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 |
945,548 |
A→G |
E142G (GAA→GGA) |
ycaK → |
NAD(P)H oxidoreductase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 945,548 | 0 | A | G | 91.7%
| 69.1
/ 0.3
| 24 | E142G (GAA→GGA) | ycaK | NAD(P)H oxidoreductase |
| Reads supporting (aligned to +/- strand): ref base A (1/1); new base G (10/12); total (11/13) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.70e-01 |
CTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGACAAAGAATCATTTGTCCAGATGGGCTGGGAAAAAAATATAAGCGATTATTTAAAAAATATGTGCAGTTATCTTGGTATTGAAGATGCCGATGTCACTTTCTTGTGTAATACAGTGGTATTCGATGGGGAAGAACTTCACGCGAGCTATTATCAGT > NZ_CP009273/945415‑945673
|
cTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGACAAAGAATCATTTGTCCAGATGGGCTGGGgaaaa > 1:291660/1‑138 (MQ=255)
tATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGACAAAGAATCATTTGTCCAGATGGGCTGGGGAAAAAATATAAGCGATTATTTaaaaa > 2:684271/1‑138 (MQ=255)
tATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGACAAAGAATCATTTGTCCAGATGGGCTGGGAAAAAAATATAAGCGATTATTTaaaaaa > 2:514282/1‑139 (MQ=255)
tGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGACAAAGAATCATTTGTCCAGATGGGCTGGGGAAAAAATATAAGCGATTATTTAAAAAATATGTGCAg < 2:517715/138‑1 (MQ=255)
tGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGACAAAGAATCATTTGTCCAGATGGGCTGGGGAAAAAATATAAGCGATTATTTAAAAAATATGTGCAg > 1:517715/1‑138 (MQ=255)
tggctTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGACAAAGAATCATTTGTCCAGATGGGCTGGGaa > 1:646059/1‑98 (MQ=255)
tggctTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGACAAAGAATCATTTGTCCAGATGGGCTGGGaa < 2:646059/98‑1 (MQ=255)
gctTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGACAAAGAATCATTTGTCCAGATGGGCTGGGGAAAAAATATAAGCGATTATTTAAAAAATATGTGCAGTTATCt < 2:702133/137‑1 (MQ=255)
tGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGACAAAGAATCATTTGTCCAGATGGGCTGGGGAAAAAATATAAGCGa > 1:295826/1‑105 (MQ=255)
tGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGACAAAGAATCATTTGTCCAGATGGGCTGGGGAAAAAATATAAGCGa < 2:295826/105‑1 (MQ=255)
aTTCAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGACAAAGAATCATTTGTCCAGATGGGCTGGGAAAAAAATATAAGCGATTATTTAAAAAATATGTGCAGTTATCTTGGTATTGAAGATGCCGATGTCACTTTc < 1:514282/139‑1 (MQ=255)
tCAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGACAAAGAATCATTTGTCCAGATGGGCTGGGGAAAAAATATAAGCGATTATTTAAAAAATATGTGCAGTTATCt < 2:545862/109‑1 (MQ=255)
tCAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGACAAAGAATCATTTGTCCAGATGGGCTGGGGAAAAAATATAAGCGATTATTTAAAAAATATGTGCAGTTATCt > 1:545862/1‑109 (MQ=255)
ttCGTTGGGTGGCGCTGGTTGGAGGAGACAAAGAATCATTTGTCCAGATGGGCTGGGGAAAAAATATAAGCGATTATTTAAAAAATATGTGCAGTTATCTTGGTATTGAAGATGCCg > 2:564409/1‑117 (MQ=255)
ttCGTTGGGTGGCGCTGGTTGGAGGAGACAAAGAATCATTTGTCCAGATGGGCTGGGGAAAAAATATAAGCGATTATTTAAAAAATATGTGCAGTTATCTTGGTATTGAAGATGCCg < 1:564409/117‑1 (MQ=255)
gTTGGGTGGCGCTGGTTGGAGGAGACAAAGAATCATTTGTCCAGATGGGCTGGGGAAAAAATATAAGCGattatt < 2:243589/75‑1 (MQ=255)
gTTGGGTGGCGCTGGTTGGAGGAGACAAAGAATCATTTGTCCAGATGGGCTGGGGAAAAAATATAAGCGattatt > 1:243589/1‑75 (MQ=255)
ggTGGCGCTGGTTGGAGGAGACAAAGAATCATTTGTCCAGATGGGCTGGGGAAAAAATATAAGCGATTATTTAAAAAATATGTGCAGTTATCTTGGTATTGAAGATGCCGATGTCACTTTCTTGTGTAATACAGTGGTa > 2:172548/1‑139 (MQ=255)
aCAAAGAATCATTTGTCCAGATGGGCTGGGGAAAAAATATAAGCGATTATTTAAAAAATATGTGCAGTTATCTTGGTATTGAAGATGCCGATGTCACTTTCTTGTGTAATACAGTGGTATTCGATGGGGAAGAACTTCa > 2:186948/1‑139 (MQ=255)
aaaGAATCATTTGTCCAGATGGGCTGGGGAAAAAATATAAGCGATTATTTAAAAAATATGTGCAGTTATCTTGGTATTGAAGATGCCGATGTCACTTTCTTGTGTAATACAGTGGTATTCGATGGGGAAGAACTTCAcg < 2:291660/139‑1 (MQ=255)
aaaGAATCATTTGTCCAGATGGGCTGGGGAAAAAATATAAGCGATTATTTAAAAAATATGTGCAGTTATCTTGGTATTGAAGATGCCGATGTCACTTTCTTGTGTAATACAGTGGTATTCGATGGGGAAGAACTTCAcg < 1:283696/139‑1 (MQ=255)
aaaGAATCATTTGTCCAGATGGGCTGGGGAAAAAATATAAGCGATTATTT‑AAAAATATGTGCAGTTATCTTGGTATTGAAGATGCCGATGTCACTTTCTTGTGTAATACAGTGGTATTCGATGGGGAAGAACTTCAcgc < 1:684271/139‑1 (MQ=255)
aaGAATCATTTGTCCAGATGGGCTGGGGAAAAAATATAAGCGATTATTTAAAAAATATGTGCAGTTATCTTGGTATTGAAGATGCCGATGTCACTTTCTTGTGTAATACAGTGGTATTCGATGGGGAAGAACTTCAcgc < 1:172548/139‑1 (MQ=255)
aGAATCATTTGTCCAGATGGGCTGGGGAAAAAATATAAGCGATTATTTAAAAAATATGTGCAGTTATCTTGGTATTGAAGATGCCGATGTCACTTTCTTGTGTAATACAGTGGTATTCGATGGGGAAGAACTTCAcgc > 1:173247/1‑138 (MQ=255)
cAGATGGGCTGGGGAAAAAATATAAGCGATTATTTAAAAAATATGTGCAGTTATCTTGGTATTGAAGATGCCGATGTCACTTTCTTGTGTAATACAGTGGTATTCGATGGGGAAGAACTTCACGCGAGCTATTATCAGt < 1:89975/139‑1 (MQ=255)
cTGGGGAAAAAATATAAGCGATTATTTAAAAAATATGTGCAGTTATCTTGGTATTGAAGATGCCGATGTCACTTTCtt > 2:94422/1‑78 (MQ=255)
cTGGGGAAAAAATATAAGCGATTATTTAAAAAATATGTGCAGTTATCTTGGTATTGAAGATGCCGATGTCACTTTCtt < 1:94422/78‑1 (MQ=255)
|
CTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGACAAAGAATCATTTGTCCAGATGGGCTGGGAAAAAAATATAAGCGATTATTTAAAAAATATGTGCAGTTATCTTGGTATTGAAGATGCCGATGTCACTTTCTTGTGTAATACAGTGGTATTCGATGGGGAAGAACTTCACGCGAGCTATTATCAGT > NZ_CP009273/945415‑945673
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGACAAAGAATCATTTGTCCAGATGGGCTGGGAAAAAAATATAAGCGATTATTTAAAAAATATGTGCAGTTATCTTGGTATTGAAGATGCCGATGTCACTTTCTTGTGTAATACAGTGGTATTCGATGGGGAAGAACTTCACGCGAGCTATTATCAGTCGTTATTATCTCAGGTACGGG > NZ_CP009273/945404‑945694
|
TCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGACAAAGAATCATTTGTCCAGATGGGCTGGGGAAAAA > SRR3722133.295626/1‑150 (MQ=60)
ataagagacAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGACAAAGAATCATTTGTCCAGATGGGCTGGGGAAAAAATATAAG < SRR3722133.644591/141‑1 (MQ=60)
GTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGACAAAGAATCATTTGTCCAGATGGGCTGGGGAAAAAATATAAGCGATTATTTAAAAAATATGTGCAGTT > SRR3722133.524698/1‑151 (MQ=60)
GAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGACAAAGAATCATTTGTCCAGATGGGCTGGGAAAAAAATATAAGCtgtctcttatacacatctccgagcccacg > SRR3722133.654499/1‑121 (MQ=60)
GGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGACAAAGAATCATTTGTCCAGATGGGCTGGGGAAAAAATATAAGCGATTATTTAAAAActgtctcttatacacatctccg > SRR3722133.299838/1‑127 (MQ=60)
ataagagacagATTCAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGACAAAGAATCATTTGTCCAGATGGGCTGGGGAAAAAATATAAGCGATTATTTAAAAAATATGTGCAGTTATCTTGGTATTGAAGATGCCGATGTCACTTTC < SRR3722133.571906/139‑1 (MQ=60)
CAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGACAAAGAATCATTTGTCCAGATGGGCTGGGGAAAAAATATAAGCGATTATTTAAAAAATATGTGCAGTTATCTTGGTATTGAAGctgtctcttatacacatctc > SRR3722133.553163/1‑131 (MQ=60)
CATTCAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGACAAAGAATCATTTGTCCAGATGGGCTGGGAAAAAAATATAAGCGATTATTTAAAAAATATGTGCAGTTATCTTGGTATTGAAGATGCCGATGTCACTTTCTTGTGTAATAC < SRR3722133.521192/151‑1 (MQ=60)
atacgagatctagtacggtctcgtgggctcggagatgtgtataagagacagGTCCAGATGGGCTGGGGAAAAAATATAAGCGATTATTTAAAAAATATGTGCAGTTATCTTGGTATTGAAGATGCCGATGTCACTTTCTTGTGTAATACAG < SRR3722133.95636/100‑1 (MQ=60)
CAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGACAAAGAATCATTTGTCCAGATGGGCTGGGGAAAAAATATAAGCGATTATTTAAAAAATATGctgtctcttatacacatctccgagcccacgagaccgtactagatctcgtatgcc > SRR3722133.246881/1‑97 (MQ=60)
GGAGGAGACAAAGAATCATTTGTCCAGATGGGCTGGGGAAAAAATATAAGCGATTATTTAAAAAATATGTGCAGTTATCTTGGTATTGAAGATGCCGATGTCACTTTCTTGTGTAATACAGTGGTATTCGATGGGGAAGAACTTCACGCG > SRR3722133.175534/1‑150 (MQ=60)
CAAAGAATCATTTGTCCAGATGGGCTGGGGAAAAAATATAAGCGATTATTTAAAAAATATGTGCAGTTATCTTGGTATTGAAGATGCCGATGTCACTTTCTTGTGTAATACAGTGGTATTCGATGGGGAAGAACTTCACGCGAGCTATTAT < SRR3722133.287568/151‑1 (MQ=60)
CAAAGAATCATTTGTCCAGATGGGCTGGGGAAAAAATATAAGCGATTATTT‑AAAAATATGTGCAGTTATCTTGGTATTGAAGATGCCGATGTCACTTTCTTGTGTAATACAGTGGTATTCGATGGGGAAGAACTTCACGCGAGCTATTATC < SRR3722133.693123/151‑1 (MQ=60)
AAAGAATCATTTGTCCAGATGGGCTGGGGAAAAAATATAAGCGATTATTTAAAAAATATGTGCAGTTATCTTGGTATTGAAGATGCCGATGTCACTTTCTTGTGTAATACAGTGGTATTCGATGGGGAAGAACTTCACGCGAGCTATTATC < SRR3722133.174826/151‑1 (MQ=60)
CCAGATGGGCTGGGGAAAAAATATAAGCGATTATTTAAAAAATATGTGCAGTTATCTTGGTATTGAAGATGCCGATGTCACTTTCTTGTGTAATACAGTGGTATTCGATGGGGAAGAACTTCACGCGAGCTATTATCAGTCGTTATTATCT < SRR3722133.91130/151‑1 (MQ=60)
GGGGAAAAAATATAAGCGATTATTTAAAAAATATGTGCAGTTATCTTGGTATTGAAGATGCCGATGTCACTTTCTTGTGTAATACAGTGGTATTCGATGGGGAAGAACTTCACGCGAGCTATTATCAGTCGTTATTATCTCAGGTACGGG < SRR3722133.96377/150‑1 (MQ=60)
|
TCCCGGCAATGCTAAAAGGATATATTGACAGAGTATGGAATAATGGGCTGGCTTATGGAGATGGGCACAAATTACCATTCAATAAAGTTCGTTGGGTGGCGCTGGTTGGAGGAGACAAAGAATCATTTGTCCAGATGGGCTGGGAAAAAAATATAAGCGATTATTTAAAAAATATGTGCAGTTATCTTGGTATTGAAGATGCCGATGTCACTTTCTTGTGTAATACAGTGGTATTCGATGGGGAAGAACTTCACGCGAGCTATTATCAGTCGTTATTATCTCAGGTACGGG > NZ_CP009273/945404‑945694
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑ |
