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 |
|
A2 F5 I179 R1
|
182 |
40.3 |
1547118 |
96.8% |
1497610 |
120.0 |
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 | . | 100.0%
| 88.8
/ NA
| 21 | coding (257/591 nt) | ycaK | NAD(P)H oxidoreductase |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base . (6/15); total (6/15) |
CGTAATTTCAACCCAGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGGTTTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTG > NZ_CP009273/945256‑945511
|
cGTAATTTCAACCCAGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCtggtg > 2:234164/1‑139 (MQ=255)
aTTTCAACCCAGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTAc < 1:335846/139‑1 (MQ=255)
aTTTCAACCCAGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTAc < 2:609371/139‑1 (MQ=255)
ggAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAg < 1:324242/139‑1 (MQ=255)
ccAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGa < 1:234164/139‑1 (MQ=255)
aGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACa < 1:248601/139‑1 (MQ=255)
gaagaaTATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTa < 1:492848/138‑1 (MQ=255)
gaagaaTATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTa < 2:303439/138‑1 (MQ=255)
aTAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATggg < 2:645272/139‑1 (MQ=255)
cGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGggctggc < 1:340233/139‑1 (MQ=255)
agGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATggg < 1:605250/139‑1 (MQ=255)
catcaGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATggg > 1:659516/1‑116 (MQ=255)
catcaGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATggg < 2:659516/116‑1 (MQ=255)
ctTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACa < 1:63810/78‑1 (MQ=255)
ctTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACa > 2:63810/1‑78 (MQ=255)
acacGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGgcg < 2:31175/139‑1 (MQ=255)
gTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGgcg < 2:416049/135‑1 (MQ=255)
gTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGgcg > 1:416049/1‑135 (MQ=255)
tggtgg‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATggg > 2:308046/1‑76 (MQ=255)
tggtgg‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATggg < 1:308046/76‑1 (MQ=255)
tggtgg‑TTTTCCTCTCTGGTGGGACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTg > 2:95154/1‑137 (MQ=255)
|
CGTAATTTCAACCCAGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGGTTTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTG > NZ_CP009273/945256‑945511
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
AATTTCAACCCAGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGGTTTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGA > NZ_CP009273/945259‑945518
|
AATTTCAACCCAGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGC < SRR3722133.340576/151‑1 (MQ=60)
CGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGAC < SRR3722133.328725/151‑1 (MQ=60)
ACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGA < SRR3722133.237354/151‑1 (MQ=60)
atacgagatctagtacggtctcgtgggctcggagatgtgtataagagacagATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAAT < SRR3722133.64628/100‑1 (MQ=60)
CAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAAT < SRR3722133.252001/151‑1 (MQ=60)
GGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGG < SRR3722133.499498/150‑1 (MQ=60)
gcatacgagatctagtacggtctcgtgggctcggagatgtgtataagagacagTGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGG < SRR3722133.312279/98‑1 (MQ=60)
ACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATG < SRR3722133.345011/151‑1 (MQ=60)
ATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACctgtctcttatacacatctccgagcccacgagaccgtactagatctcgtatgccgtcttctgcttgaaaaa > SRR3722133.98809/1‑79 (MQ=60)
CTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGctgtctcttatac > SRR3722133.668111/1‑138 (MQ=60)
GAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACC < SRR3722133.613251/151‑1 (MQ=60)
GAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGT > SRR3722133.421797/1‑151 (MQ=60)
CGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATctgtctcttatacacatctccgagcccacgagaccgtactagatctcgtatgccgtcttctgcttgaaaaaaaa > SRR3722133.510119/1‑76 (MQ=60)
CGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTctgtctcttatacacatctccgagcccacgagaccgtact > SRR3722133.187371/1‑108 (MQ=60)
|
AATTTCAACCCAGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGGTTTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGA > NZ_CP009273/945259‑945518
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
