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 F5 I102 R1
|
278 |
39.1 |
2251254 |
95.8% |
2156701 |
87.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
945,384 |
(T)5→4 |
coding (261/591 nt) |
ycaK → |
NAD(P)H oxidoreductase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 945,380 | 0 | T | . | 97.6%
| 179.3
/ ‑2.1
| 41 | coding (257/591 nt) | ycaK | NAD(P)H oxidoreductase |
| Reads supporting (aligned to +/- strand): ref base T (0/0); major base . (14/26); minor base G (1/0); total (15/26) |
| Fisher's exact test for biased strand distribution p-value = 3.66e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.87e-01 |
GACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGGTTTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATG > NZ_CP009273/945295‑945466
|
gACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGGttttcc > 2:790628/1‑89 (MQ=255)
tGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCctct < 1:1073765/91‑1 (MQ=255)
gaaTATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCtggt < 1:1112764/91‑1 (MQ=255)
gaaTATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCtggt < 2:210845/91‑1 (MQ=255)
atatGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCtggtgg > 2:524840/1‑91 (MQ=255)
aaaCGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGGGGTACCGCtt > 2:52993/1‑91 (MQ=255)
tATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGGtttt < 2:277571/65‑1 (MQ=255)
tATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGGtttt > 1:277571/1‑65 (MQ=255)
tATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGc > 1:605596/1‑91 (MQ=255)
tATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGc < 2:804490/91‑1 (MQ=255)
aTTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACCTGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCa < 1:1051516/91‑1 (MQ=255)
ttCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCaa < 2:1091281/91‑1 (MQ=255)
ttCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCaa < 1:59027/91‑1 (MQ=255)
ccAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCt > 1:645546/1‑91 (MQ=255)
tcatcaGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGat < 1:239664/91‑1 (MQ=255)
tcatcaGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGat < 2:755126/91‑1 (MQ=255)
tcatcaGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGat > 1:830394/1‑91 (MQ=255)
atcaGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCtggt < 1:953164/59‑1 (MQ=255)
atcaGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCtggt > 2:953164/1‑59 (MQ=255)
cTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCaa < 1:262006/72‑1 (MQ=255)
cTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCaa > 2:262006/1‑72 (MQ=255)
tttATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGAc < 2:114022/91‑1 (MQ=255)
tATTCAGAGCTTCATGAACATGACACGTTAGTGGTAG‑TTTTCCTCTCTGGTGGTGCAGCTTCCCGGCAATGCTAAAAGGATAAATTGACag < 2:57450/91‑1 (MQ=255)
tATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACag < 1:599092/91‑1 (MQ=255)
tATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACag < 2:662671/91‑1 (MQ=255)
tATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACag < 2:605596/91‑1 (MQ=255)
aTTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACaga > 2:336080/1‑91 (MQ=255)
ttCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACagag < 2:712835/91‑1 (MQ=255)
gagCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATg > 1:954112/1‑91 (MQ=255)
gctTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGat < 2:127981/70‑1 (MQ=255)
gctTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGat > 1:127981/1‑70 (MQ=255)
gctTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGaata > 2:116172/1‑91 (MQ=255)
gctTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGaata > 1:17105/1‑91 (MQ=255)
gctTGAACATGACACGTTAGTGG‑GGGTTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGaata > 1:149831/1‑91 (MQ=255)
ctTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGaataa < 2:875264/91‑1 (MQ=255)
aCATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGggc < 2:217247/91‑1 (MQ=255)
aCATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGggc < 1:336080/91‑1 (MQ=255)
aCATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGggc < 1:219476/91‑1 (MQ=255)
aCATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGggc < 2:612756/91‑1 (MQ=255)
aTGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGggctg < 1:546936/91‑1 (MQ=255)
gACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACag < 1:1004556/70‑1 (MQ=255)
gACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACag > 2:1004556/1‑70 (MQ=255)
gACACGTTAGTGGTAG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGggctggc > 1:718311/1‑91 (MQ=255)
acGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTa < 2:502008/91‑1 (MQ=255)
tggtgg‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGAt < 1:442184/91‑1 (MQ=255)
ggtgg‑tTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATg > 1:567898/1‑91 (MQ=255)
ggtgg‑tTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATg < 2:91876/91‑1 (MQ=255)
|
GACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGGTTTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATG > NZ_CP009273/945295‑945466
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGGTTTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTC > NZ_CP009273/945298‑945483
|
TGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTAC < SRR3722125.1097943/101‑1 (MQ=60)
cggagatgtgtataagagacagCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTT < SRR3722125.974395/79‑1 (MQ=60)
GAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTT < SRR3722125.1137865/101‑1 (MQ=60)
GGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTctgtctcttatacaca > SRR3722125.283185/1‑85 (MQ=60)
GGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGC > SRR3722125.618641/1‑101 (MQ=60)
ACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCT > SRR3722125.659470/1‑101 (MQ=60)
ATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACCTGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAG < SRR3722125.1075136/101‑1 (MQ=60)
aagagacagGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGG < SRR3722125.267283/92‑1 (MQ=60)
TTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGG < SRR3722125.60116/101‑1 (MQ=60)
CTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGAT > SRR3722125.848632/1‑101 (MQ=60)
TCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAG < SRR3722125.244467/101‑1 (MQ=60)
GCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATG > SRR3722125.975365/1‑101 (MQ=60)
tcggagatgtgtataagagacagCACGTTAGTCGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAAT < SRR3722125.1021166/78‑1 (MQ=60)
ataagagacagGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAAT < SRR3722125.1027019/90‑1 (MQ=60)
TATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAAT < SRR3722125.611985/101‑1 (MQ=60)
ATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGctgtctcttat > SRR3722125.130388/1‑90 (MQ=60)
ATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATA > SRR3722125.17414/1‑101 (MQ=60)
ATTCAGAGCTGCTTGAACATGACACGTTAGTGG‑GGGTTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATA > SRR3722125.152679/1‑101 (MQ=60)
GCTTGAACATGACACGTTAGTGGTAG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGC > SRR3722125.733814/1‑101 (MQ=60)
ACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGG < SRR3722125.343048/101‑1 (MQ=60)
ACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGG < SRR3722125.223809/101‑1 (MQ=60)
ATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAG < SRR3722125.558649/101‑1 (MQ=60)
ACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATG > SRR3722125.580042/1‑101 (MQ=60)
CGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGC > SRR3722125.257567/1‑101 (MQ=60)
TGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAAT < SRR3722125.451517/101‑1 (MQ=60)
TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCAT < SRR3722125.543790/101‑1 (MQ=60)
TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCAT < SRR3722125.883256/101‑1 (MQ=60)
TTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTC < SRR3722125.597798/101‑1 (MQ=60)
|
TGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGGTTTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTC > NZ_CP009273/945298‑945483
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
