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 |
1,848,011 |
T→C |
T76A (ACT→GCT) |
ydjE ← |
MFS transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,848,011 | 0 | T | C | 95.5%
| 132.1
/ ‑3.1
| 44 | T76A (ACT→GCT) | ydjE | MFS transporter |
| Reads supporting (aligned to +/- strand): ref base T (1/1); new base C (25/17); total (26/18) |
| 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 |
GGCCCCTGTTGCAGCAATACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGTAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTACCA > NZ_CP009273/1847925‑1848094
|
ggCCCCTGTTGCAGCAATACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAg > 2:601070/1‑90 (MQ=255)
ggCCCCTGTTGCAGCAATACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAg > 2:234740/1‑90 (MQ=255)
ggCCCCTGTTGCAGCAATACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAg > 2:1108331/1‑90 (MQ=255)
tGTTGCAGCAATACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGcc > 2:1461018/1‑90 (MQ=255)
aaTACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATa > 2:665378/1‑90 (MQ=255)
aaTACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATa > 2:1154737/1‑90 (MQ=255)
tACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAAc > 1:1409101/1‑90 (MQ=255)
tACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAAc > 2:1487884/1‑90 (MQ=255)
cgacgaTGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCaa < 1:1078228/90‑1 (MQ=255)
cgacgaTGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCaa < 2:1249372/90‑1 (MQ=255)
gacgaTGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCaaa > 1:145975/1‑90 (MQ=255)
gacgaTGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCaaa > 1:28104/1‑90 (MQ=255)
cgaTGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGTAAGTGAGCCGATGAAATAACCAAACa > 2:878145/1‑90 (MQ=255)
tGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTa < 1:229509/90‑1 (MQ=255)
tGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTa < 1:394787/90‑1 (MQ=255)
tGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTa > 1:79881/1‑90 (MQ=255)
agaTTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGcc < 1:835227/90‑1 (MQ=255)
gaTTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCg < 1:5212/90‑1 (MQ=255)
tATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGt > 1:831367/1‑90 (MQ=255)
aaaCGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAggc < 2:1014362/90‑1 (MQ=255)
ccgccCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGaa < 1:766181/90‑1 (MQ=255)
gccCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAat > 1:339521/1‑90 (MQ=255)
gccCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAat > 1:379527/1‑90 (MQ=255)
tagtCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGAc < 1:269446/90‑1 (MQ=255)
tagtCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGAc < 2:145975/90‑1 (MQ=255)
gtCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGAcca > 1:1031844/1‑90 (MQ=255)
gtCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGAcca > 1:472948/1‑90 (MQ=255)
aCCAATAAACCCACCAGTAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGAccatcc < 1:878145/90‑1 (MQ=255)
aCCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGAccatcc < 2:150658/90‑1 (MQ=255)
aCCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGAccatcc < 2:79881/90‑1 (MQ=255)
aTAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTg > 1:293473/1‑90 (MQ=255)
aTAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTg > 2:1050109/1‑90 (MQ=255)
ccaccaGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTAcc < 1:601070/90‑1 (MQ=255)
ccaccaGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTAcc < 1:1108331/90‑1 (MQ=255)
caccaGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCAtt < 1:55746/82‑1 (MQ=255)
caccaGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCAtt > 2:55746/1‑82 (MQ=255)
caccaGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTAc > 2:1385686/1‑88 (MQ=255)
caccaGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTAc < 1:1385686/88‑1 (MQ=255)
caccaGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTACCa > 2:1232303/1‑90 (MQ=255)
caccaGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTACCa > 2:268999/1‑90 (MQ=255)
caccaGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTACCa > 2:693323/1‑90 (MQ=255)
caccaGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTACCa > 2:795979/1‑90 (MQ=255)
caccaGCAAGTGAGCCGATGAAATAACCAAACATTAACGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGAc > 2:60386/1‑74 (MQ=255)
caccaGCAAGTGAGCCGATGAAATAACCAAACATTAACGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGAc < 1:60386/74‑1 (MQ=255)
|
GGCCCCTGTTGCAGCAATACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGTAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTACCA > NZ_CP009273/1847925‑1848094
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ 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
GTTGCAGCAATACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGTAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTACCAGCTTTGCTA > NZ_CP009273/1847932‑1848103
|
GTTGCAGCAATACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAAC > SRR3722078.1431956/1‑100 (MQ=60)
CAGCAATACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAA > SRR3722078.147670/1‑100 (MQ=60)
CAGCAATACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAA > SRR3722078.28451/1‑100 (MQ=60)
ATACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTA > SRR3722078.80818/1‑100 (MQ=60)
CGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGC < SRR3722078.1094532/100‑1 (MQ=60)
TGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGT > SRR3722078.842416/1‑100 (MQ=60)
TGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGT < SRR3722078.232290/100‑1 (MQ=60)
TGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGT < SRR3722078.399581/100‑1 (MQ=60)
AGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGG < SRR3722078.846341/100‑1 (MQ=60)
GATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGC < SRR3722078.5267/100‑1 (MQ=60)
GCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAAT > SRR3722078.384160/1‑100 (MQ=60)
GCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAAT > SRR3722078.343676/1‑100 (MQ=60)
CCGCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGAC < SRR3722078.776059/100‑1 (MQ=60)
GCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCA > SRR3722078.1047169/1‑100 (MQ=60)
GCCCAAAGTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCA > SRR3722078.478559/1‑100 (MQ=60)
GTAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTG > SRR3722078.297049/1‑100 (MQ=60)
agacagCCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAACGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGC < SRR3722078.61095/94‑1 (MQ=60)
TAGTCACCAATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGC < SRR3722078.272739/100‑1 (MQ=60)
ACCAATAAACCCACCAGTAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTACC < SRR3722078.889950/100‑1 (MQ=60)
AATAAACCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTACCAGC < SRR3722078.56405/100‑1 (MQ=60)
CCCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTACCAGCTTTGCT < SRR3722078.1408059/100‑1 (MQ=60)
CCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTACCAGCTTTGCTA < SRR3722078.608021/100‑1 (MQ=60)
CCACCAGCAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTACCAGCTTTGCTA < SRR3722078.1125239/100‑1 (MQ=60)
|
GTTGCAGCAATACCGACGATGAGAAGATTTATGCGAAACGCCCTGCGCCGCCCAAAGTAGTCACCAATAAACCCACCAGTAAGTGAGCCGATGAAATAACCAAACATTAATGCCGAGGTAAAGGCGGCATTGAGGAAATTATTTGACCATCCATTGCTTACCAGCTTTGCTA > NZ_CP009273/1847932‑1848103
|
| 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: ‑ |
