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 |
|
A0 F0 I1 R1
|
16 |
48.9 |
1703346 |
91.6% |
1560264 |
146.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913_3_pae_tpiA |
3,560,455 |
+G |
intergenic (‑2/+1) |
glpR ← / ← glpR |
pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913_3_pae_tpiA | 3,560,455 | 1 | . | G | 95.8%
| 148.0
/ ‑1.3
| 49 | intergenic (‑2/+1) | glpR/glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| Reads supporting (aligned to +/- strand): ref base . (0/2); new base G (19/27); total (20/29) |
| Fisher's exact test for biased strand distribution p-value = 5.12e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCC‑ACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGC‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTT > NC_000913_3_pae_tpiA/3560308‑3560592
|
ccGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCC‑ACGGCGTGTTAACCGAACTGGGAGGCAGCGCCGCACCGCCATGA‑T‑GGcg > 1:263221/1‑148 (MQ=255)
cGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGCCTGGGTGGCCTTGCGATCGTGCC‑ACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATc < 1:226559/149‑1 (MQ=255)
tAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCGCCAGCCTCTT‑TCTGAATTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAgg > 1:799441/1‑149 (MQ=255)
aaCAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTCTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCC‑ACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGtt < 1:733130/149‑1 (MQ=255)
aGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCC‑ACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTg < 1:265699/149‑1 (MQ=255)
tCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCC‑ACGGCGTGTTAACCGAACTGGAAGGCAGCACCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTcc < 1:531683/149‑1 (MQ=255)
aGCCATTGGGGATTTGCTCTGCCACTTTGAGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCC‑ACGGCGTGTTAACCGTACTGGAAGGGAGCGCCGCACCGCCGTGA‑T‑GGCGCCGGGTCAGGTTTTGCTCGGcc > 2:609989/1‑149 (MQ=255)
aGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCC‑ACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGcc > 1:512792/1‑149 (MQ=255)
gCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTCTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCC‑ACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCa > 1:492161/1‑149 (MQ=255)
ccATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCC‑ACGGCGTGTTAACCGAACTGCAAGGTAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAg < 1:379772/149‑1 (MQ=255)
cATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCC‑ACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGc > 1:490432/1‑149 (MQ=255)
gggATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCC‑ACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGTCAGCTCAtt < 2:528147/149‑1 (MQ=255)
gggATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCC‑ACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCAtt < 1:91015/149‑1 (MQ=255)
gATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCC‑ACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGa < 1:802159/149‑1 (MQ=255)
gCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCC‑ACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTcg > 1:851406/1‑149 (MQ=255)
cTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGTCTGGGGATCGTGCG‑ACGGCGTGTTAGCCGAACTGGTTTGCAGCGCCGCACCGCCTTGA‑T‑GGCTCAGGGTCAGGTTTTCCTCCTGCATCTCATAGAGGTctc > 2:349162/1‑147 (MQ=255)
tCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCC‑ACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTcgcg > 1:762791/1‑149 (MQ=255)
cTTGGCGGGCGAGGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCC‑ACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATa < 1:7582/149‑1 (MQ=255)
gCGATGCGCTCTGTTTCTTCGGGCTGGGTGGCTTTGTGATCGTGCC‑GTGGCTTGTTAACCGCACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCTAGCTCATTGAGGTCGCGGCGAATAGTCTGCgg < 2:404949/149‑1 (MQ=255)
ctTTTTCTTGGGTCTGGGTGGCCTTGCGATCGTGCC‑ACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGgag < 1:362317/149‑1 (MQ=255)
ttttCTTCGGTCTGGGTGGCCTTGCGATCGTGCC‑ACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGaa < 1:741979/149‑1 (MQ=255)
ttcttcGGGGCGGTTGTCCTTGCGGTTGTGGC‑GCGGCTTGTTAACCGTACTCGATGGCAGTGCCGACCCCCGATGA‑T‑TGCGCAGGATCAGGTTTTGACCCGCCAGCGCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAAt < 2:214606/149‑1 (MQ=255)
ctcttcGGTCTGGGTGGCGTTGCGATCGTGCC‑ACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAAt < 2:113538/148‑1 (MQ=255)
ttcGGTCTGGGTGGCCTTGCGCTCGTGCC‑ACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAACGct > 2:363979/1‑149 (MQ=255)
cGGTCTGGGTGGCCTTGCGATCGTGCC‑ACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGctct < 1:133123/149‑1 (MQ=255)
tCTGGGTGGCCTTGCGATCGTGCC‑ACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGct < 1:459575/144‑1 (MQ=255)
tCTGGGTGGCCTTGCGATCGTGCC‑ACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGct > 2:459575/1‑144 (MQ=255)
tCTGGGTGGCCTTGCGATCGTGCC‑ACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTAcc > 2:466878/1‑149 (MQ=255)
ggggTGGCCTGGCGATCGTGCC‑ACGGCGTGCTAACCGACCTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAg < 1:449374/148‑1 (MQ=255)
ccTTGCGATCGTGCC‑ACGGCGTGTTAACCGAACTTGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCg < 1:143095/149‑1 (MQ=255)
cTTGCGATCGTGCC‑ACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCgg > 1:648206/1‑149 (MQ=255)
cTTGCGATCGTGCC‑ACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCgg > 1:484269/1‑149 (MQ=255)
cTTGCGATCGTGCC‑ACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCgg > 1:231005/1‑149 (MQ=255)
ttGCGATCGTGCC‑ACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGt > 1:626056/1‑149 (MQ=255)
aTCGTGCC‑ACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGa > 1:695018/1‑149 (MQ=255)
tGCC‑ACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATa > 1:46440/1‑149 (MQ=255)
ggCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCctg < 2:851406/149‑1 (MQ=255)
gCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCctgc > 1:258962/1‑149 (MQ=255)
ggtgtTACGCGAACGGGAGGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCATGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCctgct < 2:58967/148‑1 (MQ=255)
agtgtTAACTGAACTGGGTGGCAGCGCCGCACCGCCATGA‑T‑GTCGGAGGATCAGGTTTGGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCctgct < 2:486226/148‑1 (MQ=255)
ttAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGttt < 1:741985/149‑1 (MQ=255)
aaCTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGt < 2:231005/149‑1 (MQ=255)
aaCTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGGTTTGCTCCGCCAGCCCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACCGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTCCCGTTTACCCAGt > 2:665368/1‑149 (MQ=255)
acgggAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGtt < 1:391172/146‑1 (MQ=255)
aCTGGAATGCAGCGACGCACCGCCATGA‑T‑GGCGCAGTATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCCGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGtt < 2:304027/149‑1 (MQ=255)
aCTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGtt < 1:352048/149‑1 (MQ=255)
cTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGCATGAGAAATGTTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTc < 1:378525/149‑1 (MQ=255)
ggaGGCAGCGGCGCACCGTCAGGAGG‑GGG‑CGGGATCAGGTTTTGCTTGGCCAGCTCATTGAGGGCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGat < 2:195934/147‑1 (MQ=255)
aGCGCCGCACCGCCATGA‑T‑GGCGCAGGATCAGGTTTTGCTCCGCCAGCTAATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGACTTTCGGTAATGAAATCACCATCCTGTTAGACCAGTTCGATAATAcc > 1:113013/1‑149 (MQ=255)
gCCATGA‑TGGGC‑GAGGAGGAGGGTTTGCTCCGCCAGCTCGTTGAGTGCGCGGCGAATGGTCTGCGGGCTGACGGACAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTGTCTAGTTCGATAATACCGTTGTGACGtt < 2:692665/149‑1 (MQ=255)
|
CCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCC‑ACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGA‑T‑GGC‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTT > NC_000913_3_pae_tpiA/3560308‑3560592
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
