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 |
1,673,542 |
A→G |
K287E (AAG→GAG) |
ydgH → |
DUF1471 family protein YdgH |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,673,542 | 0 | A | G | 96.8%
| 82.9
/ NA
| 31 | K287E (AAG→GAG) | ydgH | DUF1471 family protein YdgH |
| Reads supporting (aligned to +/- strand): ref base A (0/1); new base G (6/24); total (6/25) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
ATGGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGAT > NZ_CP009273/1673458‑1673616
|
atgGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGaaa < 1:1071814/90‑1 (MQ=255)
atgGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGaaa < 2:1512221/90‑1 (MQ=255)
atgGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGaaa < 2:1045479/90‑1 (MQ=255)
atgGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGaaa < 1:585036/90‑1 (MQ=255)
ggTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAgg < 1:394500/90‑1 (MQ=255)
ccGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCt < 1:846391/90‑1 (MQ=255)
ccGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCt < 2:830181/90‑1 (MQ=255)
ccGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCt < 2:1104588/90‑1 (MQ=255)
cGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTa < 1:5984/90‑1 (MQ=255)
gTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTaa < 2:920124/90‑1 (MQ=255)
gTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTaa < 2:1319893/90‑1 (MQ=255)
gTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTa > 2:257635/1‑89 (MQ=255)
gTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTa < 1:257635/89‑1 (MQ=255)
aCAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCt < 1:189110/83‑1 (MQ=255)
aCAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCt > 2:189110/1‑83 (MQ=255)
aCAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTAtt > 1:1057792/1‑90 (MQ=255)
ctctGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGaaa < 1:1364798/64‑1 (MQ=255)
ctctGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGaaa > 2:1364798/1‑64 (MQ=255)
ggCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCAccagccag < 1:762506/90‑1 (MQ=255)
cgacAACACGCCCAAATTCTCCTATAAGGTGGCGAAACGGGCGGGGGAGAAGGGTGATAATTATTCCCACATCCCCCGCCAGTGGCAGGa < 1:965054/87‑1 (MQ=255)
aaCATGCCCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAAAAAGGTGCTAAGTATTCCAACACCACCCGCCAGTGGCAGGAACGt < 1:310168/90‑1 (MQ=255)
aaCATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGGGGAAAAAGGTGCTAAGTATTACCACATCCCCCGCCAGTGGCAGGAACGt < 1:450912/90‑1 (MQ=255)
aaCATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGt < 2:557193/90‑1 (MQ=255)
aaCATGACCGAAGTCTCCTATCAGGTTGCGAAACGGGCCGCGGAGAAAGGTGCTAAGTATTCCCACATCCCCCGCCAGTGGCAGGAACGt < 1:275432/90‑1 (MQ=255)
aaCATCCCCGAACTCTCCTATCGGGTTGCCAAACGTGCCGCGGAGAAAGATGTTAATTATTACCAAATCACCCGCCAGTGGCAGGAACGt < 2:718398/90‑1 (MQ=255)
tGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCCCCCGCCAGTGGCAGGAACGTGGta < 2:1057792/90‑1 (MQ=255)
aCCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGtaat > 1:1549037/1‑90 (MQ=255)
tATCAGTTTGCGAAACGTGCCGGGGAAAAGGGTGTTAATTTTTCCCACATCCCCCGCCAGTGGCAGGAACGTGGTAATAATCTGACCGTc < 1:370637/90‑1 (MQ=255)
aGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGGAATAACCTGACCGTCAgcg > 1:86462/1‑90 (MQ=255)
gtttGCAAAACGTGCCGGGGAGAAAGGTGATAATTATTACCCCATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAgcgc < 2:728064/88‑1 (MQ=255)
gagAAAGGTGCGGAGAAGAAGGGTTTAAAATTTTCCCACACCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGAt < 1:158780/88‑1 (MQ=255)
|
ATGGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGAT > NZ_CP009273/1673458‑1673616
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ATGGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTATAAATAACTATTCAGTTACT > NZ_CP009273/1673458‑1673641
|
tgtgtataagagacagGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGT < SRR3722078.1386754/84‑1 (MQ=60)
ATGGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGT < SRR3722078.1087991/100‑1 (MQ=60)
ATGGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGT < SRR3722078.591852/100‑1 (MQ=60)
GGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTAT < SRR3722078.399294/100‑1 (MQ=60)
GTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATT > SRR3722078.1073692/1‑100 (MQ=60)
CCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACC < SRR3722078.857687/100‑1 (MQ=60)
CCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACC < SRR3722078.191354/100‑1 (MQ=60)
CGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCA < SRR3722078.6047/100‑1 (MQ=60)
CGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCA < SRR3722078.260791/100‑1 (MQ=60)
GGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCACCAGCCAGTGGCAGGAAC < SRR3722078.772307/100‑1 (MQ=60)
ACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGgaagggg > SRR3722078.727272/1‑93 (MQ=60)
cggcaaagagaccgatgcCTCCTATCCGGTTGCAAAACGGGCGGCGGAAAAAGGTGCTAAGTATTCCCACACCCCCCGCCAGTGGCAGGAACGTGGTAAT < SRR3722078.810014/82‑1 (MQ=32)
CGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAAT > SRR3722078.1574273/1‑100 (MQ=60)
AACATGCCCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAAAAAGGTGCTAAGTATTCCAACACCACCCGCCAGTGGCAGGAACGTGGTAATAACC < SRR3722078.313966/100‑1 (MQ=60)
AACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGGGGAAAAAGGTGCTAAGTATTACCACATCCCCCGCCAGTGGCAGGAACGTGGTAATAACC < SRR3722078.456296/100‑1 (MQ=60)
AACATGACCGAAGTCTCCTATCAGGTTGCGAAACGGGCCGCGGAGAAAGGTGCTAAGTATTCCCACATCCCCCGCCAGTGGCAGGAACGTGGTAATAACC < SRR3722078.278789/100‑1 (MQ=60)
GTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGGAATAACCTGACCGTCAGCG > SRR3722078.87479/1‑100 (MQ=60)
CCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGGAATAACCctgtctcttatacaca > SRR3722078.1140333/1‑84 (MQ=60)
TATCAGTTTGCGAAACGTGCCGGGGAAAAGGGTGTTAATTTTTCCCACATCCCCCGCCAGTGGCAGGAACGTGGTAATAATCTGACCGTCAGCGCAGATC < SRR3722078.375168/100‑1 (MQ=44)
GAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAAACTGACCGTCAGCGCAGATCTGTATAAATAACTATTCAGTTACT > SRR3722078.1257511/1‑100 (MQ=60)
|
ATGGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTATAAATAACTATTCAGTTACT > NZ_CP009273/1673458‑1673641
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
