCGCGCCA > NZ_CP009273/1335970‑1336145
|
| 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: ‑ |
