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 |
|
A7 F28 I1 R1
|
252 |
48.5 |
1661298 |
98.8% |
1641362 |
138.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
4,606,330 |
(G)8→9 |
noncoding (72/87 nt) |
leuQ ← |
tRNA‑Leu |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 4,606,322 | 1 | . | G | 93.8%
| 100.1
/ 0.0
| 32 | noncoding (80/87 nt) | leuQ | tRNA‑Leu |
| Reads supporting (aligned to +/- strand): ref base . (0/2); new base G (18/12); total (18/14) |
| Fisher's exact test for biased strand distribution p-value = 1.83e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.83e-01 |
TCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGA‑‑GGGGG‑GGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTA > NC_000913/4606195‑4606448
|
tCGTTTGGTGCGAGGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCTGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGA‑‑ggggg‑ggggac < 1:612108/140‑4 (MQ=255)
gTTTGGTGCGAGGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGA‑‑GGGGG‑GGG‑ACTTg < 2:177708/140‑1 (MQ=255)
ttGGTGCGAGGGGGGGGGGCCAGAACCACCAGGTCAGAAAGAACACTAGCACCTGAAGCTAGCGCGTATTCCAAGTCCGCCACCCTCGCCAAGTGCGAGAAATAAAATAGTGGTTTTTGGTGCGAG‑GGGGG‑GGG‑ACTTGa < 2:584720/140‑1 (MQ=255)
gTGCGAGGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGA‑‑ggggg‑gggg > 2:535849/1‑130 (MQ=255)
gTGCGAGGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGA‑‑ggggg‑gggg < 1:535849/131‑2 (MQ=255)
gcgagggggggggACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGAG‑GGGGG‑GGG‑ACTTGAAcccc > 1:55115/6‑140 (MQ=255)
gggggggggggACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGAG‑GGGGG‑GGG‑ACTTGAACCCCCa < 1:402660/137‑1 (MQ=255)
agggggggggACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGAG‑GGGGG‑GGG‑ACTTGAACCCCCAc < 2:82353/138‑1 (MQ=255)
agggggggggACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGAG‑GGGGG‑GGG‑ACTTGAACCCCCAc > 2:49347/3‑140 (MQ=255)
gggggggACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGAG‑GGGGG‑GGG‑ACTTGAACCCCCACGTc < 1:49347/140‑1 (MQ=255)
aCTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGAG‑GGGGG‑GGG‑ACTTGAACCCCCACGTCCGTAAgg < 2:55115/140‑1 (MQ=255)
tGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGAG‑GGGGG‑GGG‑ACTTGAACCCCCACGTCCGTAAGGaca > 1:620034/1‑140 (MQ=255)
tGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGAG‑GGGGG‑GGG‑ACTTGAACCCCCACGTCCGTAAGGaca > 2:166531/1‑140 (MQ=255)
cccccACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGAG‑GGGGG‑GGG‑ACTTGAACCCCCACGTCCGTAAGGACACTaa < 1:166531/140‑1 (MQ=255)
ccACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGAGGTTTTTGGTGCGA‑‑GGGGGAGGG‑CCTTGAACCCCCACGTCCGTAAAGTCATTAacac > 2:535496/1‑140 (MQ=25)
acacTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGAG‑GGGGG‑GGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGcgcg > 1:271053/1‑140 (MQ=255)
acacTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGAG‑GGGGG‑GGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGcgcg < 2:698706/140‑1 (MQ=255)
acacTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGAG‑GGGGG‑GGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGcgcg > 1:176293/1‑140 (MQ=255)
acacCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGAG‑GGGGG‑GGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTAcc > 1:102805/1‑140 (MQ=255)
ccTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGAG‑GGGGG‑GGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAAt > 2:659021/1‑140 (MQ=255)
cTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTACGAGCTATATCAACGTGGTTTTTGGTGCGAG‑GGGGG‑GGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAAtt > 2:490651/1‑140 (MQ=255)
tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGAG‑GGGGG‑GGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTc > 1:698706/1‑140 (MQ=255)
gAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATAAACGTGGTTTTTGGTGCGA‑‑GGGGG‑GGGCCCTTGAACCCCCACGTCCGTAAAGACACTAACACCTGAAGCTAGCGCGTCTGCCAATTca > 2:175844/1‑139 (MQ=25)
tAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGAG‑GGGGG‑GGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCAc < 2:102805/140‑1 (MQ=255)
tCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGAG‑GGGGG‑GGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCa > 2:150825/1‑140 (MQ=255)
tCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGAG‑GGGGG‑GGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCaa > 1:730316/1‑140 (MQ=255)
cACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGAG‑GGGGG‑GGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCtt > 1:241962/1‑140 (MQ=255)
cTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGAG‑GGGGG‑GGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTaaa > 1:127410/1‑140 (MQ=255)
cGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGAG‑GGGGG‑GGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAg < 2:271053/140‑1 (MQ=255)
gTGCGAGCAATATCAACGTGGTTTTTGGTGCGAG‑GGGGG‑GGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTaaa > 2:235587/1‑131 (MQ=255)
gTGCGAGCAATATCAACGTGGTTTTTGGTGCGAG‑GGGGG‑GGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTaaa < 1:235587/131‑1 (MQ=255)
gAGCAATATCAACGTGGTTTTTGGTGCGAGGGGGGG‑GGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTAc > 1:162587/1‑140 (MQ=255)
gCAATATCAACGTGGTTTTTGGTGCGA‑‑GGGGG‑GGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACg < 1:734044/140‑1 (MQ=255)
atCAACGTGGTTTTTGGTGCGAG‑GGGGG‑GGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAgg > 2:458915/1‑140 (MQ=255)
cAACGTGGTTTTTGGTGCGAG‑GGGGG‑GGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGgcg < 1:407093/140‑1 (MQ=255)
cAACGTGGTTTTTGGTGCGAG‑GGGGG‑GGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGgcg < 1:320491/140‑1 (MQ=255)
cGTGGTTTTTGGTGCGAG‑GGGGG‑GGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCAt > 1:699283/1‑140 (MQ=255)
gTTTTTGGTGCGAG‑GGGGG‑GGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTa > 2:794424/1‑140 (MQ=255)
|
TCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGA‑‑GGGGG‑GGG‑ACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTA > NC_000913/4606195‑4606448
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
