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 F2 I225 R1
|
227 |
21.4 |
1179702 |
97.1% |
1145490 |
86.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,011,010 |
A→G |
E531G (GAA→GGA) |
ygfK → |
putative selenate reductase subunit YgfK |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,011,010 | 0 | A | G | 96.5%
| 85.0
/ ‑3.4
| 29 | E531G (GAA→GGA) | ygfK | putative selenate reductase subunit YgfK |
| Reads supporting (aligned to +/- strand): ref base A (0/1); new base G (18/10); total (18/11) |
| Fisher's exact test for biased strand distribution p-value = 3.79e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.37e-01 |
GATCACCAGTGCCAATACAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGAAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGTTGCCGTGATTGGTGCA > NZ_CP009273/3010928‑3011092
|
gATCCCCAGTGCCAATACAACTGTCCCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGt < 2:101517/90‑1 (MQ=255)
aTCACCAGTGCAAATACAACTGTCCCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGtt < 2:131123/90‑1 (MQ=255)
aaTACAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAAtata > 2:107525/1‑90 (MQ=255)
aaTACAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAAtata > 1:562568/1‑90 (MQ=255)
tACAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGa > 1:57750/1‑80 (MQ=255)
tACAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGa < 2:57750/80‑1 (MQ=255)
aaCTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCaa > 1:196772/1‑90 (MQ=255)
aaCTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCaa > 1:250891/1‑90 (MQ=255)
gtccccGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCt < 2:126504/87‑1 (MQ=255)
gTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGAAAAAGGTTGGGATGAATATAAGCAACGCt < 1:484220/90‑1 (MQ=255)
aCCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTgg > 2:356820/1‑90 (MQ=255)
cGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGcac > 1:467615/1‑90 (MQ=255)
ggATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAAcc > 2:425010/1‑90 (MQ=255)
ggATTACGACAGTGCGCTGAATATCCGCGAACTG‑AAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCa > 2:29818/1‑90 (MQ=255)
gACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGt > 1:25792/1‑90 (MQ=255)
gTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGgaa < 2:374734/42‑1 (MQ=255)
gTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGgaa > 1:374734/1‑42 (MQ=255)
gTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTg > 2:417821/1‑90 (MQ=255)
gTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTg > 1:82618/1‑90 (MQ=255)
gTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTg > 1:575493/1‑90 (MQ=255)
gTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTg > 2:466624/1‑90 (MQ=255)
gTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTg > 1:330335/1‑90 (MQ=255)
cgcTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGctggttctggtt < 2:332295/90‑1 (MQ=255)
tGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCAc < 2:412637/90‑1 (MQ=255)
aaaaaGTCGCG‑‑GGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGTTGCCGTGAtt < 1:235375/90‑1 (MQ=255)
aaaGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGTTGCCGTGAtt < 1:258831/90‑1 (MQ=255)
aaaGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGTTGCCGTGAtt < 1:180322/90‑1 (MQ=255)
gcgcTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGTTGCCGTg > 1:496034/1‑81 (MQ=255)
gcgcTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGTTGCCGTg < 2:496034/81‑1 (MQ=255)
gcgcTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGTTGCCGTGATTGGTGCa > 1:18007/1‑90 (MQ=255)
gcgcTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGTTGCCGTGATTGGTGCa > 1:35723/1‑90 (MQ=255)
|
GATCACCAGTGCCAATACAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGAAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGTTGCCGTGATTGGTGCA > NZ_CP009273/3010928‑3011092
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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
GTCATATTTGCGATCACCAGTGCCAATACAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGAAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGTTGCCGTGATTGGTGCAGGTC > NZ_CP009273/3010917‑3011096
|
ttcttttttgcgacccccagtccaaataaAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGG < SRR3722109.249925/71‑1 (MQ=60)
CACCAGTGCCAATACAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATA > SRR3722109.571103/1‑100 (MQ=60)
CCAGTGCCAATACAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAG > SRR3722109.58434/1‑100 (MQ=60)
GTGCCAATACAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAA > SRR3722109.199175/1‑100 (MQ=60)
GTGCCAATACAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAA > SRR3722109.253850/1‑100 (MQ=60)
CATCTCTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCAC < SRR3722109.444205/100‑1 (MQ=60)
CAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCAC > SRR3722109.474650/1‑100 (MQ=60)
GTCCCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGAAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACC < SRR3722109.491513/100‑1 (MQ=60)
CCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGT > SRR3722109.26109/1‑100 (MQ=60)
GATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGActgtctcttatacacatctgacgctgccgacgaatgtc > SRR3722109.380029/1‑62 (MQ=60)
GATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTG > SRR3722109.83634/1‑100 (MQ=60)
GATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTG > SRR3722109.584219/1‑100 (MQ=60)
GATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTG > SRR3722109.334703/1‑100 (MQ=60)
GAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGTTGCCGTGATTGGTGCA > SRR3722109.36140/1‑100 (MQ=60)
GAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGTTGCCGTGATTGGTGCA > SRR3722109.503523/1‑100 (MQ=60)
GAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGTTGCCGTGATTGGTGCA > SRR3722109.18241/1‑100 (MQ=60)
AAAAAGTCGCG‑‑GGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGTTGCCGTGATTGGTGCAGGTC < SRR3722109.238157/100‑1 (MQ=60)
AAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGTTGCCGTGATTGGTGCAGGTC < SRR3722109.261963/100‑1 (MQ=60)
AAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGTTGCCGTGATTGGTGCAGGTC < SRR3722109.182536/100‑1 (MQ=60)
|
GTCATATTTGCGATCACCAGTGCCAATACAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGAAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGTTGCCGTGATTGGTGCAGGTC > NZ_CP009273/3010917‑3011096
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
