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 |
834,509 |
T→C |
37.5% |
N989N (AAT→AAC) ‡ |
narG → |
nitrate reductase 1, alpha subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 834,509 | 0 | T | C | 37.5%
| 33.6
/ 47.4
| 48 | N989N (AAT→AAC) ‡ | narG | nitrate reductase 1, alpha subunit |
| Reads supporting (aligned to +/- strand): ref base T (13/17); new base C (10/8); total (23/25) |
| Fisher's exact test for biased strand distribution p-value = 5.52e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.25e-01 |
GGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGA > minE/834440‑834576
|
ggTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATa < 1:3896094/71‑1 (MQ=255)
gTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATa > 1:1021293/1‑70 (MQ=255)
aGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATa > 1:2346364/1‑68 (MQ=255)
gCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATAaag < 1:2065168/70‑1 (MQ=255)
gTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATaa > 1:2907642/1‑65 (MQ=255)
gTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATAAagaaga < 1:2445255/71‑1 (MQ=255)
tGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAAt < 1:3687186/62‑1 (MQ=255)
aaaGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAAt > 1:834706/1‑60 (MQ=255)
aaaGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGACg < 1:1527250/70‑1 (MQ=255)
cTGGGCTGCCCTGAGCGAATTTACCGGTCGTGCCCATACGCATCTGGCGCTGAATAAAGAAGACgag > 1:800475/1‑67 (MQ=255)
cccTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGACGAGAAGAt > 1:2332549/1‑64 (MQ=255)
cccTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCtt < 1:2870825/70‑1 (MQ=255)
cccTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCtt < 1:1227682/70‑1 (MQ=255)
cccTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCt < 1:3683722/69‑1 (MQ=255)
ccTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCtt < 1:485273/69‑1 (MQ=255)
tGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCcg > 1:243645/1‑70 (MQ=255)
aGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCCGCGa > 1:288234/1‑71 (MQ=255)
gCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCCGCGa > 1:210116/1‑70 (MQ=255)
cGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCCGCGat < 1:2344688/70‑1 (MQ=255)
aaTTTACCGGTCGTGACCATACGCATCTGGCGCTGAAt < 1:2719780/38‑1 (MQ=255)
tcaCCGGGCGCGAACATACCCATCTGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAg < 1:544803/69‑1 (MQ=255)
caCCGGGCGCGAACATACCCATCTGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAgg > 1:833000/2‑71 (MQ=255)
caCCGGGCGCGAACATACCCATCTGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAgg > 1:1978356/2‑71 (MQ=255)
ccGGTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCCGCGATAtt < 1:3300136/65‑1 (MQ=255)
ccGGGCGCGAACATACCCATCTGGCGCTGCACAAAGAGGACGAGAAGATTCGCt < 1:1319235/54‑1 (MQ=255)
ccGGGCGCGAACATACCCATCTGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAGGcg < 1:1850715/71‑2 (MQ=255)
ccGGGCGCGAACATACCCATCTGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAGGcg < 1:525403/71‑2 (MQ=255)
cGGTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCCGCGatat < 1:3829395/63‑1 (MQ=255)
cGGTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCCGCGATATTCAGGcac < 1:708986/71‑1 (MQ=255)
gTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGAc < 1:3301163/38‑1 (MQ=255)
gTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCCGCGATATTCAGGCACAg < 1:3711096/71‑1 (MQ=255)
cGTGACCATACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCCGCGATATTCAGGCACAGcc > 1:1505855/1‑71 (MQ=255)
gaacATACCCATCTGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAGGCGCAGCcgcg > 1:2012385/4‑71 (MQ=255)
aCCATACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCCGCGATATTCAGGCACAGCcgcg > 1:3373149/1‑70 (MQ=255)
cATACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCCGCGATATTCa > 1:1686105/1‑56 (MQ=255)
aTACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCcgc > 1:2100489/1‑47 (MQ=255)
aTACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCCGCGATATTCAGGCACAGCCGCGCaaa < 1:444828/71‑1 (MQ=255)
aTACCCATCTGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAg > 1:1265997/1‑56 (MQ=255)
cccATCTGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAGGCGCAGCCGCGTAAAAt > 1:726047/3‑70 (MQ=255)
gCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCCGCGATATTCAGGCACAGCCGCGCAAAATTa < 1:1798718/71‑1 (MQ=255)
ccATCTGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAGGCGCAGCcgc > 1:71946/2‑62 (MQ=255)
cATCTGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAGGCGCAGCCGCGTAAAATTAt < 1:501873/71‑1 (MQ=255)
cATCTGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAGGCGCAGCCGCGTAAAATTAt < 1:2869360/71‑1 (MQ=255)
aTCTGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAGGCGCAGCCGCGTAAAAtt > 1:2402586/1‑68 (MQ=255)
aTCTGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAGGCGCAGCCGCGTAAAATTAtc < 1:1834838/71‑1 (MQ=255)
tCTGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTcgc < 1:461865/40‑1 (MQ=255)
tGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAgg > 1:3407723/1‑48 (MQ=255)
tGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAgg > 1:3069163/1‑48 (MQ=255)
gcgcTGAATAAAGAAGACGAGAAGATCCGCTTCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTcc < 1:715014/69‑1 (MQ=255)
cgcTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAGGCGCAGCCGCGTAAAATTATCTCCAGc > 1:3406273/1‑71 (MQ=255)
gAATAAAGAAGACGAGAAGATCCGCTTCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGa > 1:1145938/1‑71 (MQ=255)
|
GGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGA > minE/834440‑834576
|
| 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
