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 I1 R1
|
67 |
31.4 |
1402038 |
96.1% |
1347358 |
109.5 |
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 | 84.9%
| 97.7
/ 10.7
| 33 | intergenic (‑27/‑298) | upp/purM | uracil phosphoribosyltransferase/phosphoribosylaminoimidazole synthetase |
| Reads supporting (aligned to +/- strand): ref base . (3/2); new base A (13/15); total (16/17) |
| Fisher's exact test for biased strand distribution p-value = 6.56e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.53e-01 |
TACCCACTTCGGAAGCGAGTTCGCGAAAGCGCTTGGTGCTGATATCTTGCTCACGCATCAGTCCCAGCTTGTGTTTGACGAGTGGGTGTTTGACTTCCACGATCTTCATACTCTTTCTCCTTTGAGGGGCAGCCAC‑‑AAA‑AAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGTTATGAAAGAAGATTATTC > NC_000913/2620764‑2621028
|
tACCCACTTCGGAAGCGAGTTCGCGAAAGCGCTTGGTGCTGATATCTTGCTCACGCATCAGTCCCAGCTTGTGTTTGACGAGTGGGTGTTTGACTTCCACGATCTTCATACTCTTTCTCCTTTGAGGGGCAGCCAC‑‑aaa > 1:258306/1‑139 (MQ=255)
tACCCACTTCGGAAGCGAGTTCGCGAAAGCGCTTGGTGCTGATATCTTGCTCACGCATCAGTCCCAGCTTGTGTTTGACGAGTGGGTGTTTGACTTCCACGATCTTCATACTCTTTCTCCTTTGAGGGGCAGCCAC‑‑aaa > 1:665168/1‑139 (MQ=255)
tCGGAAGCGAGTTCGCGAAAGCGCTTGGTGCTGATATCTTGCTCACGCATCAGTCCCAGCTTGTGTTTGACGAGTGGGTGTTTGACTTCCACGATCTTCATACTCTTTCTCCTTTGAGGGGCAGCCAC‑‑AAA‑AAAAATCg > 1:43037/1‑139 (MQ=255)
aaGCGAGTTCGCGAAAGCGCTTGGTGCTGATATCTTGCTCACGCATCAGTCCCAGCTTGTGTTTGACGAGTGGGTGTTTGACTTCCACGATCTTCATACTCTTTCTCCTTTGAGGGGCAGCCACA‑AAA‑AAAAATCGACg < 2:346424/139‑1 (MQ=255)
ggTGCTGATATCTTGCTCACGCATCAGTCCCAGCTTGTGTTTGACGAGTGGGTGTTTGACTTCCACGATCTTCATACTCTTTCTCCTTTGAGGGGCAGCCAC‑‑AAA‑AAAAATCGACGGATTATACCTCCTTTCTTCAAgg < 2:43037/139‑1 (MQ=255)
gCTCACGCATCAGTCCCAGCTTGTGTTTGACGAGTGGGTGTTTGACTTCCACGATCTTCATACTCTTTCTCCTTTGAGGGGCAGCCAC‑‑AAAGAAAAATCGAc > 2:417354/1‑102 (MQ=255)
gCTCACGCATCAGTCCCAGCTTGTGTTTGACGAGTGGGTGTTTGACTTCCACGATCTTCATACTCTTTCTCCTTGGAGGGGCAGCCACA‑AAA‑AAAAATCGAc < 1:417354/102‑1 (MQ=255)
cTCACGCATCAGTCCCAGCTTGTGTTTGACGAGTGGGTGTTTGACTTCCACGATCTTCATACTCTTTCTCCTTTGAGGGGCAGCCACA‑AAA‑AAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCttt > 1:265154/1‑139 (MQ=255)
cACGCATCAGTCCCAGCTTGTGTTTGACGAGTGGGTGTTTGACTTCCACGATCTTCATACTCTTTCTCCTTTGAGGGGCAGCCACA‑AAA‑AAAAATCGACGGATTATACCTCCTTTCTTTAAGGCGGCAATATTCtt > 2:74901/1‑136 (MQ=255)
cACGCATCAGTCCCAGCTTGTGTTTGACGAGTGGGTGTTTGACTTCCACGATCTTCATACTCTTTCTCCTTTGAGGGGCAGCCACA‑AAA‑AAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCtt < 1:74901/136‑1 (MQ=255)
tgtTTGACGAGTGGGTGTTTGACTTCCACGATCTTCATTCTCTTTCTCCTTTGAGGGGCAGCCACA‑AAA‑AAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGt < 1:23575/131‑1 (MQ=255)
tgtTTGACGAGTGGGTGTTTGACTTCCACGATCTTCATACTCTTTCTCCTTTGAGGGGCAGCCACA‑AAA‑AAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGt > 2:23575/1‑131 (MQ=255)
tgtTTGACGAGTGGGTGTTTGACTTCCACGATCTTCATACTCTTTCTCCTTTGAGGGGCAGCCAC‑‑aaa‑aaaaaatcga < 2:480672/78‑6 (MQ=255)
tgtTTGACGAGTGGGTGTTTGACTTCCACGATCTTCATACTCTTTCTCCTTTGAGGGGCAGCCAC‑‑aaa‑aaaaaatcga > 1:480672/1‑73 (MQ=255)
tttGACGAGTGGGTGTTTGACTTCCACGATCTTCATACTCTTTCTCCTTTGAGGGGCAGCCACA‑AAA‑AAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGTCAAAATGATa < 2:665168/139‑1 (MQ=255)
ttGACGAGTGGGTGTTTGACTTCCACGATCTTCATACTCTTTCTCCTTTGAGGGGCAGCCACA‑AAA‑AAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGTCAAAATGATaa < 2:265154/139‑1 (MQ=255)
gTGGGTGTTTGACTTCCACGATCTTCATACTCTTTCTCCTTTGAGGGGCAGCCACA‑AAA‑AAAAATCGACGGATTATACCTCCTTTCTTCAAgg > 1:594976/1‑93 (MQ=255)
gTGGGTGTTTGACTTCCACGATCTTCATACTCTTTCTCCTTTGAGGGGCAGCCACA‑AAA‑AAAAATCGACGGATTATACCTCCTTTCTTCAAgg < 2:594976/93‑1 (MQ=255)
tCATACTCTTTCTCCTTTGAGGGGCAGCCACA‑AAA‑AAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGa < 2:258306/139‑1 (MQ=255)
aTACTCTTTCTCCTTTGAGGGGCAGCCACA‑AAA‑AAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATg > 1:384619/1‑139 (MQ=255)
tctTTCTCCTTTGAGGGGCAGCCACA‑AAA‑AAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGTTa < 2:384619/139‑1 (MQ=255)
ctTTCTCCTTTGAGGGGCAGCCACA‑AAA‑AAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTc < 2:31065/73‑1 (MQ=255)
ctTTCTCCTTTGAGGGGCAGCCACA‑AAA‑AAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTc > 1:31065/1‑73 (MQ=255)
ctTTCTCCTTTGAGGGGCAGCCACA‑AAA‑AAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGTCaa < 1:554084/93‑1 (MQ=255)
ctTTCTCCTTTGAGGGGCAGCCACA‑AAA‑AAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGTCaa > 2:554084/1‑93 (MQ=255)
tttCTCCTTTGAGGGGCAGCCACAAAAA‑AAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAg < 2:180625/131‑1 (MQ=255)
tttCTCCTTTGAGGGGCAGCCACAAAAA‑AAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAg > 1:180625/1‑131 (MQ=255)
tttCTCCTTTGAGGGGCAGCCACA‑AAA‑AAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGTTATg > 2:659528/1‑139 (MQ=255)
tttCTCCTTTGAGGGGCAGCCACA‑AAA‑AAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGTTATg > 2:396664/1‑139 (MQ=255)
ctcCTTTGAGGGGCAGCCACA‑AAA‑AAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGTTATGaaa > 1:551911/1‑139 (MQ=255)
cTTTGAGGGGCAGCCACA‑AAA‑AAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCa > 2:660758/1‑60 (MQ=255)
cTTTGAGGGGCAGCCACA‑AAA‑AAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCa < 1:660758/60‑1 (MQ=255)
gggCAGCCACA‑AAA‑AAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATa < 2:398260/99‑1 (MQ=255)
gggCAGCCACA‑AAA‑AAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATa > 1:398260/1‑99 (MQ=255)
ggCAGCCACA‑AAA‑AAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGTTATGAAAGAAGATTATTc < 2:551911/139‑1 (MQ=255)
gCCAC‑‑AAA‑AAAAATCGACGGATTATACCTCCTTTCTTCAAgg > 2:564164/1‑42 (MQ=255)
gCCAC‑‑AAA‑AAAAATCGACGGATTATACCTCCTTTCTTCAAgg < 1:564164/42‑1 (MQ=255)
|
TACCCACTTCGGAAGCGAGTTCGCGAAAGCGCTTGGTGCTGATATCTTGCTCACGCATCAGTCCCAGCTTGTGTTTGACGAGTGGGTGTTTGACTTCCACGATCTTCATACTCTTTCTCCTTTGAGGGGCAGCCAC‑‑AAA‑AAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGTTATGAAAGAAGATTATTC > NC_000913/2620764‑2621028
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
