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 |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,119,719 |
G→T |
49.1% |
intergenic (‑8/+239) |
ydiV ← / ← nlpC |
conserved hypothetical protein/predicted lipoprotein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,119,719 | 0 | G | T | 49.1%
| 6.1
/ 64.0
| 59 | intergenic (‑8/+239) | ydiV/nlpC | conserved hypothetical protein/predicted lipoprotein |
| Reads supporting (aligned to +/- strand): ref base G (20/10); new base T (16/13); total (36/23) |
| Fisher's exact test for biased strand distribution p-value = 4.30e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.45e-01 |
GTCTCTTATCGGCAGGAAATAGCAATCAGAATGATAAAGATTCTCCAAAAAAATCTTCATGGTAACCGTCCCTCTCGAAGGATGTTTTTCAGTATCCGGCTAAAAGGGATGAGGCCATAAGACATAACAAT > minE/1119652‑1119782
|
gTCTCTTATCGGCAGGAAATAGCAATCAGAATGATAAAGATTCTCCAAAAAAATCTTCATGGTAACCGt < 1:1917359/69‑1 (MQ=255)
tctTATCGGCAGGAAATAGCAATCAGAATGATAAAGATTCTCCAAAAAAATCTTCATGGTAACCGTccc < 1:542286/69‑1 (MQ=255)
aTAGCAATCAGAATGATAAAGATTCTCCAAAAAAATCTTCATGGTAACCGTCCCTCTCGAAGGATGttt < 1:3326406/69‑1 (MQ=255)
aTAGCAATCAGAATGATAAAGATTCTCCAAAAAAATCTTCATGGTAACCGTCCCTCTCGAAGGATGttt < 1:3432435/69‑1 (MQ=255)
aTAGCAATCAGAATGATAAAGATTCTCCAAAAAAATCTTCATGGTAACCGTCCCTCTCGAAGGATGttt < 1:1172216/69‑1 (MQ=255)
aGCAATCAGAATGATAAAGATTCTCCAAAAAAATCTTCATGGTAACCGTCCCTCTCGAAgg > 1:1030910/1‑61 (MQ=255)
aGCAATCAGAATGATAAAGATTCTCCAAAAAAATCTTCATGGTAACCGTCCCTCTCGAAGGATGttt > 1:2762627/1‑67 (MQ=255)
aGCAATCAGAATGATAAAGATTCTCCAAAAAAATCTTCATGGTAACCGTCCCTCTCGAAGGATGttt > 1:1957334/1‑67 (MQ=255)
aGCAATCAGAATGATAAAGATTCTCCAAAAAAATCTTCATGGTAACCGTCCCTCTCGAAGGATGttt > 1:405057/1‑67 (MQ=255)
aGCAATCAGAATGATAAAGATTCTCCAAAAAAATCTTCATGGTAACCGTCCCTCTCGAAGGATGttt > 1:3025973/1‑67 (MQ=255)
agaaTCAGAATGATAAAGATTCTCCAAAAAAATCTTCATGGTAACCGTCCCTCTCGAAGGATGTTTTTc > 1:3255867/3‑69 (MQ=255)
aGAATGATAAAGATTCTCCAAAAAAATCTTCATGGTAACCGTCCCtctc > 1:3226433/1‑49 (MQ=255)
aGAATGATAAAGATTCTCCAAAAAAATCTTCATGGTAACCGTCCCTCTCGAAGGATGTTTTTc > 1:2527773/1‑63 (MQ=255)
aGAATGATAAAGATTCTCCAAAAAAATCTTCATGGTAACCGTCCCTCTCGAAGGATGTTTTTc > 1:507977/1‑63 (MQ=255)
aGAATGATAAAGATTCTCCAAAAAAATCTTCATGGTAACCGTCCCTCTCGAAGGATGTTTTTc > 1:3044607/1‑63 (MQ=255)
aGAATGATAAAGATTCTCCAAAAAAATCTTCATGGTAACCGTCCCTCTCGAAGGATGTTTTTc > 1:2291412/1‑63 (MQ=255)
aTAAAGATTCTCCAAAAAAATCTTCATGGTAACCGTCCCTCTCGAAGGATGTTTTTCAGTATCCGGCt > 1:1585763/1‑68 (MQ=255)
aTAAAGATTCTCCAAAAAAATCTTCATGGTAACCGTCCCTCTCGAAGGATGTTTTTCAGTATCCGGCt > 1:1586536/1‑68 (MQ=255)
aTAAAGATTCTCCAAAAAAATCTTCATGGTAACCGTCCCTCTCGAAGGATGTTTTTCAGTATCCGGCt > 1:1587521/1‑68 (MQ=255)
aTAAAGATTCTCCAAAAAAATCTTCATGGTAACCGTCCCTCTCGAAGGATGTTTTTCAGTATCCGGCt > 1:1373882/1‑68 (MQ=255)
aTAAAGATTCTCCAAAAAAATCTTCATGGTAACCGTCCCTCTCGAAGGATGTTTTTCAGTATCCGGCt > 1:356158/1‑68 (MQ=255)
aTAAAGATTCTCCAAAAAAATCTTCATGGTAACCGTCCCTCTCGAAGGATGTTTTTCAGTATCCGGCt > 1:622277/1‑68 (MQ=255)
aTAAAGATTCTCCAAAAAAATCTTCATGGTAACCGTCCCTCTCGAAGGATGTTTTTCAGTATCCGGCt > 1:1211279/1‑68 (MQ=255)
aTAAAGATTCTCCAAAAAAATCTTCATGGTAACCGTCCCTCTCGAAGGATGTTTTTCAGTATCCGGCt > 1:11259/1‑68 (MQ=255)
gATTCTCCAAAAAAATCTTCATGGTAACCTTCCCTCTCGAAgg > 1:149140/1‑43 (MQ=255)
gATTCTCCAAAAAAATCTTCATGGTAACCTTCCCTCTCGAAGGATGTTTTTCAGTATcc > 1:932117/1‑59 (MQ=255)
gATTCTCCAAAAAAATCTTCATGGTAACCTTCCCTCTCGAAGGATGTTTTTCAGTATcc > 1:2757031/1‑59 (MQ=255)
gATTCTCCAAAAAAATCTTCATGGTAACCTTCCCTCTCGAAGGATGTTTTTCAGTATcc > 1:3272839/1‑59 (MQ=255)
gATTCTCCAAAAAAATCTTCATGGTAACCTTCCCTCTCGAAGGATGTTTTTCAGTATcc > 1:3299109/1‑59 (MQ=255)
gATTCTCCAAAAAAATCTTCATGGTAACCTTCCCTCTCGAAGGATGTTTTTCAGTATcc > 1:44068/1‑59 (MQ=255)
gATTCTCCAAAAAAATCTTCATGGTAACCTTCCCTCTCGAAGGATGTTTTTCAGTATcc > 1:451389/1‑59 (MQ=255)
gATTCTCCAAAAAAATCTTCATGGTAACCTTCCCTCTCGAAGGATGTTTTTCAGTATcc > 1:805037/1‑59 (MQ=255)
gATTCTCCAAAAAAATCTTCATGGTAACCTTCCCTCTCGAAGGATGTTTTTCAGTATcc > 1:1019568/1‑59 (MQ=255)
gATTCTCCAAAAAAATCTTCATGGTAACCTTCCCTCTCGAAGGATGTTTTTCAGTATcc > 1:1121215/1‑59 (MQ=255)
gATTCTCCAAAAAAATCTTCATGGTAACCTTCCCTCTCGAAGGATGTTTTTCAGTATcc > 1:1740102/1‑59 (MQ=255)
gATTCTCCAAAAAAATCTTCATGGTAACCTTCCCTCTCGAAGGATGTTTTTCAGTATcc > 1:1194786/1‑59 (MQ=255)
gATTCTCCAAAAAAATCTTCATGGTAACCTTCCCTCTCGAAGGATGTTTTTCAGTATcc > 1:2660586/1‑59 (MQ=255)
gATTCTCCAAAAAAATCTTCATGGTAACCTTCCCTCTCGAAGGATGTTTTTCAGTATcc > 1:2390051/1‑59 (MQ=255)
gATTCTCCAAAAAAATCTTCATGGTAACCTTCCCTCTCGAAGGATGTTTTTCAGTATcc > 1:2362275/1‑59 (MQ=255)
gATTCTCCAAAAAAATCTTCATGGTAACCTTCCCTCTCGAAGGATGTTTTTCAGTATcc > 1:2186295/1‑59 (MQ=255)
ccAAAAAAATCTTCATGGTAACCGTCCCTCTCGAAGGATGTTTTTCAGTATCCGGCTAAAAGGGATGa < 1:2791961/68‑1 (MQ=255)
aaaaaaTCTTCATGGTAACCGTCCCTCTCGAAGGATGTTTTTCAGTATCCGGCTAAAAGGGATGAGGc < 1:2354370/68‑1 (MQ=255)
aaaaaaTCTTCATGGTAACCGTCCCTCTCGAAGGATGTTTTTCAGTATCCGGCTAAAAGGGATGAGGc < 1:2008039/68‑1 (MQ=255)
aaaaaTCTTCATGGTAACCGTCCCTCTCGAAGGATGTTTTTCAGTATCCGGCTAAAAGGGATGAGGc < 1:730350/67‑1 (MQ=255)
aaaaTCTTCATGGTAACCTTCCCTCTCGAAGGATGTTTTTCAGTATCCGGCTAAAAGGGATGAGGCCAt < 1:1822101/69‑1 (MQ=255)
aaaaTCTTCATGGTAACCTTCCCTCTCGAAGGATGTTTTTCAGTATCCGGCTAAAAGGGATGAGGCCAt < 1:1248383/69‑1 (MQ=255)
aaaaTCTTCATGGTAACCTTCCCTCTCGAAGGATGTTTTTCAGTATCCGGCTAAAAGGGATGAGGCCAt < 1:752463/69‑1 (MQ=255)
aaaaTCTTCATGGTAACCTTCCCTCTCGAAGGATGTTTTTCAGTATCCGGCTAAAAGGGATGAGGCCAt < 1:829798/69‑1 (MQ=255)
aaaaTCTTCATGGTAACCTTCCCTCTCGAAGGATGTTTTTCAGTATCCGGCTAAAAGGGATGAGGCCAt < 1:575171/69‑1 (MQ=255)
aaaaTCTTCATGGTAACCTTCCCTCTCGAAGGATGTTTTTCAGTATCCGGCTAAAAGGGATGAGGCCAt < 1:546378/69‑1 (MQ=255)
aaaaTCTTCATGGTAACCTTCCCTCTCGAAGGATGTTTTTCAGTATCCGGCTAAAAGGGATGAGGCCAt < 1:1382285/69‑1 (MQ=255)
aaaaTCTTCATGGTAACCTTCCCTCTCGAAGGATGTTTTTCAGTATCCGGCTAAAAGGGATGAGGCCAt < 1:1447192/69‑1 (MQ=255)
aaaaTCTTCATGGTAACCTTCCCTCTCGAAGGATGTTTTTCAGTATCCGGCTAAAAGGGATGAGGCCAt < 1:163076/69‑1 (MQ=255)
aaaaTCTTCATGGTAACCTTCCCTCTCGAAGGATGTTTTTCAGTATCCGGCTAAAAGGGATGAGGCCAt < 1:1855903/69‑1 (MQ=255)
aaaaTCTTCATGGTAACCTTCCCTCTCGAAGGATGTTTTTCAGTATCCGGCTAAAAGGGATGAGGCCAt < 1:2188837/69‑1 (MQ=255)
aaaaTCTTCATGGTAACCTTCCCTCTCGAAGGATGTTTTTCAGTATCCGGCTAAAAGGGATGAGGCCAt < 1:2462523/69‑1 (MQ=255)
aaaaTCTTCATGGTAACCTTCCCTCTCGAAGGATGTTTTTCAGTATCCGGCTAAAAGGGATGAGGCCAt < 1:2471525/69‑1 (MQ=255)
ttCATGGTAACCGTCCCTCTCGAAGGATGTTTTTCAGTATCCGGCTAAAAGGGATGAGGCCATAAGAc > 1:3177040/1‑68 (MQ=255)
aaCCGTCCCTCTCGAAGGATGTTTTTCAGTATCCGGCTAAAAGGGATGAGGCCATAAGACATAACAAt < 1:2613682/68‑1 (MQ=255)
|
GTCTCTTATCGGCAGGAAATAGCAATCAGAATGATAAAGATTCTCCAAAAAAATCTTCATGGTAACCGTCCCTCTCGAAGGATGTTTTTCAGTATCCGGCTAAAAGGGATGAGGCCATAAGACATAACAAT > minE/1119652‑1119782
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
