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 |
|
A13 F52 I1 R1
|
14 |
89.3 |
4518203 |
92.8% |
4192892 |
99.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
4,196,209 |
Δ1 bp |
intergenic (‑110/+123) |
thiC ← / ← rsd |
phosphomethylpyrimidine synthase/stationary phase protein, binds sigma 70 RNA polymerase subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 4,196,209 | 0 | T | . | 98.7%
| 369.8
/ ‑2.0
| 79 | intergenic (‑110/+123) | thiC/rsd | phosphomethylpyrimidine synthase/stationary phase protein, binds sigma 70 RNA polymerase subunit |
| Reads supporting (aligned to +/- strand): ref base T (1/0); new base . (32/46); total (33/46) |
| Fisher's exact test for biased strand distribution p-value = 4.18e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.20e-01 |
GTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTG > NC_000913/4196115‑4196301
|
gTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGc > 1:1545839/1‑100 (MQ=255)
ttAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGcc < 1:1360821/100‑1 (MQ=255)
ttAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGcc < 1:1397984/100‑1 (MQ=255)
tAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAgtc < 2:779339/99‑3 (MQ=255)
tAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCt > 1:1619570/1‑100 (MQ=255)
aGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGa < 2:698115/100‑1 (MQ=255)
tctgTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATc < 2:1601219/97‑1 (MQ=255)
cGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGGAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAg < 2:1586135/100‑1 (MQ=255)
gTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAga > 1:1601228/1‑99 (MQ=255)
ggCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGtt < 2:643647/100‑1 (MQ=255)
gTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCcgcg < 1:362016/100‑1 (MQ=255)
tCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCgg < 1:346785/100‑1 (MQ=255)
aGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATGAGGTTCCGCGGAt > 1:1314558/1‑100 (MQ=255)
aGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGAt > 1:1788199/1‑100 (MQ=255)
gacgacGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATc < 2:779524/100‑1 (MQ=255)
cgacgGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGTTTCCGCGGATccc > 2:1354216/1‑100 (MQ=255)
gacgGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCg < 2:1619561/100‑1 (MQ=255)
acgGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGa < 2:1435839/100‑1 (MQ=255)
acgGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGa > 2:361907/1‑100 (MQ=255)
acgGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGa < 1:922391/100‑1 (MQ=255)
acgGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGa < 1:1086222/100‑1 (MQ=255)
ggATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAAt < 2:1873108/100‑1 (MQ=255)
ggATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAAt > 2:902865/1‑100 (MQ=255)
ggATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAAt > 2:1002139/1‑100 (MQ=255)
gATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATa > 1:2167566/1‑100 (MQ=255)
aTGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATaa > 1:468267/1‑100 (MQ=255)
aaGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACg < 1:1905894/100‑1 (MQ=255)
aaGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACg > 2:1844690/1‑100 (MQ=255)
aaGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACg < 1:1174855/100‑1 (MQ=255)
aGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACgg > 1:1025739/1‑100 (MQ=255)
aGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACgg < 2:1593149/100‑1 (MQ=255)
aGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACgg < 1:844184/100‑1 (MQ=255)
cAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGtc > 1:1550634/1‑100 (MQ=255)
aaGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGtct > 1:2112617/1‑100 (MQ=255)
agagACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGtctc < 2:1545830/100‑1 (MQ=255)
gagaCGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCa < 2:1725212/100‑1 (MQ=255)
gagaCGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTGCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGtctc < 1:625416/99‑1 (MQ=255)
agaCGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAg < 1:1865547/100‑1 (MQ=255)
gATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCa > 2:2053730/1‑100 (MQ=255)
gATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAg < 2:211871/100‑1 (MQ=255)
gATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAg > 2:445603/1‑100 (MQ=255)
aTCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGt > 2:2248123/1‑100 (MQ=255)
aTCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGt > 2:2180044/1‑100 (MQ=255)
cgccgcAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTa < 2:1550625/100‑1 (MQ=255)
cgccgcAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTa < 1:1391427/100‑1 (MQ=255)
ggccctgcggCGAAGCGATAGCAGATTAACTATTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTaa > 1:1517688/9‑100 (MQ=255)
cccctgcggCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAg > 2:2084187/8‑100 (MQ=255)
gcAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGc < 1:2180059/100‑1 (MQ=255)
gcAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGc < 1:2248138/100‑1 (MQ=255)
aGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCAc < 2:1553591/100‑1 (MQ=255)
ggggCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACt > 1:2141191/1‑100 (MQ=255)
ggCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTcc > 2:1534238/1‑100 (MQ=255)
ggCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTcc > 2:690999/1‑100 (MQ=255)
cgatgcgatAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGa < 2:2229810/100‑1 (MQ=255)
cgatgcgatAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAACGCACTcc > 1:2147319/1‑98 (MQ=255)
cgatgcgatAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAAAGGTCTCAGCGAGTTAAGGCACTACGa > 1:1871556/1‑100 (MQ=255)
gcgatAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAg < 2:2182636/100‑1 (MQ=255)
gcgatAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAg > 1:1444885/1‑100 (MQ=255)
gcgatAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCACCCAGTTAAGGCACTCCGACAAg < 2:1314549/100‑1 (MQ=255)
gatAGCAGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGaa < 1:1479492/100‑1 (MQ=255)
aGATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGc > 2:2005021/1‑100 (MQ=255)
gATTAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGcc > 2:1467272/1‑100 (MQ=255)
tAACTCTTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCg < 1:304415/100‑1 (MQ=255)
ctctTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCaa > 2:2128596/1‑100 (MQ=255)
ctTGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAAt < 2:1025732/100‑1 (MQ=255)
tGTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATgg > 1:421162/1‑100 (MQ=255)
gTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATggg < 1:445606/100‑1 (MQ=255)
gTTCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATggg < 2:1444876/100‑1 (MQ=255)
ttCCCTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATgggg < 1:1534247/100‑1 (MQ=255)
ctccTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGc < 1:2183707/98‑1 (MQ=255)
ccTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCag > 2:2183692/1‑99 (MQ=255)
ccTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCAt > 2:1661097/1‑100 (MQ=255)
cTTCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCAtt < 1:1026648/100‑1 (MQ=255)
ttCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTg < 2:1993103/100‑1 (MQ=255)
ttCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTg < 2:1683903/100‑1 (MQ=255)
ttCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTg < 2:1682985/100‑1 (MQ=255)
ttCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTg < 2:1211403/100‑1 (MQ=255)
ttCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTg < 1:1844702/100‑1 (MQ=255)
ttCGCAGG‑ATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCGCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTg < 2:770615/100‑1 (MQ=255)
|
GTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTG > NC_000913/4196115‑4196301
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
