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 |
|
A1 F999 I1 R1
|
225 |
156.4 |
11709729 |
83.8% |
9812752 |
75.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
3,873,627 |
Δ1 bp |
coding (506/672 nt) |
yidX → |
putative replicase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 3,873,625 | 0 | G | . | 99.1%
| 515.0
/ ‑2.2
| 117 | coding (504/672 nt) | yidX | putative replicase |
| Reads supporting (aligned to +/- strand): ref base G (0/1); new base . (72/42); total (72/45) |
| Fisher's exact test for biased strand distribution p-value = 3.74e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
Only 100 of 127 total aligned reads displayed.
TTACTCAAAGGTGATGGCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCCGGGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACTGCACCGCTGCAATTTC > NC_000913/3873550‑3873696
|
ttACTCAAAGGTGATGGCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCCg > 2:2628729/1‑76 (MQ=255)
tACTCAAAGCTGATGGCGTTCTACCATCCATCTAAAGTGCGCTTTTATGAATACTCTTCCCCCAGAGCCACTCCgg < 2:5062109/76‑1 (MQ=255)
cTCAAAGGTGATGGCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCCggat > 2:2526729/1‑74 (MQ=255)
cTCAAAGGTGATGGCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCCggat < 2:5799413/76‑3 (MQ=255)
cTCAAAGGTGATGGCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCCggat > 2:5610885/1‑74 (MQ=255)
tCAAAGGTGATGGCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCCggatg > 1:1032009/1‑73 (MQ=255)
tCAAAGGTGATGGCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCCggatg > 2:5051606/1‑73 (MQ=255)
tCAAAGGTGATGGCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATGCACCCAGAGGCATTCCggatg > 2:5104145/1‑73 (MQ=255)
aaaGGTGATGGCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGgt > 1:369252/1‑76 (MQ=255)
aaGGTGATGGCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGgtg > 1:1795695/1‑76 (MQ=255)
aGGTGATGGCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGgtgt > 1:4140190/1‑76 (MQ=255)
aGGTGATGGCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGgtgt > 1:2801963/1‑76 (MQ=255)
ggTGATGGCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGtt > 2:5638731/1‑76 (MQ=255)
ggTGATGGCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGtt > 2:3273154/1‑76 (MQ=255)
gTGATGGCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGttt < 2:4761740/76‑1 (MQ=255)
tGATGGCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTc < 2:3955707/76‑1 (MQ=255)
tGATGGCATTCTACCATCCATTTAAAGTGCGATTTGATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTc < 1:1674353/76‑1 (MQ=255)
gATGGCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTcc < 1:4470310/76‑1 (MQ=255)
gATGGCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTcc > 2:2733408/1‑76 (MQ=255)
ggCGTTCTACCATCCCTTTAAAGTGCGCTTTTATGAATCCTATTCACCCAGAGGCATTCC‑TGATTGTGTTTCCgca > 1:2196250/1‑76 (MQ=255)
ggCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCgca > 1:2153480/1‑76 (MQ=255)
gCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCgcag < 2:447450/76‑1 (MQ=255)
gCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCgcag > 1:2445388/1‑76 (MQ=255)
cGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCgcagc < 2:4669173/76‑1 (MQ=255)
cGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCgcagc > 1:2428917/1‑76 (MQ=255)
gTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCgcagca < 2:3241132/76‑1 (MQ=255)
gTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCgcagca > 2:873595/1‑76 (MQ=255)
ttCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCAt < 1:2510910/76‑1 (MQ=255)
ttCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCAt > 2:656074/1‑76 (MQ=255)
ttCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCAt < 2:2031135/76‑1 (MQ=255)
cTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTa > 2:1649954/1‑76 (MQ=255)
cTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTa < 1:2640576/76‑1 (MQ=255)
aCCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACt < 2:3600594/76‑1 (MQ=255)
ccatccatTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTg > 2:3994178/1‑76 (MQ=255)
catccatTTAAAGTGCGATTTTATGTATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGc > 2:1111144/1‑76 (MQ=255)
catccatTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGc > 1:403645/1‑76 (MQ=255)
tccatTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCACTACTGCCa > 1:5317877/1‑76 (MQ=255)
ccatTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAg > 2:2053009/1‑76 (MQ=255)
ccatTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAg > 1:2782666/1‑76 (MQ=255)
ccatTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAg < 1:342084/76‑1 (MQ=255)
ccatTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAg > 2:1404459/1‑76 (MQ=255)
catTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGt > 2:2439166/1‑76 (MQ=255)
catTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGt < 2:2741433/76‑1 (MQ=255)
atTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTg > 2:1027122/1‑76 (MQ=255)
atTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTg > 2:5766014/1‑76 (MQ=255)
tttAAAGTGGGATTTTATGAATACTATTCACCCAGAGGCATT‑CAGGATGGGGTTTCCGCAGCATTACTGCCAGTGa < 2:420042/76‑1 (MQ=255)
nttAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGa > 1:1939114/2‑76 (MQ=255)
ttAAAGTGCGATTTTATGAATATTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGAc > 2:4235851/1‑76 (MQ=255)
ttAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGAc > 2:361691/1‑76 (MQ=255)
ttAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGAc > 1:1273184/1‑76 (MQ=255)
aaaGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTg > 2:1373955/1‑76 (MQ=255)
aaGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGt < 2:3441432/76‑1 (MQ=255)
aGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGtt > 1:960075/1‑76 (MQ=255)
gTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTa > 2:2707751/1‑76 (MQ=255)
gTGCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTa > 2:622693/1‑76 (MQ=255)
ggCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTAc < 2:1903011/75‑1 (MQ=255)
gCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACg > 2:1553408/1‑76 (MQ=255)
gCGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACg > 1:5176703/1‑76 (MQ=255)
cGATTTTCTGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGc > 2:3556800/1‑76 (MQ=255)
cGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGc > 1:881242/1‑76 (MQ=255)
cGATTTTATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGc > 2:5625071/1‑76 (MQ=255)
tttttATGAGTCCTATTCGCCGAGAGGCATTCC‑GAATGGTGTTTCCGCACCATTACTGCCAGTGACTGTTACGCTg < 1:5667220/75‑1 (MQ=255)
ttttATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTgg < 2:415260/76‑1 (MQ=255)
ttttATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTgg > 2:1770/1‑76 (MQ=255)
tttATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGa > 2:2048821/1‑76 (MQ=255)
tttATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGa > 1:1875489/1‑76 (MQ=255)
tttATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGAACGTTACGCTGGa > 2:5274683/1‑76 (MQ=255)
tttATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCCCAGCATTACTGCCAGTGACTGTTACGCTggc > 2:899007/1‑75 (MQ=255)
ttATGAATATTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGAc < 1:4235852/76‑1 (MQ=255)
ttATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGAc < 1:1010495/76‑1 (MQ=255)
ttATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGAc > 1:3278976/1‑76 (MQ=255)
tATGAATACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGAca > 2:3968493/1‑76 (MQ=255)
aaTACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGAcctcat > 2:5748158/1‑76 (MQ=255)
atccTATCCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCAtt < 1:13634/73‑1 (MQ=255)
aTACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCAtt < 1:1572884/76‑1 (MQ=255)
tACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTa > 2:5713539/1‑76 (MQ=255)
tACTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTa > 2:546204/1‑76 (MQ=255)
aCTATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTAc > 1:68244/1‑76 (MQ=255)
cTAGTCCCCCAGAGGCATTCCGGG‑TGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACt < 2:5591430/76‑1 (MQ=255)
tATTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACTg < 1:3817337/76‑1 (MQ=255)
aTTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACTGc < 1:656074/76‑1 (MQ=255)
aTTCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACTGc > 1:1741270/1‑76 (MQ=255)
ttCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACTGCa > 1:4673337/1‑76 (MQ=255)
tCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACTGCAc < 2:2445388/76‑1 (MQ=255)
tCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACTGCAc > 1:2107380/1‑76 (MQ=255)
tCACCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTAATGCAc > 1:5542833/1‑76 (MQ=255)
cACCCAGAGGCATTCC‑GTATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACTGCAcc < 1:4995732/76‑1 (MQ=255)
aCCCAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACTGCACCg < 2:3452068/76‑1 (MQ=255)
cccAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACTGCACCGc > 1:4810644/1‑76 (MQ=255)
ccAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACTGCACCGCt > 2:1262265/1‑76 (MQ=255)
ccAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACTGCACCGCt > 2:3738085/1‑76 (MQ=255)
cAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACCTCATTACTGCACCCCTg > 2:5686785/1‑76 (MQ=255)
cAGAGGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACTGCACCGCTg > 2:4264629/1‑76 (MQ=255)
agagGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACTGCACCGCTGc > 1:1689137/1‑76 (MQ=255)
agagGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACTGCACCGCTGc < 1:4414206/76‑1 (MQ=255)
agagGCATTCC‑GGATGGTGTTTCCGCAGCATCACTGCCAGTGACTGTTACGCTGGACATCATTACTGCACCGCTGc < 1:1770/76‑1 (MQ=255)
agGCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACTGCACCGCTGCaa > 2:4508590/1‑76 (MQ=255)
ggCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACTGCACCGCTGCAAt > 1:3499279/1‑76 (MQ=255)
gCATTCC‑GGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACTGCACCGCTGCAAtt < 1:4141670/76‑1 (MQ=255)
catCCCGGATGGTGTTTCCCCAGCATTCCTGCCAGTGACTGTTACGCTGGACATCATTACTGCACCGCTGCAAttt < 1:899007/74‑1 (MQ=255)
|
TTACTCAAAGGTGATGGCGTTCTACCATCCATTTAAAGTGCGATTTTATGAATACTATTCACCCAGAGGCATTCCGGGATGGTGTTTCCGCAGCATTACTGCCAGTGACTGTTACGCTGGACATCATTACTGCACCGCTGCAATTTC > NC_000913/3873550‑3873696
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
