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 I97 R1
|
275 |
44.0 |
1733530 |
96.5% |
1672856 |
122.0 |
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%
| 117.0
/ NA
| 27 | coding (257/591 nt) | ycaK | NAD(P)H oxidoreductase |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base . (9/18); total (9/18) |
TATCGGCGTAATTTCAACCCAGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGGTTTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTG > NZ_CP009273/945250‑945511
|
tatCGGCGTAATTTCAACCCAGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGGttttcctc < 1:545933/138‑5 (MQ=255)
ggCGTAATTTCAACCCAGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCAACAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCtgg < 1:458455/139‑1 (MQ=255)
aTTTCAACCCAGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTAc < 1:9164/139‑1 (MQ=255)
aCCCAGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTc > 1:334178/1‑139 (MQ=255)
gTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGc < 2:320472/139‑1 (MQ=255)
gTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGc < 1:753606/139‑1 (MQ=255)
tgatgaCGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCa < 2:698753/139‑1 (MQ=255)
tgatgaCGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCa < 2:545474/139‑1 (MQ=255)
aCGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGc > 1:390479/1‑138 (MQ=255)
ccGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTaaa < 1:149525/139‑1 (MQ=255)
cGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTaa > 2:422442/1‑137 (MQ=255)
ggAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTAc > 1:670119/1‑117 (MQ=255)
ggAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTAc < 2:670119/117‑1 (MQ=255)
ggAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAg < 2:283356/139‑1 (MQ=255)
aaGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGa < 2:488493/139‑1 (MQ=255)
ccAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGa < 2:334178/139‑1 (MQ=255)
aGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACa < 2:390479/139‑1 (MQ=255)
tatGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGaata < 2:773652/139‑1 (MQ=255)
aTAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATggg < 2:20105/139‑1 (MQ=255)
cAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGAt < 1:267126/139‑1 (MQ=255)
catcaGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGcaca > 1:394044/1‑138 (MQ=255)
ctTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGAc > 1:708186/1‑77 (MQ=255)
ctTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGAc < 2:708186/77‑1 (MQ=255)
acacGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGgcg < 2:404863/139‑1 (MQ=255)
gTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTgg > 2:498151/1‑139 (MQ=255)
tggtgg‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGc > 2:339880/1‑36 (MQ=255)
tggtgg‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGc < 1:339880/36‑1 (MQ=255)
tggtgg‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTg > 1:576815/1‑137 (MQ=255)
|
TATCGGCGTAATTTCAACCCAGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGGTTTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTG > NZ_CP009273/945250‑945511
|
| 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
TCGATTTATATCGGCGTAATTTCAACCCAGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGGTTTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGACAAAGAATCATTT > NZ_CP009273/945242‑945531
|
cattgtgcggttgtgttttttgttttttttttttttcaagcagaagacggcatacgagattcgccttagtctcgtgggctcggagatgtgtataagagacagATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGG < SRR3722120.318947/49‑1 (MQ=60)
ATATCGGCGTAATTTCAACCCAGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTAC < SRR3722120.553623/150‑1 (MQ=60)
CGGCGTAATTTCAACCCAGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCAACAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTT < SRR3722120.465120/151‑1 (MQ=60)
GCGTAATTTCAACCCAGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCC > SRR3722120.338961/1‑151 (MQ=60)
AATTTCAACCCAGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGC < SRR3722120.9278/151‑1 (MQ=60)
ACCCAGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCT > SRR3722120.396207/1‑150 (MQ=60)
AGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAG < SRR3722120.763791/151‑1 (MQ=60)
gtagatgtgctacttcttttttttttcaagcagaagacggcatacgatattcgccttagtctcgtgggctcggagatgtgtataagagacagTGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAG < SRR3722120.344781/58‑1 (MQ=60)
GTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCctgtctcttat > SRR3722120.679300/1‑139 (MQ=60)
GCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTG < SRR3722120.151542/151‑1 (MQ=60)
CTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAA > SRR3722120.399818/1‑150 (MQ=60)
CCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATT < SRR3722120.270960/151‑1 (MQ=60)
cgccttagtctcgtgggctcggagatgtgtataagagacagTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAG < SRR3722120.302548/109‑1 (MQ=60)
ATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAActgtctcttatacacatctccgagcccacgagactaaggcgaatatcgtatg > SRR3722120.717852/1‑99 (MQ=60)
TGACACGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTGG > SRR3722120.584844/1‑149 (MQ=60)
CGTTAGTGGTGG‑TTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATctgtctcttatacacatctccgagcccacgagactaaggcgaatctcgtatgccgccttctgcttgaaaaaaaa > SRR3722120.535500/1‑76 (MQ=60)
GGTTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGACAAAGAATCAT > SRR3722120.472490/1‑151 (MQ=60)
TTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGACAAAGAATCATTT < SRR3722120.7695/150‑1 (MQ=60)
|
TCGATTTATATCGGCGTAATTTCAACCCAGTGATGACGCCGGAAGATGAACCAGACTGGAAGAATATGGATAAACGTTATTCTCCAGAGGTTCATCAGCTTTATTCAGAGCTGCTTGAACATGACACGTTAGTGGTGGTTTTTCCTCTCTGGTGGTACAGCTTCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGACAAAGAATCATTT > NZ_CP009273/945242‑945531
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
