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 |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,475,715 |
T→G |
37.8% |
P260P (CCT→CCG) |
nrdB → |
ribonucleoside diphosphate reductase 1, beta subunit, ferritin‑like |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,475,715 | 0 | T | G | 37.8%
| 24.3
/ 46.1
| 53 | P260P (CCT→CCG) | nrdB | ribonucleoside diphosphate reductase 1, beta subunit, ferritin‑like |
| Reads supporting (aligned to +/- strand): ref base T (11/22); new base G (13/7); total (24/29) |
| Fisher's exact test for biased strand distribution p-value = 4.51e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.77e-01 |
GACGAAGCCCTGCACCTGACCGGCACCCAGCATATGCTGAATCTGCTGCGCAGCGGCGCGGACGATCCTGAGATGGCGGAAATTGCCGAAGAGTGTAAGCAGGAGTGCTATGACCTGTTTGTT > minE/1475647‑1475769
|
gacgaAGCCCTGCACCTGACCGGCACCCAGCATATGCTGAATCTGCTGCGCAGCGGCGCGGACGATCCt < 1:1038486/69‑1 (MQ=255)
gacgaAGCCCTGCACCTGACCGGCACCCAGCATATGCTGAATCTGCTGCGCAGCGGCGCGGACGATCCt < 1:1251946/69‑1 (MQ=255)
cgaAGCCCTGCACCTGACCGGCACCCAGCATATGCTGAATCTGCTGCGCAGCGGCGCGGACGATCCTga < 1:118851/69‑1 (MQ=255)
cgaAGCCCTGCACCTGACCGGCACCCAGCATATGCTGAATCTGCTGCGCAGCGGCGCGGACGATCCTga < 1:490062/69‑1 (MQ=255)
gCACCTGCCCGGCACCCAGCATATGCTGAATCTGCTGCGCAGCGGCGCGGACGATCCTGAGATGGCGGa < 1:1545754/69‑1 (MQ=255)
gCACCTGACCGGCACCCAGCATATGCTGAATCTGCTGCGCAGCGGCGCGGACGATCCTGAGATGGCGGa < 1:3376370/69‑1 (MQ=255)
gCACCTGACCGGCACCCAGCATATGCTGAATCTGCTGCGCAGCGGCGCGGACGATCCTGAGATGGCGGa < 1:2045880/69‑1 (MQ=255)
gCACCTGACCGGCACCCAGCATATGCTGAATCTGCTGCGCAGCGGCGCGGACGATCCTGAGATGGCGGa < 1:2613154/69‑1 (MQ=255)
gCACCTGACCGGCACCCAGCATATGCTGAATCTGCTGCGCAGCGGCGCGGACGATCCTGAGATGGCGGa < 1:2877702/69‑1 (MQ=255)
gCACCTGACCGGCACCCAGCATATGCTGAATCTGCTGCGCAGCGGCGCGGACGATCCTGAGATGGCGGa < 1:2934152/69‑1 (MQ=255)
gCACCTGACCGGCACCCAGCATATGCTGAATCTGCTGCGCAGCGGCGCGGACGATCCTGAGATGGCGGa < 1:1226463/69‑1 (MQ=255)
gCACCTGACCGGCACCCAGCATATGCTGAATCTGCTGCGCAGCGGCGCGGACGATCCTGAGATGGCGGa < 1:1003043/69‑1 (MQ=255)
cATATGCTGAATCTGCTGCGCAGCGGCGCGGACGATCCTGAGATGGCGGAAATTGCCGAAGAGTGTa > 1:1451685/1‑67 (MQ=255)
tGCTGAATCTGCTGCGCAGCGGCGCGGACGATCCTGAGATGGCGGAAATTGCCGAAGAGTGTAAGCAgg > 1:1288012/1‑69 (MQ=255)
tGCTGAATCTGCTGCGCAGCGGCGCGGACGATCCTGAGATGGCGGAAATTGCCGAAGAGTGTAAGCAgg > 1:3136153/1‑69 (MQ=255)
tGCTGAATCTGCTGCGCAGCGGCGCGGACGATCCTGAGATGGCGGAAATTGCCGAAGAGTGTAAGCAgg > 1:2207443/1‑69 (MQ=255)
gCTGAATCTGCTGCGCAGCGGCGCGTATGATCCGGAGATGGCGGAAATTGcc > 1:291931/1‑52 (MQ=255)
gCTGAATCTGCTGCGCAGCGGCGCGGATGATCCGGAGATGGCGGAAATTGcc > 1:3053007/1‑52 (MQ=255)
gCTGAATCTGCTGCGCAGCGGCGCGGATGATCCGGAGATGGCGGAAATTGcc > 1:3173641/1‑52 (MQ=255)
gCTGAATCTGCTGCGCAGCGGCGCGGATGATCCGGAGATGGCGGAAATTGcc > 1:386241/1‑52 (MQ=255)
gCTGAATCTGCTGCGCAGCGGCGCGGATGATCCGGAGATGGCGGAAATTGcc > 1:2218700/1‑52 (MQ=255)
gCTGAATCTGCTGCGCAGCGGCGCGGATGATCCGGAGATGGCGGAAATTGcc > 1:1028374/1‑52 (MQ=255)
gCTGAATCTGCTGCGCAGCGGCGCGGATGATCCGGAGATGGCGGAAATTGcc > 1:971035/1‑52 (MQ=255)
gCTGAATCTGCTGCGCAGCGGCGCGGATGATCCGGAGATGGCGGAAATTGcc > 1:1214541/1‑52 (MQ=255)
gCTGAATCTGCTGCGCAGCGGCGCGGATGATCCGGAGATGGCGGAAATTGcc > 1:1230536/1‑52 (MQ=255)
gCTGAATCTGCTGCGCAGCGGCGCGGATGATCCGGAGATGGCGGAAATTGcc > 1:1270838/1‑52 (MQ=255)
gCTGAATCTGCTGCGCAGCGGCGCGGATGATCCGGAGATGGCGGAAATTGcc > 1:1382930/1‑52 (MQ=255)
gCTGAATCTGCTGCGCAGCGGCGCGGATGATCCGGAGATGGCGGAAATTGcc > 1:1765327/1‑52 (MQ=255)
gCTGAATCTGCTGCGCAGCGGCGCGGATGATCCGGAGATGGCGGAAATTGcc > 1:1672748/1‑52 (MQ=255)
tCTGCTGCGCAGCGGCGCGGACGATCCTGAGATGGCGGAAATTGCCGAAGAGTGTAAg < 1:1939024/58‑1 (MQ=255)
tCTGCTGCGCAGCGGCGCGGACGATCCTGAGATGGCGGAAATTGCCGAAGAGTGTAAg > 1:3307807/1‑58 (MQ=255)
tCTGCTGCGCAGCGGCGCGGACGATCCTGAGATGGCGGAAATTGCCGAAGAGTGTAAg > 1:301190/1‑58 (MQ=255)
tCTGCTGCGCAGCGGCGCGGACGATCCTGAGATGGCGGAAATTGCCGAAGAGTGTAAg < 1:819833/58‑1 (MQ=255)
tCTGCTGCGCAGCGGCGCGGACGATCCTGAGATGGCGGAAATTGCCGAAGAGTGTAAg > 1:1439314/1‑58 (MQ=255)
tCTGCTGCGCAGCGGCGCGGACGATCCTGAGATGGCGGAAATTGCCGAAGAGTGTAAg > 1:1545109/1‑58 (MQ=255)
tCTGCTGCGCAGCGGCGCGGACGATCCTGAGATGGCGGAAATTGCCGAAGAGTGTAAg > 1:2432094/1‑58 (MQ=255)
tCTGCTGCGCAGCGGCGCGGACGATCCTGAGATGGCGGAAATTGCCGAAGAGTGTAAg < 1:541220/58‑1 (MQ=255)
tCTGCTGCGCAGCGGCGCGGACGATCCTGAGATGGCGGAAATTGCCGAAGAGTGTAAg < 1:769841/58‑1 (MQ=255)
tCTGCTGCGCAGCGGCGCGGACGATCCTGAGATGGCGGAAATTGCCGAAGAGTGTAAg < 1:1893055/58‑1 (MQ=255)
tCTGCTGCGCAGCGGCGCGGACGATCCTGAGATGGCGGAAATTGCCGAAGAGTGTAAg < 1:1976293/58‑1 (MQ=255)
tCTGCTGCGCAGCGGCGCGGACGATCCTGAGATGGCGGAAATTGCCGAAGAGTGTAAGCAGGAGTGCt > 1:1802165/1‑68 (MQ=255)
ctgctgCGCAGCGGCGCGGACGATCCTGAGATGGCGGAAATTGCCGAAGAGTGTAAGc > 1:2361399/1‑58 (MQ=255)
cAGCGGCGCGGATGATCCGGAGATGGCGGAAATTGCCGAAGAATGTAAGCAGGAGTGCTATGACCtgt < 1:795756/68‑1 (MQ=255)
cAGCGGCGCGGATGATCCGGAGATGGCGGAAATTGCCGAAGAATGTAAGCAGGAGTGCTATGACCtgt < 1:990304/68‑1 (MQ=255)
cAGCGGCGCGGATGATCCGGAGATGGCGGAAATTGCCGAAGAATGTAAGCAGGAGTGCTATGACCtgt < 1:3258232/68‑1 (MQ=255)
cAGCGGCGCGGATGATCCGGAGATGGCGGAAATTGCCGAAGAATGTAAGCAGGAGTGCTATGACCtgt < 1:1426151/68‑1 (MQ=255)
cAGCGGCGCGGATGATCCGGAGATGGCGGAAATTGCCGAAGAATGTAAGCAGGAGTGCTATGACCtgt < 1:1192164/68‑1 (MQ=255)
cAGCGGCGCGGATGATCCGGAGATGGCGGAAATTGCCGAAGAATGTAAGCAGGAGTGCTATGACCtgt < 1:1034958/68‑1 (MQ=255)
cAGCGGCGCGGATGATCCGGAGATGGCGGAAATTACCGAAGAATGTAAGCAGGAGTGCTATGACCtgt < 1:563799/68‑1 (MQ=255)
ggcgCGGACGATCCTGAGATGGCGGAAATTGCCGAAGAGTGTaat < 1:3429027/45‑2 (MQ=255)
ggcgCGGACGATCCTGAGATGGCGGAAATTGCCGAAGAGTGTAAg < 1:3032749/45‑1 (MQ=255)
ggcgCGGACGATCCTGAGATGGCGGAAATTGCCGAAGAGTGTAAg < 1:2083532/45‑1 (MQ=255)
ggcgCGGACGATCCTGAGATGGCGGAAATTGCCGAAGAGTGTAAg < 1:1938563/45‑1 (MQ=255)
ggcgCGGACGATCCTGAGATGGCGGAAATTGCCGAAGAGTGTAAGCAGGAGTGCTATGACCtgtttgtt < 1:2155817/69‑1 (MQ=255)
ggcgCGGACGATCCTGAGATGGCGGAAATTGCCGAAGAGTGTAAGCAGGAGTGCTATGACCtgtttgtt < 1:95354/69‑1 (MQ=255)
|
GACGAAGCCCTGCACCTGACCGGCACCCAGCATATGCTGAATCTGCTGCGCAGCGGCGCGGACGATCCTGAGATGGCGGAAATTGCCGAAGAGTGTAAGCAGGAGTGCTATGACCTGTTTGTT > minE/1475647‑1475769
|
| 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
