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 R1
|
2169 |
63.0 |
3952800 |
76.2% |
3012033 |
62.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
975,257:1 |
+A |
43.5% |
coding (358/375 nt) |
ydeH ← |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 975,257 | 1 | . | A | 43.5%
| 6.9
/ 156.9
| 69 | coding (358/375 nt) | ydeH | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base . (15/24); new base A (18/12); total (33/36) |
| Fisher's exact test for biased strand distribution p-value = 9.27e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01 |
GAACCCGACGACCCGGCAATCCCGTCAAAACATCCATATTGCTACGGATCGTCAGCAAATAAATTTTGT‑ATCGGTTAATGCCGCAGTAAAAGAAAGCAACCCCTCCTGAAAGGCGTCGAAATGCGCGTCCTGCCAGTGA > minE/975189‑975327
|
gAACCCGACGACCCGGCAATCCCGTCAAAACATCCATATTGCTACGGATCGTCAGCAAATAAATTTTGT‑At > 1:3878904/1‑71 (MQ=255)
gAACCCGACGACCCGGCAATCCCGTCAAAACATCCATATTGCTACGGATCGTCAGCAAATAAATTTTGT‑At > 1:3601563/1‑71 (MQ=255)
ccGACGACCCGGCAATCCCGTCAAAACATCCATATTGCTACGGATCGTCAGCAAATAAATTTTGT‑ATCGGt > 1:2437555/1‑71 (MQ=255)
acgacCCGGCAATCCCGTCAAAACATCCATATTGCTACGGATCGTCAGCAAATAAATTTTGT‑ATCGGTTaa < 1:3443201/71‑1 (MQ=255)
acgacCCGGCAATCCCGTCAAAACATCCATATTGCTACGGATCGTCAGCAAATAAATTTTGT‑ATCGGTTaa < 1:1912099/71‑1 (MQ=255)
cgacCCGGCAATCCCGTCAAAACATCCATATTGCTACGGATCGTCAGCAAATAAATTTTGT‑ATCGGTTAAt > 1:2389228/1‑71 (MQ=255)
cgacCCGGCAATCCCGTCAAAACATCCATATTGCTACGGATCGTCAGCAAATAAATTTTGT‑ATCGGTTAAt > 1:130917/1‑71 (MQ=255)
acCCGGCAATCCCGTCAAAACATCCATATTGCTACGGATCGTCAGCAAATAAATTTTGT‑ATCGGTTAATGc < 1:1407503/71‑1 (MQ=255)
cccGGCAATCCCGTCAAAACATCCATATTGCTACGGATCGTCAGCAAATAAATTTTGT‑ATCGGTTAATGcc > 1:3646093/1‑71 (MQ=255)
cGGCAATCCCGTCAAAACATCCATATTGCTACGGATCGTCAGCAAATAAATTTTGTAATCGGTTAATGCCg > 1:1404873/1‑71 (MQ=255)
cGGCAATCCCGTCAAAACATCCATATTGCTACGGATCGTCAGCAAATAAATTTTGT‑ATCGGTTAATGCCg > 1:788586/1‑70 (MQ=255)
ggCAATCCCGTCAAAACATCCATATTGCTACGGATCGTCAGCAAATAAATTTTGTAATCGGTTAATGCCg > 1:881086/1‑70 (MQ=255)
ggCAATCCCGTCAAAACATCCATATTGCTACGGATCGTCAGCAAATAAATTTTGTAATCGGTTAATGCCg > 1:3038044/1‑70 (MQ=255)
ggCAATCCCGTCAAAACATCCATATTGCTACGGATCGTCAGCAAATAAATTTTGT‑ATCGGTTAATGCCg > 1:1452960/1‑69 (MQ=255)
gCAATCCCGTCAAAACATCCATATTGCTACGGATCGTCAGCAAATAAATTTTGTAATCGGTTAATGCCg > 1:2763301/1‑69 (MQ=255)
gCAATCCCGTCAAAACATCCATATTGCTACGGATCGTCAGCAAATAAATTTTGTAATCGGTTAATGCCGCa < 1:3639760/71‑1 (MQ=255)
gCAATCCCGTCAAAACATCCATATTGCTACGGATCGTCAGCAAATAAATTTTGTAATCGGTTAATGCCGCa < 1:615850/71‑1 (MQ=255)
aaTCCCGTCAAAACATCCATATTGCTACGGATCGTCAGCAAATAAATTTTGT‑ATCGGTTAATGCCGCAGTa < 1:1376465/71‑1 (MQ=255)
aTCCCGTCAAAACATCCATATTGCTACGGATCGTCAGCAAATAAATTTTGT‑ATCGGTTAATGCCGCAGTaa < 1:2343895/71‑1 (MQ=255)
tCCCGTCAAAACATCCATATTGCTACGGATCGTCAGCAAATAAATTTTGTAATCGGTTAATg > 1:3686787/1‑62 (MQ=255)
cGTCAAAACATCCATATTGCTACGGATCGTCAGCAAATAAATTTTGTAATCGGTTAATGCCGCAGTaa > 1:2845407/1‑68 (MQ=255)
cGTCAAAACATCCATATTGCTACGGATCGTCAGCAAATAAATTTTGT‑ATCGGTTAATGCCGCAGTAaaaga < 1:3244414/71‑1 (MQ=255)
gTCAAAACATCCATATTGCTACGGATCGTCAGCAAATAAATTTTGT‑ATCGGTTAATGCCGCAGTAaaaga < 1:1856739/70‑1 (MQ=255)
aaaaCATCCATATTGCTACGGATCGTCAGCAAATAAATTTTGT‑ATCGGTTAATGCCGCAGTAAAAGAAAGc < 1:3813719/71‑1 (MQ=255)
aaaaCATCCATATTGCTACGGATCGTCAGCAAATAAATTTTGT‑ATCGGTTAATGCCGCAGTAAAAGAAAGc < 1:2792644/71‑1 (MQ=255)
aaaCATCCATATTGCTACGGATCGTCAGCAAATAAATTTTGTAATCGGTTAATGCCGCAGt > 1:3401939/1‑61 (MQ=255)
aaaCATCCATATTGCTACGGATCGTCAGCAAATAAATTTTGTAATCGGTTAATGCCGCAGTAAAAGAAAGc < 1:3847473/71‑1 (MQ=255)
aaaCATCCATATTGCTACGGATCGTCAGCAAATAAATTTTGT‑ATCGGTTAATGCCGCAGTAAAAGAAAGCa < 1:1826960/71‑1 (MQ=255)
aTCCATATTGCTACGGATCGTCAGCAAATAAATTTTGT‑ATCGGTTaa > 1:2821104/1‑47 (MQ=255)
ccATATTGCTACGGATCGTCAGCAAATAAATTTTGTAATCGGTTAATGCCGCAGTAaaagaaa > 1:1275683/1‑63 (MQ=255)
ccATATTGCTACGGATCGTCAGCAAATAAATTTTGTAATCGGTTAATGCCGCAGTAAAAGAAAGCAAcccc > 1:1111070/1‑71 (MQ=255)
ccATATTGCTACGGATCGTCAGCAAATAAATTTTGTAATCGGTTAATGCCGCAGTAAAAGAAAGCAAcccc > 1:2257694/1‑71 (MQ=255)
cATATTGCTACGGATCGTCAGCAAATAAATTTTGTAATCGGTTAATGCCGCAGTAAAAGAAAGCAAcccc < 1:2933535/70‑1 (MQ=255)
tatTGCTACGGATCGTCAGCAAATAAATTTTGTAATCGGTTAATGCCGCAGTAAAAGAAAGc < 1:3847284/62‑1 (MQ=255)
ttGCTACGGATCGTCAGCAAATAAATTTTGT‑ATCGGTTaa > 1:3069977/1‑40 (MQ=255)
ttGCTACGGATCGTCAGCAAATAAATTTTGT‑ATCGGTTAATGCCGCAGTAaaaga < 1:1196094/55‑1 (MQ=255)
tGCTACGGATCGTCAGCAAATAAATTTTGTAATCGGt > 1:1959725/1‑37 (MQ=37)
tGCTACGGATCGTCAGCAAATAAATTTTGTAATCGGTTaa > 1:2195304/1‑40 (MQ=38)
gCTACGGATCGTCAGCAAATAAATTTTGTAATCGGTTAATGCCGCAGTAAAAGAAAGCAACCCCTCCTGa < 1:2723537/70‑1 (MQ=255)
gCTACGGATCGTCAGCAAATAAATTTTGT‑ATCGGTTAATGCCGCAGTAAAAGAAAGCAACCCCTCCTGa > 1:3020899/1‑69 (MQ=255)
cTACGGATCGTCAGCAAATAAATTTTGTAATCGGTTAATGCCGCAGTaaa < 1:3597050/50‑1 (MQ=255)
cTACGGATCGTCAGCAAATAAATTTTGT‑ATCGGTTAATGCCg < 1:3208804/42‑1 (MQ=255)
cTACGGATCGTCAGCAAATAAATTTTGT‑ATCGGTTAATGCCg < 1:676898/42‑1 (MQ=255)
cTACGGATCGTCAGCAAATAAATTTTGT‑ATCGGTTAATGCCg < 1:1999922/42‑1 (MQ=255)
cTACGGATCGTCAGCAAATAAATTTTGT‑ATCGGTTAATGCCGCAGTAaaagaaag > 1:591406/1‑55 (MQ=255)
tACGGATCGTCAGCAAATAAATTTTGT‑ATCGTTTAATGCCGCAGTAAAAGAAAGCAAc < 1:1502967/58‑1 (MQ=255)
tACGGATCGTCAGCAAATAAATTTTGT‑ATCGGTTAATGCCGCAGTAAAAGAAAGCAAc < 1:321851/58‑1 (MQ=255)
tACGGATCGTCAGCAAATAAATTTTGT‑ATCGGTTAATGCCGCAGTAAAAGAAAGCAACCcctc > 1:1068004/1‑63 (MQ=255)
cGGATCGTCAGCAAATAAATTTTGTAATCGGTTAATGCCGCAGTAAAAGAAAGCAACCCCTCCTGAAAg < 1:3683191/69‑1 (MQ=255)
cGGATCGTCAGCAAATAAATTTTGTAATCGGTTAATGCCGCAGTAAAAGAAAGCAACCCCTCCTGAAAGGc > 1:3944412/1‑71 (MQ=255)
gTCAGCAAATAAATTTTGTAATCGGTTAATGCCGCAGTAAAAGAAAGCAACCCCTCCTGAAAGGCGTCGaa < 1:669875/71‑1 (MQ=255)
gTCAGCAAATAAATTTTGTAATCGGTTAATGCCGCAGTAAAAGAAAGCAACCCCTCCTGAAAGGCGTCGaa < 1:1653402/71‑1 (MQ=255)
tCAGCAAATAAATTTTGT‑ATCGGTTAATGCCGCAGTAAAAGAAAGCAACCCCTCCTGAAAGGCGTCGAAAt < 1:2336573/71‑1 (MQ=255)
tCAGCAAATAAATTTTGT‑ATCGGTTAATGCCGCAGTAAAAGAAAGCAACCCCTCCTGAAAGGCGTCGAAAt < 1:620087/71‑1 (MQ=255)
aGCAAATAAATTTTGTAATCGGTTAATGCCGCAGTAAAAGAAAGCAACCCCTCCTGAAAGGCGTCGAAATg > 1:2094386/1‑71 (MQ=255)
aGCAAATAAATTTTGT‑ATCGGTTAATGCCGCAGTAAAAGAAAGCAACCCCTCCTGAAAGGCGTCGAAATgc < 1:1526653/71‑1 (MQ=255)
aGCAAATAAATTTTGT‑ATCGGTTAATGCCGCAGTAAAAGAAAGCAACCCCTCCTGAAAGGCGTCGAAATgc < 1:892505/71‑1 (MQ=255)
aGCAAATAAATTTTGT‑ATCGGTTAATGCCGCAGTAAAAGAAAGCAACCCCTCCTGAAAGGCGTCGAAATg < 1:1644395/70‑1 (MQ=255)
gCAAATAAATTTTGTAATCGGTTAATGCCGCAGTAAAAGAAAGCAACCCCTCCTGAAAGGCGt < 1:649113/63‑1 (MQ=255)
taaatTTTGTAATCGGTTAATGCCGCAGTAAAAGAAAGCAACCCCTCCTGAAAGGCGTCGAAATg < 1:948106/65‑1 (MQ=255)
aaatTTTGTAATCGGTTAATGCCGCAGTAAAAGAAAGCAACCCCTCCTGAAAGGCGTCGAAATgc > 1:3353168/1‑65 (MQ=255)
aaatTTTGTAATCGGTTAATGCCGCAGTAAAAGAAAGCAACCCCTCCTGAAAGGCGTCGAAATGCGCGTcc > 1:2800911/1‑71 (MQ=255)
aatTTTGT‑ATCGGTTAATGCCGCAGTAAAAGAAAGCaa > 1:1762927/1‑38 (MQ=255)
aatTTTGT‑ATCGGTTAATGCCGCAGTAAAAGAAAGCaa > 1:801386/1‑38 (MQ=255)
atTTTGTAATCGGTTAATGCCGCAGTAAAAGAAAGc > 1:1800650/1‑36 (MQ=37)
atTTTGTAATCGGTTAATGCCGCAGTAAAAGAAAGCAAccc > 1:1350853/1‑41 (MQ=38)
ttttGT‑ATCGGTTAATGCCGCAGTAAAAGAAAGCAACCCCTCCTGAAAGGCGTCGAAAt < 1:1236784/59‑1 (MQ=255)
ttttGT‑ATCGGTTAATGCCGCAGTAAAAGAAAGCAACCCCTCCTGAAAGGCGTCGAAAt < 1:2770408/59‑1 (MQ=255)
ttttGT‑ATCGGTTAATGCCGCAGTAAAAGAAAGCAACCCCTCCTGAAAGGCGTCGAAATGCGCGTCCTGcc < 1:719016/71‑1 (MQ=255)
t‑ATCGGTTAATGCCGCAGTAAAAGAAAGCAACCCCTCCTGAAAGGCGTCGAAATGCGCGTCCTGCCAGTGa < 1:3532633/71‑1 (MQ=255)
|
GAACCCGACGACCCGGCAATCCCGTCAAAACATCCATATTGCTACGGATCGTCAGCAAATAAATTTTGT‑ATCGGTTAATGCCGCAGTAAAAGAAAGCAACCCCTCCTGAAAGGCGTCGAAATGCGCGTCCTGCCAGTGA > minE/975189‑975327
|
| 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
