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 I200 R1
|
216 |
30.8 |
1683622 |
97.2% |
1636480 |
87.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,057,664 |
T→C |
G95G (GGA→GGG) |
cobT ← |
nicotinate‑nucleotide‑‑dimethylbenzimidazole phosphoribosyltransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,057,664 | 0 | T | C | 87.1%
| 69.0
/ 5.7
| 31 | G95G (GGA→GGG) | cobT | nicotinate‑nucleotide‑‑dimethylbenzimidazole phosphoribosyltransferase |
| Reads supporting (aligned to +/- strand): ref base T (1/3); new base C (13/14); total (14/17) |
| Fisher's exact test for biased strand distribution p-value = 6.07e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.87e-01 |
CCGGGGATAGGCTCAGCAGTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTTCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGTGATCGGC > NZ_CP009273/2057575‑2057747
|
ccGGGGATAGGCTCAGCAGTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGgttgtt > 2:681576/1‑90 (MQ=255)
gggATAGGCTCAGCAGTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCa < 2:320261/90‑1 (MQ=255)
gggATAGGCTCAGCAGTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCa < 1:644500/90‑1 (MQ=255)
cTCAGCAGTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTTCCACGGGTCat < 1:52195/90‑1 (MQ=255)
cagcagTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCatat > 1:87838/1‑90 (MQ=255)
agcagTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATAtt > 1:411222/1‑90 (MQ=255)
gTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCa > 2:380551/1‑90 (MQ=255)
aTCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGc > 2:734800/1‑90 (MQ=255)
aTCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGc > 2:558863/1‑90 (MQ=255)
tCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACCCGCCGGTTGTCCCACGGGTCATATTTTCAGcc < 2:607310/90‑1 (MQ=255)
cAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATgg > 2:350215/1‑90 (MQ=255)
aTCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGt > 1:782020/1‑90 (MQ=255)
ttACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTTCCACGGGTCATATTTTCAGCCTGTATGGCTGTCActt < 1:681576/90‑1 (MQ=255)
gTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCttt > 2:102579/1‑90 (MQ=255)
gTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCttt > 1:90650/1‑90 (MQ=255)
tGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCtttt < 2:87838/90‑1 (MQ=255)
tAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGaaa > 1:536791/1‑90 (MQ=255)
ccGCTTGTTCTGCCAGCACACACACGCCGGTTGTTCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGa < 1:308652/90‑1 (MQ=255)
cGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGAc < 1:729916/90‑1 (MQ=255)
gCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGAcc < 1:171008/90‑1 (MQ=255)
gTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCtt < 2:593927/90‑1 (MQ=255)
gTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCtt < 2:800535/90‑1 (MQ=255)
gCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGcc > 1:619799/1‑45 (MQ=255)
gCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGcc < 2:619799/45‑1 (MQ=255)
acacGCCGGTTGTTCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGt > 1:360881/1‑90 (MQ=255)
acacGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGt > 1:388923/1‑90 (MQ=255)
cacGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGTg < 2:536791/90‑1 (MQ=255)
acGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGTGa < 1:188118/90‑1 (MQ=255)
ccGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGTGATCg > 1:67468/1‑90 (MQ=255)
ggTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGTGATCGGc < 2:154137/90‑1 (MQ=255)
ggTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGTGATCGGc < 2:793987/90‑1 (MQ=255)
ggTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGTGATCGGc < 1:110653/90‑1 (MQ=255)
|
CCGGGGATAGGCTCAGCAGTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTTCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGTGATCGGC > NZ_CP009273/2057575‑2057747
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 33 ≤ 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
GGGATAGGCTCAGCAGTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTTCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGTGATCGGCACACATAACCAGTAC > NZ_CP009273/2057578‑2057762
|
GGGATAGGCTCAGCAGTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATAT > SRR3722079.88536/1‑100 (MQ=60)
GGGATAGGCTCAGCAGTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATAT < SRR3722079.651162/100‑1 (MQ=60)
GGATAGGCTCAGCAGTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATT > SRR3722079.414738/1‑100 (MQ=60)
CTCAGCAGTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTTCCACGGGTCATATTTTCAGCC < SRR3722079.52605/100‑1 (MQ=60)
CAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGT > SRR3722079.790407/1‑100 (MQ=60)
CATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTT > SRR3722079.91365/1‑100 (MQ=60)
TTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTTCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGA < SRR3722079.688734/100‑1 (MQ=60)
ACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAA > SRR3722079.541833/1‑100 (MQ=60)
CCGCTTGTTCTGCCAGCACACACACGCCGGTTGTTCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTC < SRR3722079.311169/100‑1 (MQ=60)
CGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGctgtctcttatacacatctccgagcccacgagacc > SRR3722079.626102/1‑65 (MQ=60)
CGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCC < SRR3722079.737721/100‑1 (MQ=60)
GCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCC < SRR3722079.172497/100‑1 (MQ=60)
GCCAGCACACACACGCCGGTTGTTCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGT > SRR3722079.363700/1‑100 (MQ=60)
GCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGT > SRR3722079.392137/1‑100 (MQ=60)
CACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGTGATCG > SRR3722079.68024/1‑100 (MQ=60)
ACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGTGATCGGCACACA < SRR3722079.189756/100‑1 (MQ=60)
GGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGTGATCGGCACACATAACC < SRR3722079.111551/100‑1 (MQ=60)
TCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGTGATCGGCACACATAACCAGTAC > SRR3722079.600837/1‑100 (MQ=60)
|
GGGATAGGCTCAGCAGTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTTCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGTGATCGGCACACATAACCAGTAC > NZ_CP009273/2057578‑2057762
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
