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 F3 I96 R1
|
172 |
34.7 |
2005794 |
96.2% |
1929573 |
85.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,149,054 |
G→C |
A213P (GCG→CCG) |
oxyR → |
DNA‑binding transcriptional regulator OxyR |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,149,054 | 0 | G | C | 90.6%
| 166.7
/ 9.7
| 53 | A213P (GCG→CCG) | oxyR | DNA‑binding transcriptional regulator OxyR |
| Reads supporting (aligned to +/- strand): ref base G (2/3); new base C (18/30); total (20/33) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.68e-01 |
GATCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTT > NZ_CP009273/4148970‑4149132
|
gATCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGAt < 1:301114/90‑1 (MQ=255)
gATCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGAt < 2:549483/90‑1 (MQ=255)
gATCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGAt < 2:236320/90‑1 (MQ=255)
tCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGa < 1:8512/90‑1 (MQ=255)
tCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGa < 1:98058/90‑1 (MQ=255)
cTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGaa < 2:668172/90‑1 (MQ=255)
gggAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATacac < 1:954221/90‑1 (MQ=255)
ggAAAAACAGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGa < 1:9560/84‑1 (MQ=255)
ggAAAAACAGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGa > 2:9560/1‑84 (MQ=255)
gAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGAt > 2:492450/1‑78 (MQ=255)
gAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGAt < 1:492450/78‑1 (MQ=255)
aaaCTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTc > 2:199384/1‑90 (MQ=255)
ctgctgATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCcgc < 2:367389/90‑1 (MQ=255)
tgctgATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCcgcg > 1:497743/1‑90 (MQ=255)
gctgATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCTGGGGCGGATGAAGACACACACTTCcgcgc > 1:956339/1‑90 (MQ=255)
gATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGAc < 2:705568/90‑1 (MQ=255)
gATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGAc < 1:822371/90‑1 (MQ=255)
gATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGAc < 1:420365/90‑1 (MQ=255)
aTGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGAcc < 2:42981/90‑1 (MQ=255)
tGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCa < 1:115062/90‑1 (MQ=255)
tGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCa < 2:397909/90‑1 (MQ=255)
tGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCa < 2:47093/90‑1 (MQ=255)
tGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCa < 1:821524/90‑1 (MQ=255)
tGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCa < 2:918285/90‑1 (MQ=255)
cTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGc < 2:263096/90‑1 (MQ=255)
cTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGc < 2:666874/90‑1 (MQ=255)
tGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCa > 1:309202/1‑87 (MQ=255)
tGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCa < 2:309202/87‑1 (MQ=255)
tGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAAc < 1:428951/90‑1 (MQ=255)
gTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAActc < 2:413422/90‑1 (MQ=255)
aCTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTgc < 2:1000920/90‑1 (MQ=255)
gcgcGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAActc < 2:549187/80‑1 (MQ=255)
gcgcGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAActc > 1:549187/1‑80 (MQ=255)
gcgcGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTgcgc > 2:726828/1‑85 (MQ=255)
gcgcGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTgcgc < 1:726828/85‑1 (MQ=255)
gATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACAtggtg > 2:36362/1‑90 (MQ=255)
gATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACAtggtg > 1:614855/1‑90 (MQ=255)
tCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTggc > 2:163998/1‑90 (MQ=255)
ggCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTggcggc < 2:102359/90‑1 (MQ=255)
gggTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAg > 2:915866/1‑90 (MQ=255)
ttCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCggg > 2:94395/1‑90 (MQ=255)
ttCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCa > 2:970494/1‑81 (MQ=255)
ttCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCa < 1:970494/81‑1 (MQ=255)
ttCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCggg > 2:534941/1‑90 (MQ=255)
ttCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCggg > 2:519464/1‑90 (MQ=255)
ttCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCggg < 2:290254/90‑1 (MQ=255)
ttCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCggg > 1:474746/1‑90 (MQ=255)
tCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGa < 1:534941/90‑1 (MQ=255)
cTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGAt < 1:199384/90‑1 (MQ=255)
tGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATc < 1:422131/90‑1 (MQ=255)
ttGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACtt > 2:29220/1‑90 (MQ=255)
ttGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACtt > 1:515312/1‑90 (MQ=255)
ttGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGGGGCGGCAGGTAGCGGGATCACtt > 1:552753/1‑90 (MQ=255)
|
GATCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTT > NZ_CP009273/4148970‑4149132
|
| 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
GATCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGC > NZ_CP009273/4148970‑4149138
|
agTCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACAC < SRR3722236.499873/98‑1 (MQ=60)
GATCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACAC < SRR3722236.305468/100‑1 (MQ=60)
TCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACAC < SRR3722236.99420/100‑1 (MQ=60)
TCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACAC < SRR3722236.8628/100‑1 (MQ=60)
GGCAGGGGAAAAACAGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTC < SRR3722236.9690/100‑1 (MQ=60)
GGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCG > SRR3722236.505265/1‑100 (MQ=60)
GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCTGGGGCGGATGAAGACACACACTTCCGCGC > SRR3722236.973211/1‑100 (MQ=60)
GGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGC < SRR3722236.971056/100‑1 (MQ=60)
CTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCC > SRR3722236.313651/1‑100 (MQ=60)
GATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAA < SRR3722236.836708/100‑1 (MQ=60)
GATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAA < SRR3722236.426228/100‑1 (MQ=60)
gagatctacacctaagccttcgtcggcagcgtcagatgtgtataagagacagAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAAC < SRR3722236.509311/48‑1 (MQ=60)
TGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAAC < SRR3722236.116666/100‑1 (MQ=60)
TGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAAC < SRR3722236.835848/100‑1 (MQ=60)
TGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAAC < SRR3722236.434929/100‑1 (MQ=60)
GTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACAT > SRR3722236.557646/1‑100 (MQ=60)
CTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTG > SRR3722236.624741/1‑100 (MQ=60)
TGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGG < SRR3722236.739163/100‑1 (MQ=60)
GGCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGG > SRR3722236.481820/1‑100 (MQ=60)
GCAATGGGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGA < SRR3722236.987610/100‑1 (MQ=60)
GGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTT > SRR3722236.523149/1‑100 (MQ=60)
GGTTTCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGGGGCGGCAGGTAGCGGGATCACTT > SRR3722236.561263/1‑100 (MQ=60)
TCTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACT < SRR3722236.543165/100‑1 (MQ=60)
CTGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTG < SRR3722236.202358/100‑1 (MQ=60)
TGTTTTGAAGCCGGGCCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGC < SRR3722236.428021/100‑1 (MQ=60)
|
GATCTGGCAGGGGAAAAACTGCTGATGCTGGAAGATGGTCACTGTTTGCGCGATCAGGCAATGGGTTTCTGTTTTGAAGCCGGGGCGGATGAAGATACACACTTCCGCGCGACCAGCCTGGAAACTCTGCGCAACATGGTGGCGGCAGGTAGCGGGATCACTTTACTGC > NZ_CP009273/4148970‑4149138
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
