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 |
|
A3 F2 I1 R1
|
2892 |
75.3 |
5698161 |
66.1% |
3766484 |
59.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
Exported |
834,266 |
G→C |
27.0% |
E908D (GAG→GAC) |
narG → |
nitrate reductase 1, alpha subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | Exported | 834,266 | 0 | G | C | 27.0%
| 126.0
/ 47.2
| 74 | E908D (GAG→GAC) | narG | nitrate reductase 1, alpha subunit |
| Reads supporting (aligned to +/- strand): ref base G (16/38); new base C (10/10); total (26/48) |
| Fisher's exact test for biased strand distribution p-value = 1.69e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.48e-01 |
TTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTACCTCTATCGGCCCGCTGATGGAGAAAATCGGTAATGGCGGTAAAGGGATTGCCTGGAACACCCAGAGCGAGATGGATCTGCTGCGTAAGCTCA > Exported/834199‑834336
|
ttATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTACCTCTATCGGCCCGCTGATGGAGaaa < 1:276779/71‑1 (MQ=255)
gTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTACCTCTATCGGCCCGCTGATGGAGAAAATCgg < 1:2863443/71‑1 (MQ=255)
gTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTACCTCTATCGGCCCGCTGATGGAGAAAATCgg < 1:512139/71‑1 (MQ=255)
tCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTACCTCTATCGGCCCGCTGATGGGGAAAATCGGt < 1:918393/71‑1 (MQ=255)
tCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTACCTCTATCGGCCCGCTGATGGAGAAAATCGGt < 1:4618116/71‑1 (MQ=255)
tCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTACCTCTATCGGCCCGCTGATGGAGAAAATCGGt < 1:2213556/71‑1 (MQ=255)
gTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTACCTCTATCGGCCCGCTGATGGAGAAAATCGGTaa > 1:2423121/1‑71 (MQ=255)
agagCGCGATTATCCGGCGACTTACGAACGCTTTACCTCTATCGGCCCGCTGATGGAGAAAATCGGTAATg > 1:1718139/1‑71 (MQ=255)
agagCGCGATTATCCGGCGACTTACGAACGCTTTACCTCTATCGGCCCGCTGATGGAGAAAATCGGTAATg > 1:2292926/1‑71 (MQ=255)
gagCGCGACTACCCTGCTACGTATGAACGCTTTACCTCGCTCGGGCCATTGATGGACAAACTTGGCAATgg < 1:2331647/71‑1 (MQ=255)
gagCGCGACTACCCTGCTACGTATGAACGCTTTACCTCGCTCGGGCCATTGATGGACAAACTTGGCAATgg < 1:2770130/71‑1 (MQ=255)
agCGCGACTACCCTGCTACGTATGAACGCTTTACCTCGCTCGGGCCATTGATGGACAAACTTGGCAATGGc < 1:2732854/71‑1 (MQ=255)
cgcgATTATCCGGCGACTTACGAACGCTTTACCTCTATCGGCCCGCTGATGGAGAAAAt < 1:2180099/59‑1 (MQ=255)
cgATTATCCGGCGACTTACGAACGCTTTACCTCTATCGGCCCGCTGATGGAGAAAATCGGTAATGGCGGt > 1:2191912/1‑70 (MQ=255)
aTTATCCGGCGACTTACGAACGCTTTACCTCTATCGGCCCGCTGATGGAGAAAATCgg < 1:3378964/58‑1 (MQ=255)
ttATCCGGCGACTTACGAACGCTTTACCTCTATCGGCCCGCTGATGGAGAAAATCGGTaa > 1:5053776/1‑60 (MQ=255)
ttATCCGGCGACTTACGAACGCTTTACCTCTATCGGCCCGCTGATGGAGAAAATCGGTAATGGCGGt > 1:2175296/1‑67 (MQ=255)
ttATCCGGCGACTTACGAACGCTTTACCTCTATCGGCCCGCTGATGGAGAAAATCGGTAATGGCGGTAAAg > 1:4055910/1‑71 (MQ=255)
aTCCGGCGACTTACGAACGCTTTACCTCTATCGGCCCGCTGATGGAGAAAATCGGTAATGGCGGTAAAgg < 1:3738083/70‑1 (MQ=255)
cGGCGACTTACGAACGCTTTACCTCTATCGGCCCGCTGATGGAGAAAATCGGTAATGGCGGTAAAgg < 1:4685043/67‑1 (MQ=255)
ggCGACTTACGAACGCTTTACCTCTATCGGCCCGCTGATGGAGAAAATCGGTAATGGCGGTAAAGGGATTg < 1:2770132/71‑1 (MQ=255)
aCTTACGAACGCTTTACCTCTATCGGCCCGCTGATGGAGAAAATCGGTAATGGCGG‑AAAGGGATTGCCTgg < 1:419840/71‑1 (MQ=255)
ttACAAACGCTTTACCTCTATCGGCCCGCTGATGGAGAAAATCGGTAATGGCGGTAAAggg < 1:3928344/61‑1 (MQ=255)
aCGAACGCTTTACCTCTATCGGCCCGCTGATGGAGAAAATCGGTAATGGCGGTAAAGGGATTGCCTGGaa < 1:291860/70‑1 (MQ=255)
tgAACGCTTTACCTCGCTCGGGCCATTGATGGACAAACTTGGCAAt < 1:271263/45‑1 (MQ=255)
aaCGCTTTACCTCGCTCGGGCCATTGATGGACAAACTTGGCAATGGCGGTAAAGGGATTTCGTgg < 1:267508/65‑1 (MQ=255)
aaCGCTTTACCTCGCTCGGGCCATTGATGGACAAACTTGGCAATGGCGGTAAAGGGATTTCGTGGAATAcc > 1:4518783/1‑71 (MQ=255)
cGCTTTACCTCTATCGGCCCGCTGATGGAGAAAATCGGt < 1:3049915/39‑1 (MQ=255)
cGCTTTACCTCTATCGGCCCGCTGATGGAGAAAATCGGt < 1:1646611/39‑1 (MQ=255)
cGCTTTACCTCGCTCGGGCCATTGATGGACAAACTTGGCAATGGCGGTAAAggg < 1:584154/54‑1 (MQ=255)
gCTTTACCTCGCTCGGGCCATTGATGGACAAACTTGGCAATGGCGGTAAAGGGa < 1:2556674/54‑1 (MQ=255)
gCTTTACCTCGCTCGGGCCATTGATGGACAAACTTGGCAATGGCGGTAAAGGGa < 1:2753986/54‑1 (MQ=255)
gCTTTACCTCGCTCGGGCCATTGATGGACAAACTTGGCAATGGCGGTAAAGGGATTTCGTgg < 1:3178416/62‑1 (MQ=255)
cTTTACCTCTATCGGCCCGCTGATGGAGAAAATCGGTaa > 1:3443090/1‑39 (MQ=255)
cTTTACCTCTATCGGCCCGCTGATGGAGAAAATCGGTaa > 1:4420579/1‑39 (MQ=255)
cTTTACCTCTATCGGCCCGCTGATGGAGAAAATCGGTaa > 1:2996780/1‑39 (MQ=255)
cTTTACCTCTATCGGCCCGCTGATGGAGAAAATCGCTAATGGCGGTAAAGGGATTGCCTGGAACACCCaga < 1:761213/71‑1 (MQ=255)
tttACCTCTATCGGCCCGCGGATGGAGAAAATCGGTa > 1:2821064/1‑37 (MQ=255)
ttACCTCTATCGGCCCGCTGATGGAGAAAATCGGTAATGGCGGTAAAGGGATTGc < 1:1780629/55‑1 (MQ=255)
ttACCTCTATCGGCCCGCTGATGGAGAAAATCGGTAATGGCGGTAAAGGGATTGc < 1:2732616/55‑1 (MQ=255)
tACCTCTATCGGCCCGCTGATGGAGAAAATCGGTAATGGCGGTa > 1:2957626/1‑44 (MQ=255)
tACCTCTATCGGCCCGCTGATGGAGAAAATCGGTAATGGCGGTAAAGGGATTGCCTGGAACACCCAGAGc < 1:3115838/70‑1 (MQ=255)
tACCTCGCTCGGGCCATTGATGGACAAACTTGGCAATGGCGGTAAAGGGATTTCGTGGAATACCCaggat < 1:4847850/70‑4 (MQ=255)
aCCTCTATCGGCCCGCTGATGGAGAAAATCGGTAATGGCGGTAAAGGGATTGCCTGGAACACCCAGAGCg < 1:5329022/70‑1 (MQ=255)
ccTCTATCGGCCCGCTGATGGAGAAAATCGGTAATGGCGGTAAAGGGATTGCCTGGAACACCCAGAGCga < 1:3160474/70‑1 (MQ=255)
ccTCTATCGGCCCGCTGATGGAGAAAATCGGTAATGGCGGTAAAGGGATTGCCTGGAACACCCAGAGCga < 1:2660199/70‑1 (MQ=255)
ctctATCGGCCCGCTGATGGAGAAAATCGGTAATgg < 1:2364127/36‑1 (MQ=255)
ctctATCGGCCCGCTGATGGAGAAAATCGGTAATGGCGGTAAAGGGATTGCCTGGAACACCCAGAGCgaga < 1:4396547/71‑1 (MQ=255)
ctATCGGCCCGCTGATGGAGAAAATCGGTAATGGCGGTAAAGGGATTGCCTGGAACACCCAGAGc < 1:210801/65‑1 (MQ=255)
tATCGGCCCGCTGATGGAGAAAATCGGTAATGGCGGTAAAGGGATTGCCTGGAACACCCAGAGCGAGATg > 1:1766222/1‑70 (MQ=255)
aTCGGCCCGCTGATGGAGAAAATCGGTAATGGCGGTAAAGGGATTGCCTGGAACACCCAGAGCGAGATGGa > 1:894272/1‑71 (MQ=255)
aTCGGCCCGCTGATGGAGAAAATAGGTAATGGCGGTAAAGGGATTGCCTGGAACACCCAGAGCGAGATGGa > 1:4372801/1‑71 (MQ=255)
tCGGCCCGCTGATGGAGAAAATCGGTAATGGCGGTAAAGGGATTGCCTgg < 1:4481599/50‑1 (MQ=255)
tCGGCCCGCTGATGGAGAAAATCGGTAATGGCGGTAAAGGGATTGCCTGGAACACCCAGAGCGAGATGGAt > 1:3797728/1‑71 (MQ=255)
cGGCCCGCTGATGGAGAAAATCGGTAATGGCGGTAAAGGGATTGCCTGGAACACCCAGAGCGAGATgg < 1:802142/68‑1 (MQ=255)
cGCTGATGGAGAAAATCGGTAATGGCGGTAAAGGGATTGCCTgg < 1:2551366/44‑1 (MQ=255)
cGCTGATGGAGAAAATCGGTAATGGCGGTAAAGGGATTGCCTgg < 1:2845189/44‑1 (MQ=255)
cGCTGATGGAGAAAATCGGTAATGGCGGTAAAGGGATTGCCTgg < 1:4663557/44‑1 (MQ=255)
cGCTGATGGAGAAAATCGGTAATGGCGGTAAAGGGATTGCCTGGAACACCCAGAGCga < 1:5435845/58‑1 (MQ=255)
cGCTGATGGAGAAAATCGGTAATGGCGGTAAAGGGATTGCCTGGAACACCCAGAGCga < 1:3581008/58‑1 (MQ=255)
gCTGATGGAGAAAATCGGTAATGGCGGTAAAGGGATTGCCTgg < 1:1579095/43‑1 (MQ=255)
cTGATGGAGAAAATCGGTAATGGCGGTAAAGGGATTGCCTgt < 1:4322964/42‑2 (MQ=255)
gATGGACAAACTTGGCAATGGCGGTAAAGGGATTTCGTGGaa > 1:5430540/1‑42 (MQ=16)
gATGGACAAACTTGGCAATGGCGGTAAAGGGATTTCGTGGaa > 1:2891107/1‑42 (MQ=16)
gATGGACAAACTTGGCAATGGCGGTAAAGGGATTTCGTGGaa > 1:5658164/1‑42 (MQ=16)
gATGGACAAACTTGGCAATGGCGGTAAAGGGATTTCGTGGaa > 1:935884/1‑42 (MQ=16)
gATGGACAAACTTGGCAATGGCGGTAAAGGGATTTCGTGGa > 1:198260/1‑41 (MQ=16)
gATGGACAAACTTGGCAATGGCGGTAAAGGGATTTCGTGGa > 1:1536115/1‑41 (MQ=16)
gATGGACAAACTTGGCAATGGCGGTAAAGGGATTTCGTGGAATAcc > 1:515111/1‑46 (MQ=255)
gATGGACAAACTTGGCAATGGCGGTAAAGGGATTTCGTGGAATAcc > 1:2966700/1‑46 (MQ=255)
gATGGACAAACTTGGCAATGGCGGTAAAGGGATTTCGTGGAATAcc > 1:2030043/1‑46 (MQ=255)
tGGAGAAAATCGGTAATGGCGGTAAAGGGATTGCCTGGAACAccc < 1:4887448/45‑1 (MQ=255)
tGGAGAAAATCGGTAATGGCGGTAAAGGGATTGCCTGGAACAccc < 1:2677410/45‑1 (MQ=255)
tGGAGAAAATCGGTAATGGCGGTAAAGGGATTGCCTGGAACAccc < 1:1775653/45‑1 (MQ=255)
agaAAATCGGTAATGGCGGTAAAGGGATTGCCTGGAACACCCAGAGCGAGATGGATCTGCTGCGTAAGCt > 1:5344887/1‑70 (MQ=255)
agaAAATCGGTAATGGCGGTAAAGGGATTGCCTGGAACACCCAGAGCGAGATGGATCTGCTGCGTAAGCt > 1:998717/1‑70 (MQ=255)
gaAAATCGGTAATGGCGGTAAAGGGATTGCCTGGAACACCCAGAGCGAGATGGATCTGCTGCGTAAGCTCa < 1:4824569/71‑1 (MQ=255)
|
TTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTACCTCTATCGGCCCGCTGATGGAGAAAATCGGTAATGGCGGTAAAGGGATTGCCTGGAACACCCAGAGCGAGATGGATCTGCTGCGTAAGCTCA > Exported/834199‑834336
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
