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 |
|
A6 F21 I0 R2
|
370 |
72.1 |
3738297 |
91.5% |
3420541 |
62.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
775,547 |
C→T |
6.6% |
T390T (ACC→ACT) |
icd → |
isocitrate dehydrogenase, specific for NADP+ |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 775,547 | 0 | C | T | 6.6%
| 296.4
/ 7.8
| 91 | T390T (ACC→ACT) | icd | isocitrate dehydrogenase, specific for NADP+ |
| Reads supporting (aligned to +/- strand): ref base C (44/41); new base T (2/4); total (46/45) |
| Fisher's exact test for biased strand distribution p-value = 4.34e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.05e-01 |
GGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCG > minE/775479‑775617
|
ggTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCt < 1:1580269/70‑1 (MQ=255)
aCCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACtt > 1:2124198/1‑71 (MQ=255)
aCCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACtt > 1:2989566/1‑71 (MQ=255)
ccGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTc < 1:358606/71‑1 (MQ=255)
ccGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTc < 1:799059/71‑1 (MQ=255)
ccGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTc < 1:147683/71‑1 (MQ=255)
ccGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTc < 1:735793/71‑1 (MQ=255)
cGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTc < 1:2343621/70‑1 (MQ=255)
gAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTc > 1:1316175/1‑69 (MQ=255)
gAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGa < 1:299497/71‑1 (MQ=255)
aaGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAg > 1:2997238/1‑71 (MQ=255)
gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAg > 1:3392326/1‑66 (MQ=255)
cTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCt < 1:2268823/70‑1 (MQ=255)
cTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGc < 1:299933/62‑1 (MQ=255)
cTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatg > 1:1841684/1‑70 (MQ=255)
cTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatg > 1:2564693/1‑70 (MQ=255)
cTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatg > 1:383624/1‑70 (MQ=255)
cTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTga > 1:2883717/1‑68 (MQ=255)
cTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTga > 1:729976/1‑68 (MQ=255)
cTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTga > 1:111326/1‑68 (MQ=255)
ttAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCt < 1:2872751/65‑1 (MQ=255)
ttAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCt < 1:3462876/65‑1 (MQ=255)
tAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatggat > 1:2905505/1‑71 (MQ=255)
tAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatggat > 1:2401662/1‑71 (MQ=255)
tAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatggat > 1:97970/1‑71 (MQ=255)
aaTTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatggatg > 1:3383743/1‑71 (MQ=255)
tAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCt > 1:2685110/1‑57 (MQ=255)
tAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCt > 1:3363553/1‑57 (MQ=255)
aGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatggat > 1:3037691/1‑61 (MQ=255)
aGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAAc > 1:2725117/1‑71 (MQ=255)
aGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAAc > 1:2162471/1‑71 (MQ=255)
aGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAAc > 1:2653645/1‑71 (MQ=255)
ggTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatg < 1:455388/57‑1 (MQ=255)
ggTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatg < 1:389699/57‑1 (MQ=255)
ggTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatg < 1:2406373/57‑1 (MQ=255)
ggTATGGAAGGCGCAATCAACGCGAAAACCGCAACCTATGACTTCGAGCGTCTgatg < 1:810680/57‑1 (MQ=255)
gTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGctg < 1:2020763/71‑1 (MQ=255)
aTGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAActgct > 1:947763/1‑71 (MQ=255)
aTGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAActgct > 1:3227925/1‑71 (MQ=255)
aTGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAActgct > 1:257647/1‑71 (MQ=255)
aTGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAActgct > 1:462304/1‑71 (MQ=255)
aTGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAActgct > 1:1981864/1‑71 (MQ=255)
ggAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAActgct < 1:1197818/69‑1 (MQ=255)
gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACt > 1:926072/1‑37 (MQ=255)
gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACt > 1:2346304/1‑37 (MQ=255)
gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACt > 1:3463852/1‑37 (MQ=255)
gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACt > 1:2315324/1‑37 (MQ=255)
gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACt > 1:1256360/1‑37 (MQ=255)
gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGatggatgg < 1:865985/56‑1 (MQ=255)
gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGatggatgg < 1:850966/56‑1 (MQ=255)
gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGa < 1:27788/70‑1 (MQ=255)
gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGa < 1:2949979/70‑1 (MQ=255)
gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGa < 1:1088655/70‑1 (MQ=255)
gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGa < 1:1786808/70‑1 (MQ=255)
gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGa < 1:565330/70‑1 (MQ=255)
aGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAAt < 1:3096395/71‑1 (MQ=255)
gcgcAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGt < 1:831941/71‑1 (MQ=255)
gcgcAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGt < 1:1772844/71‑1 (MQ=255)
cgcAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGt > 1:2298059/1‑40 (MQ=255)
cgcAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGatggatgg > 1:1141043/1‑51 (MQ=255)
gcAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGt < 1:1362592/69‑1 (MQ=255)
gcAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGt < 1:3233730/69‑1 (MQ=255)
gcAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGt < 1:1983688/69‑1 (MQ=255)
gcAATCAACGCGAATACCGTAACCTATGACTTCGAGc < 1:1598405/37‑1 (MQ=255)
aaTCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGt < 1:1612837/67‑1 (MQ=255)
tCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGa > 1:1675238/1‑60 (MQ=25)
tCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGa > 1:3710811/1‑60 (MQ=25)
tCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCa < 1:1345910/68‑1 (MQ=255)
tCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCa < 1:3367238/68‑1 (MQ=255)
tCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCa < 1:2149317/68‑1 (MQ=255)
aaCGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatggat > 1:833945/1‑42 (MQ=255)
aaCGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatggat > 1:2577245/1‑42 (MQ=255)
aaCGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGtt > 1:1676387/1‑71 (MQ=255)
aaCGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGtt > 1:1790612/1‑71 (MQ=255)
cgcgAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTg < 1:3490477/71‑1 (MQ=255)
cgcgAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTg < 1:707240/71‑1 (MQ=255)
aaaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGATAAACTGCTGAAATGTTCAGAGTTTGGTg < 1:1192230/70‑1 (MQ=255)
aaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAcg > 1:998428/1‑71 (MQ=255)
aaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAcg > 1:2773391/1‑71 (MQ=255)
aaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAcg > 1:1701850/1‑71 (MQ=255)
tAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGatc < 1:1080245/71‑1 (MQ=255)
tAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGat > 1:698805/1‑70 (MQ=255)
tAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGat > 1:2500039/1‑70 (MQ=255)
tAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGat > 1:1718344/1‑70 (MQ=255)
tAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGat > 1:1284236/1‑70 (MQ=255)
aaCCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTg < 1:3143671/59‑1 (MQ=255)
aCCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGatca < 1:54397/70‑1 (MQ=255)
aCCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGatca < 1:3105006/70‑1 (MQ=255)
aCCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGatca < 1:1958724/70‑1 (MQ=255)
aCCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGatca < 1:1844675/70‑1 (MQ=255)
aCCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGatca < 1:1672524/70‑1 (MQ=255)
cTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGatcatc > 1:1050187/1‑70 (MQ=255)
cTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCg < 1:1942565/71‑1 (MQ=255)
|
GGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCG > minE/775479‑775617
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
