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 |
|
A6 F1 I2 R1
|
67 |
27.9 |
1239648 |
95.3% |
1181384 |
112.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,620,907 |
(A)8→9 |
intergenic (‑35/‑290) |
upp ← / → purM |
uracil phosphoribosyltransferase/phosphoribosylaminoimidazole synthetase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,620,899 | 1 | . | A | 94.7%
| 57.1
/ ‑2.9
| 19 | intergenic (‑27/‑298) | upp/purM | uracil phosphoribosyltransferase/phosphoribosylaminoimidazole synthetase |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base A (9/9); total (9/10) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.31e-01 |
CCACTTCGGAAGCGAGTTCGCGAAAGCGCTTGGTGCTGATATCTTGCTCACGCATCAGTCCCAGCTTGTGTTTGACGAGTGGGTGTTTGACTTCCACGATCTTCATACTCTTTCTCCTTTGAGGGGCAGCCAC‑AAAAAAA‑ATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGTTATGAAAGAAGATTATTC > NC_000913/2620767‑2621028
|
ccACTTCGGAAGCGAGTTCGCGAAAGCGCTTGGTGCTGATATCTTGCTCACGCATCAGTCCCAGCTTGTGTTTGACGAGTGGGTGTTTGACTTCCACGATCTTCATACTCTTTCTCCTTTGAGGGGCAGCCAC‑aaaaaa < 2:145568/139‑1 (MQ=255)
aGTTCGCGAAAGCGCTTGGTGCTGATATCTTGCTCACGCATCAGTCCCAGCTTGTGTTTGACGAGTGGGTGTTTGACTTCCACGATCTTCATACTCTTTCTCCTTTGAGGGGCAGCCACAAAAAAAA‑ATCGACGGATta > 2:451939/1‑139 (MQ=255)
tCGCGAAAGCGCTTGGTGCTGATATCTTGCTCACGCATCAGTCCCAGCTTGTGTTTGACGAGTGGGTGTTTGACTTCCACGATCTTCATACTCTTTCTCCTTTGAGGGGCAGCCACAAAAAAAA‑ATCGACGGATTATAc < 2:420413/139‑1 (MQ=255)
ttGCTCACGCATCAGTCCCAGCTTGTGTTTGACGAGTGGGTGTTTGACTTCCACGATCTTCATACTCTTTCTCCTTTGAGGGGCAGCCACAAAAAAAA‑ATCGACGGATTATACCTCCTTTCTTCAAgg < 1:151679/128‑1 (MQ=255)
ttGCTCACGCATCAGTCCCAGCTTGTGTTTGACGAGTGGGTGTTTGACTTCCACGATCTTCATACTCTTTCTCCTTTGAGGGGCAGCCACAAAAAAAA‑ATCGACGGATTATACCTCCTTTCTTCAAgg > 2:151679/1‑128 (MQ=255)
ccAGCTTGTGTTTGACGAGTGGGTGTTTCACTTCCACGATCTTCATACTCTTTCTCCTTTGAGGGGCAGCCACAAAAAAAA‑ATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGt < 1:451939/139‑1 (MQ=255)
gCTTGTGTTTGACGAGTGGGTGTTTGACTTCCACGATCTTCATACTCTTTCTCCTTTGAGGGGCAGCCACAAAAAAAA‑ATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGt < 1:236000/136‑1 (MQ=255)
gCTTGTGTTTGACGAGTGGGTGTTTGACTTCCACGATCTTCATACTCTTTCTCCTTTGAGGGGCAGCCACAAAAAAAA‑ATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGt > 2:236000/1‑136 (MQ=255)
tgtTTGACGAGTGGGTGTTTGACTTCCACGATCTTCATACTCTTTCTCCTTTGAGGGGCAGCCACAAAAAAAA‑ATCGACGGATTATAc > 1:43791/1‑88 (MQ=255)
tgtTTGACGAGTGGGTGTTTGACTTCCACGATCTTCATACTCTTTCTCCTTTGAGGGGCAGCCACAAAAAAAA‑ATCGACGGATTATAc < 2:43791/88‑1 (MQ=255)
gACTTCCACGATCTTCATACTCTTTCTCCTTTGAGGGGCAGCCACAAAAAAAA‑ATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGTGATAAAGtt < 2:413318/139‑1 (MQ=255)
tttCTCCTTTGAGGGGCAGCCACAAAAAAAA‑ATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGa > 2:360104/1‑131 (MQ=255)
tttCTCCTTTGAGGGGCAGCCACAAAAAAAA‑ATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGa < 1:360104/131‑1 (MQ=255)
ttGAGGGGCAGCCACAAAAAAAA‑ATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGTTATGAAagaaga > 2:115401/1‑139 (MQ=255)
ttGAGGGGCAGCCACAAAAAAAA‑ATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGTTATGAAagaaga > 1:558548/1‑139 (MQ=255)
gAGGGGCAGCCACAAAAAAAA‑ATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGTCAAAATGATaa > 2:357999/1‑90 (MQ=255)
gAGGGGCAGCCAC‑AAAAAAAGATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGTCAAAATGATaa < 1:357999/90‑1 (MQ=255)
ggCAGCCACAAAAAAAA‑ATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGTTATGAAAGAAGATTATTc < 2:558548/139‑1 (MQ=255)
cAGCCACAAAAAAAA‑ATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGTTATGAaag > 1:428063/1‑127 (MQ=255)
cAGCCACAAAAAAAA‑ATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGTTATGAaag < 2:428063/127‑1 (MQ=255)
|
CCACTTCGGAAGCGAGTTCGCGAAAGCGCTTGGTGCTGATATCTTGCTCACGCATCAGTCCCAGCTTGTGTTTGACGAGTGGGTGTTTGACTTCCACGATCTTCATACTCTTTCTCCTTTGAGGGGCAGCCAC‑AAAAAAA‑ATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGTTATGAAAGAAGATTATTC > NC_000913/2620767‑2621028
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
