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 |
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 | 96.0%
| 71.6
/ ‑3.6
| 25 | G95G (GGA→GGG) | cobT | nicotinate‑nucleotide‑‑dimethylbenzimidazole phosphoribosyltransferase |
| Reads supporting (aligned to +/- strand): ref base T (1/0); new base C (15/9); total (16/9) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.40e-01 |
AGGCTCAGCAGTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTTCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGTGATCGGCAC > NZ_CP009273/2057583‑2057749
|
aGGCTCAGCAGTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGt > 2:10874/1‑90 (MQ=255)
cagcagTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCatat > 1:13065/1‑90 (MQ=255)
cagcagTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCatat > 2:268958/1‑90 (MQ=255)
cagcagTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCatat > 1:188668/1‑90 (MQ=255)
tATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAg < 2:541951/90‑1 (MQ=255)
aTCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGc > 2:81577/1‑90 (MQ=255)
cAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATgg > 1:191580/1‑90 (MQ=255)
cAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATgg > 2:56107/1‑90 (MQ=255)
cAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATgg > 2:434198/1‑90 (MQ=255)
aCATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCt > 2:149840/1‑90 (MQ=255)
gTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCttt > 2:346728/1‑90 (MQ=255)
tGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCtttt < 1:10874/90‑1 (MQ=255)
tGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCtttt < 2:214223/90‑1 (MQ=255)
gACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTgg > 1:318657/1‑90 (MQ=255)
tAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGcc < 1:52431/62‑1 (MQ=255)
tAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGcc > 2:52431/1‑62 (MQ=255)
tAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGaaa > 1:16883/1‑90 (MQ=255)
cGCTTGTTCTGCCAGCACACACACGCCGGTTGTTCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGAc > 2:234496/1‑90 (MQ=255)
gCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTtcctcc > 1:527880/1‑90 (MQ=255)
gCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGa < 1:149840/90‑1 (MQ=255)
cacacacGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGc < 2:191580/90‑1 (MQ=255)
ggTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGTGATCGGc < 1:230633/90‑1 (MQ=255)
ggTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGTGATCGGc < 1:550868/90‑1 (MQ=255)
ggTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGTGATCGGc < 1:473506/90‑1 (MQ=255)
ggTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGTGATCGGc > 1:343033/1‑90 (MQ=255)
gttgtcCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGTGATCGGc < 1:164776/89‑1 (MQ=255)
gttgtcCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGTGATCGGc > 2:164776/1‑89 (MQ=255)
ttgtcCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGTGATCGGcac < 1:76490/90‑1 (MQ=255)
|
AGGCTCAGCAGTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTTCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGTGATCGGCAC > NZ_CP009273/2057583‑2057749
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TTGATAAGCCCGGGGATAGGCTCAGCAGTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTTCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGTGATCGGCACACATAACCAGTAC > NZ_CP009273/2057566‑2057762
|
TTGATAAGCCCGGGGATAGGCTCAGCAGTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCC < SRR3722109.80251/100‑1 (MQ=60)
GGGATAGGCTCAGCAGTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATAT > SRR3722109.190982/1‑100 (MQ=60)
GGGACAGGCTCAGCAGTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATAT > SRR3722109.13246/1‑100 (MQ=60)
GTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGG > SRR3722109.193925/1‑100 (MQ=60)
gatgtgtataagagacagACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTG < SRR3722109.53056/82‑1 (MQ=60)
CAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGG > SRR3722109.322857/1‑100 (MQ=60)
ACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAA > SRR3722109.17103/1‑100 (MQ=60)
TGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAG < SRR3722109.11021/100‑1 (MQ=60)
CGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCC > SRR3722109.535920/1‑100 (MQ=60)
GCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGTGATC < SRR3722109.151691/100‑1 (MQ=60)
CACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGTGATCGGC > SRR3722109.347604/1‑100 (MQ=60)
GGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGTGATCGGCACACATAACC < SRR3722109.166817/100‑1 (MQ=60)
GGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGTGATCGGCACACATAACC < SRR3722109.233368/100‑1 (MQ=60)
GGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGTGATCGGCACACATAACC < SRR3722109.480639/100‑1 (MQ=60)
GGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGTGATCGGCACACATAACC < SRR3722109.559242/100‑1 (MQ=60)
TTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGTGATCGGCACACATAACCAG < SRR3722109.77414/100‑1 (MQ=60)
TCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGTGATCGGCACACATAACCAGTAC < SRR3722109.343241/100‑1 (MQ=60)
TCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGTGATCGGCACACATAACCAGTAC > SRR3722109.440396/1‑100 (MQ=60)
|
TTGATAAGCCCGGGGATAGGCTCAGCAGTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTTCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGTGATCGGCACACATAACCAGTAC > NZ_CP009273/2057566‑2057762
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
