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 |
|
A12 F56 I1 R1
|
165 |
53.8 |
2611523 |
96.4% |
2517508 |
99.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
3,783,402 |
A→G |
V87A (GTC→GCC) |
gpsA ← |
glycerol‑3‑phosphate dehydrogenase (NAD+) |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 3,783,402 | 0 | A | G | 97.7%
| 151.8
/ ‑4.3
| 45 | V87A (GTC→GCC) | gpsA | glycerol‑3‑phosphate dehydrogenase (NAD+) |
| Reads supporting (aligned to +/- strand): ref base A (0/1); new base G (20/23); total (21/24) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.63e-01 |
ACGTCCGGTTTCCGCTTCCAGCCCTTTGGTCGCCCACACCAGACGCGCATCAGGACGCATCAGTGGTTTAATCTGGCGCAGCACTTCACCAAAGACATGGCTGGGTACGACGACGAGAATATTACGGCTGGCTGCCAGCGCAGTGGCGAGATCGCTTTCAAGATGGAGCGTATCGGGAAAAGGCACATC > NC_000913/3783308‑3783496
|
aCGTCCGGTTTCCGCTTCCAGCCCGTTGGTCGCCCACACCAGACGCGCATCAGGACGCATCAGTGGTTTAATCTGGCGCAGCACTTCACCAAAGGCATgn < 2:1076551/100‑2 (MQ=255)
cGTCCGGTTTCCGCTTCCAGCCCTTTGGTCGCCCACACCCGACGCGCATCAGGACGCATCAGTGGTTTAATCTGGCGCAGCACTTCACCACAGTCATGGc > 2:638129/1‑100 (MQ=255)
cGTCCGGTTTCCGCTTCCAGCCCTTTGGTCGCCCACACCAGACGCGCATCAGGACGCATCAGTGGTTTAATCTGGCGCAGCACTTCACCAAAGGCATGGc < 2:69972/100‑1 (MQ=255)
cGGTTTCCGCTTCCAGCCCTTTGGTCGCCCACACCAGACGCGCATCAGGACGCATCAGTGGTTTAATCTGGCGCAGCACTTCACCAAAGGCATGGCTggg < 1:62225/100‑1 (MQ=255)
gTTTCCGCTTCCAGCCCTTTGGTCGCCCACACCAGACGCGCATCAGGACGCATCAGTGGTTTAATCTGGCGCAGCACTTCACCAAAGGCATGGCTGGGTa < 2:982351/100‑1 (MQ=255)
ttCCGCTTCCAGCCCTTTGGTCGCCCACACCAGACGCGCATCAGGACGCATCAGTGGTTTAATCTGGCGCAGCACTTCACCAAAGGCATGGCTGGGTacg > 2:862532/1‑100 (MQ=255)
ttCCGCTTCCAGCCCTTTGGTCGCCCACACCAGACGCGCATCAGGACGCATCAGTGGTTTAATCTGGCGCAGCACTTCACCAAAGGCATGGCTGGGTacg < 1:731227/100‑1 (MQ=255)
ttCCGCTTCCAGCCCTTTGGTCGCCCACACCAGACGCGCATCAGGACGCATCAGTGGTTTAATCTGGCGCAGCACTTCACCAAAGGCATGGCTGGGTac > 2:175325/1‑99 (MQ=255)
cTTCCAGCCCTTTGGTCGCCCACACCAGACGCGCATCAGGACGCATCAGTGGTTTAATCTGGCGCAGCACTTCACCAAAGGCATGGCTGGGTacgacgac < 2:726819/100‑1 (MQ=255)
gCCCTTTGGTCGCCCACACCAGACGCGCATCAGGACGCATCAGTGGTTTAATCTGGCGCAGCACTTCACCAAAGGCATGGCTGGGTACGACGACGAGAat < 2:1101914/100‑1 (MQ=255)
cTTTGGTCGCCCACACCAGACGCGCATCAGGACGCATCAGTGGTTTAATCTGGCGCAGCACTTCACCAAAGGCATGGCTGGGTACGACGACGAGAATAtt > 2:1298245/1‑100 (MQ=255)
tttGGTCGCCCACACCAGACGCGCATCAGGACGCATCAGTGGTTTAATCTGGCGCAGCACTTCACCAAAGGCATGGCTGGGTACGACGACGAGAATATTa < 2:384571/100‑1 (MQ=255)
cGCCCACACCAGACGCGCATCAGGACGCATCAGTGGTTTAATCTGGCGCAGCACTTCACCAAAGGCATGGCTGGGTACGACGACGAGAATATTACggctg < 2:336865/100‑1 (MQ=255)
acCAGACGCGCATCAGGACGCATCAGTGGTTTAATCTGGCGCAGCACTTCACCAAAGGCATGGCTGGGTACGACGACGAGAATATTACGGCTGGCTGCCa > 1:494262/1‑100 (MQ=255)
ccAGACGCGCATCAGGACGCATCAGTGGTTTAATCTGGCGCAGCACTTCACCAAAGGCATGGCTGGGTACGACGACGAGAATATTACGGCTGGCTGCCAg > 1:722665/1‑100 (MQ=255)
gACGCGCATCAGGACGCATCAGTGGTTTAATCTGGCGCAGCACTTCACCAAAGGCATGGCTGGGTACGACGACGAGAATATTACGGCTGGCTGCCAgcgc < 1:996473/100‑1 (MQ=255)
cgcgCATCAGGACGCATCAGTGGTTTAATCTGGCGCAGCACTTCACCAAAGGCATGGCTGGGTACGACGACGAGAATATTACGGCTGGCTGCCAGCGCAg > 2:241097/1‑100 (MQ=255)
cgcgCAGCAGGACGCATCAGTGGTTTAATCTGGCGCAGCACTTCACCAAAGGCATGGCTGGGTACGACGACGAGAATATTACGGCTGGCTGCCAGCGCAg < 1:1119377/100‑1 (MQ=255)
cgcATCAGGACGCATCAGTGGTTTAATCTGGCGCAGCACTTCACCAAAGACATGGCTGGGTACGACGACGAGAATATTACGGCTGGCTGCCAGCGCAGTg < 2:1287336/100‑1 (MQ=255)
gcATCAGGACGCATCAGTGGTTTAATCTGGCGCAGCACTTCACCAAAGGCATGGCTGGGTACGACGACGAGAATATTACGGCTGGCTGCCAGCGCAGTgg < 2:82753/100‑1 (MQ=255)
aTCAGGACGCATCAGTGGTTTAATCTGGCGCAGCACTTCACCAAAGGCATGGCTGGGTACGACGACGAGAATATTACGGCTGGCTGCCAGCGCAGTGGCg < 2:884871/100‑1 (MQ=255)
cAGGACGCATCAGTGGTTTAATCTGGCGCAGCACTTCACCAAAGGCATGGCTGGGTACGACGACGAGAATATTACGGCTGGCTGCCAGCGCAGTGGCgag < 1:231014/100‑1 (MQ=255)
ggACGCATCAGTGGTTTAATCTGGCGCAGCACTTCACCAAAGGCATGGCTGGGTACGACGACGAGAATATTACGGCTGGCTGCCAGCGCAGTGGCGAGAt > 1:91810/1‑100 (MQ=255)
cGCATCAGTGGTTTAATCTGGCGCAGCACTTCACCAAAGGCATGGCTGGGTACGACGACGAGAATATTACGGCTGGCTGCCAGCGCAGTGGCTAGATCg < 2:106872/99‑1 (MQ=255)
cATCAGTGGTTTAATCTGGCGCAGCACTTCACCAAAGGCATGGCTGGGTACGACGACGAGAATATTACGGCTGGCTGCCAGCGCAGTGGCGAGATCGCtt > 1:439340/1‑100 (MQ=255)
tCAGTGGTTTAATCTGGCGCAGCACTTCACCAAAGGCATGGCTGGGTACGACGACGAGAATATTACGGCTGGCTGCCAGCGCAGTGGCGAGATCGCTTTc > 2:733328/1‑100 (MQ=255)
cAGGGGTTTAATCTGGCGCAGCACTTCACCAAAGGCATGGCGGGGTACGACGACGAGAATATTACGGCTGGCTGCCAGCACAGTGGCGAGATCGCttt < 2:202608/98‑1 (MQ=255)
aGTGGTTTAATCTGGCGCAGCACTTCACCAAAGGCATGGCTGGGTACGACGACGAGAATATTACGGCTGGCTGCCAGCGCAGTGGCGAGATCGCTTTCaa > 1:1099970/1‑100 (MQ=255)
tGGTTTAATCTGGCGCAGCACTTCACCAAAGGCATGGCTGGGTACGACGACGAGAATATTACGGCTGGCTGCCAGCGCAGTGGCGAGATCGCTTTCAAGa > 1:471847/1‑100 (MQ=255)
ggTTTAATCTGGCGCAGCACTTCACCAAAGGCATGGCTGGGTACGACGACGAGAATATTACGGCTGGCTGCCAGCGCAGTGGCGAGATCGCTTTCAAGAt < 2:321714/100‑1 (MQ=255)
gTTTAATCTGGCGCAGCACTTCACCAAAGGCATGGCTGGGTACGACGACGAGAATATTACGGCTGGCTGCCAGCGCAGTGGCGAGATCGCTTTCAAGATg > 1:870141/1‑100 (MQ=255)
tAATCTGGCGCAGCACTTCACCAAAGGCATGGCTGGGTACGACGACGAGAATATTACGGCTGGCTGCCAGCGCAGTGGCGAGATCGCTTTCAAGATGGAg < 1:519820/100‑1 (MQ=255)
cTGGCGCAGCACTTCACCAAAGGCATGGCTGGGTACGACGACGAGAATATTACGGCTGGCTGCCAGCGCAGTGGCGAGATCGCTTTCAAGATGGAGCGTa > 1:630549/1‑100 (MQ=255)
ggCGCAGCACTTCACCAAAGGCATGGCTGGGTACGACGACGAGAATATTACGGCTGGCTGCCAGCGCAGTGGCGAGATCGCTTTCAAGATGGAGCGTATc > 2:347456/1‑100 (MQ=255)
gcgcAGCACTTCACCAAAGGCATGGCTGGGTACGACGACGAGAATATTACGGCTGGCTGCCAGCGCAGTGGCGAGATCGCTTTCAAGATGGAGCGTATCg > 1:1073966/1‑100 (MQ=255)
gcagcaCTTCACCAAAGGCATGGCTGGGTACGACGACGAGAATATTACGGCTGGCTGCCAGCGCAGTGGCGAGATCGCTTTCAAGATGGAGCGTATCggg < 1:811120/100‑1 (MQ=255)
aCTTCACCAAAGGGATGGCTGGGTACGACGACGAGAATATTACGGCTGGCTGCCAGCGCAGTGGCGAGATCGCTTTCAAGATGGAGCGTATCGGGAAAAg > 1:884901/1‑100 (MQ=255)
aCTTCACCAAAGGCATGGCTGGGTACGACGACGAGAATATTACGGCTGGCTGCCAGCGCAGTGGCGAGATCGCTTTCAAGATGGAGCGTATCGGGAAAAg < 1:241099/100‑1 (MQ=255)
aCTTCACCAAAGGCATGGCTGGGTACGACGACGAGAATATTACGGCTGGCTGCCAGCGCAGTGGCGAGATCGCTTTCAAGATGGAGCGTATCGGGAAAAg < 2:602779/100‑1 (MQ=255)
cTTCACCAAAGGCATGGCTGGGTACGACGACGAGAATATTACGGCTGGCTGCCAGCGCAGTGGCGAGATCGCTTTCAAGATGGAGCGTATCGGGAAAAgg > 1:437001/1‑100 (MQ=255)
ttCACCAAAGGCATGGCTGGGTACGACGACGAGAATATTACGGCTGGCTGCCAGCGCAGTGGCGAGATCGCTTTCAAGATGGAGCGTATCGGGAAAAGGc < 1:1196699/100‑1 (MQ=255)
ttCACCAAAGGCATGGCTGGGTACGACGACGAGAATATTACGGCTGGCTGCCAGCGCAGTGGCGAGATCGCTTTCAAGATGGAGCGTATCGGGAAAAGGc < 2:870135/100‑1 (MQ=255)
ccAAAGGCATGGCTGGGTACGACGACGAGAATATTACGGCTGGCTGCCAGCGCAGTGGCGAGATCGCTTTCAAGATGGAGCGTATCGGGAAAAGGCACAt > 2:336084/1‑100 (MQ=255)
cAAAGGCATGGCTGGGTACGACGACGAGAATATTACGGCTGGCTGCCAGCGCAGTGGCGAGATCGCTTTCAAGATGGAGCGTATCGGGAAAAGGCACATc > 2:501418/1‑100 (MQ=255)
aaaGGCGTGACTGGGTACGACGACGAGAATATTACGGCTGGCTGCCAGCGCAGTGGCAAGATCGCTTTCACGATGGAGCGTATCGGGAAAAGGCACATc > 2:1243654/1‑99 (MQ=255)
|
ACGTCCGGTTTCCGCTTCCAGCCCTTTGGTCGCCCACACCAGACGCGCATCAGGACGCATCAGTGGTTTAATCTGGCGCAGCACTTCACCAAAGACATGGCTGGGTACGACGACGAGAATATTACGGCTGGCTGCCAGCGCAGTGGCGAGATCGCTTTCAAGATGGAGCGTATCGGGAAAAGGCACATC > NC_000913/3783308‑3783496
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
