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 |
2,144,062 |
T→C |
43.4% |
G111G (GGT→GGC) |
argG → |
argininosuccinate synthetase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,144,062 | 0 | T | C | 43.4%
| 10.3
/ 39.7
| 53 | G111G (GGT→GGC) | argG | argininosuccinate synthetase |
| Reads supporting (aligned to +/- strand): ref base T (13/17); new base C (4/19); total (17/36) |
| Fisher's exact test for biased strand distribution p-value = 7.40e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.91e-01 |
TCATAACACCACCGGCGGCCTGACCTATTTCAACACGACGCCGCTGGGCCGCGCCGTGACTGGTACCATGCTGGTTGCTGCGATGAAAGAAGATGGCGTGAATATCTGGGGTGACGGTAGCACCTA > minE/2143999‑2144124
|
tCATAACCCCACCGGCGGCCTGACCTATTTCAACACGACGCCGCTGGGCCGCGCCGTGACTGGTACCAt > 1:5895/1‑69 (MQ=255)
tCATAACACCACCGGCGGCCTGACCTATTTCAACACGACGCCGCTGGGCCGCGCCGTGACTGGTACCAt > 1:1127425/1‑69 (MQ=255)
tCATAACACCACCGGCGGCCTGACCTATTTCAACACGACGCCGCTGGGCCGCGCCGTGACTGGTACCAt > 1:1030747/1‑69 (MQ=255)
tCATAACACCACCGGCGGCCTGACCTATTTCAACACGACGCCGCTGGGCCGCGCCGTGACTGGTACCAt > 1:1908741/1‑69 (MQ=255)
tCATAACACCACCGGCGGCCTGACCTATTTCAACACGACGCCGCTGGGCCGCGCCGTGACTGGTACCAt > 1:3162161/1‑69 (MQ=255)
tCATAACACCACCGGCGGCCTGACCTATTTCAACACGACGCCGCTGGGCCGCGCCGTGACTGGTACCAt > 1:1483234/1‑69 (MQ=255)
tCATAACACCACCGGCGGCCTGACCTATTTCAACACGACGCCGCTGGGCCGCGCCGTGACTGGTACCAt > 1:820487/1‑69 (MQ=255)
cTATTTCAACACGACGCCGCTGGGCCGCGCCGTGACTGGTACCATGCTGGTTGTTGCGATGAaagaa < 1:1244348/67‑1 (MQ=255)
cTATTTCAACACGACGCCGCTGGGCCGCGCCGTGACTGGTACCATGCTGGTTGCTGCGTTGAaagaa < 1:1974269/67‑1 (MQ=255)
cTATTTCAACACGACGCCGCTGGGCCGCGCCGTGACTGGTACCATGCTGGTTGCTGCGATGAaagaa < 1:1551113/67‑1 (MQ=255)
cTATTTCAACACGACGCCGCTGGGCCGCGCCGTGACTGGTACCATGCTGGTTGCTGCGATGAaagaa < 1:2652208/67‑1 (MQ=255)
cTATTTCAACACGACGCCGCTGGGCCGCGCCGTGACTGGTACCATGCTGGTTGCTGCGATGAaagaa < 1:3009025/67‑1 (MQ=255)
cTATTTCAACACGACGCCGCTGGGCCGCGCCGTGACTGGTACCATGCTGGTTGCTGCGATGAaagaa < 1:773254/67‑1 (MQ=255)
tCAACACGACGCCGCTGGGCCGCGCCGTGACTGGTACCATGCTGGTTGCTGCGATGAaagaa < 1:2230357/62‑1 (MQ=255)
tCAACACGACGCCGCTGGGCCGCGCCGTGACTGGTACCATGCTGGTTGCTGCGATGAAAGAAGATGGc > 1:3190904/1‑68 (MQ=255)
tCAACACGACGCCGCTGGGCCGCGCCGTGACCGGCACCATGCTGGTTGCTGCTATGAaag < 1:1797970/60‑1 (MQ=255)
tCAACACGACGCCGCTGGGCCGCGCCGTGACCGGCACCATGCTGGTTGCTGCTATGAaag < 1:877111/60‑1 (MQ=255)
tCAACACGACGCCGCTGGGCCGCGCCGTGACCGGCACCATGCTGGTTGCTGCTATGAaag < 1:3076906/60‑1 (MQ=255)
tCAACACGACGCCGCTGGGCCGCGCCGTGACCGGCACCATGCTGGTTGCTGCTATGAaag < 1:1624884/60‑1 (MQ=255)
tCAACACGACGCCGCTGGGCCGCGCCGTGACCGGCACCATGCTGGTTGCTGCTATGAaag < 1:2011778/60‑1 (MQ=255)
tCAACACGACGCCGCTGGGCCGCGCCGTGACCGGCACCATGCTGGTTGCTGCTATGAaag < 1:2380063/60‑1 (MQ=255)
acacGACGCCGCTGGGCCGCGCCGTGACTGGTACCATGCTGGTTGCTGCGATGAAAGAAGATGGCGTg < 1:294338/68‑1 (MQ=255)
acacGACGCCGCTGGGCCGCGCCGTGACTGGTACCATGCTGGTTGCTGCGATGAAAGAAGATGGCGTg < 1:2844686/68‑1 (MQ=255)
acacGACGCCGCTGGGCCGCGCCGTGACTGGTACCATGCTGGTTGCTGCGATGAAAGAAGATGGCGTg < 1:283399/68‑1 (MQ=255)
cacGACGCCGCTGGGCCGCGCCGTGACTGGTACCATGCTGGTTGCTGCGATGAAAGAAGATGGCGTg < 1:244073/67‑1 (MQ=255)
cgcTGGGCCGCGCCGTGACCGGCACCATGCTGGTTGCTGCTATGAAAGAAGATGGCGTGAATATCTggg < 1:855328/69‑1 (MQ=255)
cgcTGGGCCGCGCCGTGACCGGCACCATGCTGGTTGCTGCTATGAAAGAAGATGGCGTGAATATCTggg < 1:325636/69‑1 (MQ=255)
cgcTGGGCCGCGCCGTGACCGGCACCATGCTGGTTGCTGCTATGAAAGAAGATGGCGTGAATATCTggg < 1:3432133/69‑1 (MQ=255)
cgcTGGGCCGCGCCGTGACCGGCACCATGCTGGTTGCTGCTATGAAAGAAGATGGCGTGAATATCTggg < 1:1917956/69‑1 (MQ=255)
cgcTGGGCCGCGCCGTGACCGGCACCATGCTGGTTGCTGCTATGAAAGAAGATGGCGTGAATATCTggg < 1:1964643/69‑1 (MQ=255)
cgcTGGGCCGCGCCGTGACCGGCACCATGCTGGTTGCTGCTATGAAAGAAGATGGCGTGAATATCTggg < 1:141164/69‑1 (MQ=255)
cgcTGGGCCGCGCCGTGACCGGCACCATGCTGGTTGCTGCTATGAAAGAAGATGGCGTGAATATCTggg < 1:2199669/69‑1 (MQ=255)
cgcTGGGCCGCGCCGTGACCGGCACCATGCTGGTTGCTGCTATGAAAGAAGATGGCGTGAATATCTggg < 1:2591391/69‑1 (MQ=255)
cgcTGGGCCGCGCCGTGACCGGCACCATGCTGGTTGCTGCTATGAAAGAAGATGGCGTGAATATCTggg < 1:2545385/69‑1 (MQ=255)
cgcTGGGCCGCGCCGTGACCGGCACCATGCTGGTTGCTGCTATGAAAGAAGATGGCGTGAATATCTggg < 1:998510/69‑1 (MQ=255)
cgcTGGGCCGCGCCGTGACCGGCACCATGCTGGTTGCTGCTATGAAAGAAGATGGCGTAAATATCTggg < 1:1961665/69‑1 (MQ=255)
gcTTGGCCGCGCCGTGACCGGCACCATGCTGGTTGCTGCTATGAAAGAAGATGGCGTGAATATCTggg < 1:2511519/68‑1 (MQ=255)
gggCCGCGCCGTGACTGGTACCATGCTGGTTGCTGCGATGAAAGAAGATGGCGTGAATATCTGGGGTGa > 1:2068318/1‑69 (MQ=255)
ggCCGCGCCGTGACCGGCACCATGCTGGTTGCTGCTATGAtag < 1:1716358/43‑1 (MQ=25)
cgcCGTGACCGGCACCATGCTGGTTGCTGCTATGAaaga > 1:1206981/1‑39 (MQ=37)
cgcCGTGACCGGCACCATGCTGGTTGCTGCTATGAAAGAAGATGGCGTg > 1:972206/1‑49 (MQ=255)
cgcCGTGACCGGCACCATGCTGGTTGCTGCTATGAAAGAAGATGGCGTGAATATCt > 1:224418/1‑56 (MQ=255)
cgcCGTGACCGGCACCATGCTGGTTGCTGCTATGAAAGAAGATGGCGTGAATATCTGGGGTgctg > 1:1689584/1‑62 (MQ=255)
gcCGTGACTGGTACCATGCTGGTTGCTGCGATGAAAGAAGATGGCGTGAATATCTGGGGTGACGGTAGc < 1:584123/69‑1 (MQ=255)
gcCGTGACTGGTACCATGCTGGTTGCTGCGATGAAAGAAGATGGCGTGAATATCTGGGGTGACGGTAGc < 1:2850778/69‑1 (MQ=255)
gcCGTGACTGGTACCATGCTGGTTGCTGCGATGAAAGAAGATGGCGTGAATATCTGGGGTGACGGTAGc < 1:2489416/69‑1 (MQ=255)
gcCGTGACTGGTACCATGCTGGTTGCTGCGATGAAAGAAGATGGCGTGAATATCTGGGGTGACGGTAGc < 1:2477991/69‑1 (MQ=255)
ccGTGACTGGTACCATGCTGGTTGCTGCGATGAAAGAAGATGGCGTGAATATCTGGGGTGACGGTAGc < 1:1873490/68‑1 (MQ=255)
ccGTGACTGGTACCATGCTGGTTGCTGCGATGAAAGAAGATGGCGTGAATATCTGGGGTGACGGTAGc < 1:226024/68‑1 (MQ=255)
aCTGGTACCATGCTGGTTGCTGCGATGAAAGAAGATGGCGTGAATATCTGGGGTGACgg > 1:127178/1‑59 (MQ=255)
aCTGGTACCATGCTGGTTGCTGCGATGAAAGAAGATGGCGTGAATATCTGGGGTGACGGTAGCACCTa > 1:3249592/1‑68 (MQ=255)
aCTGGTACCATGCTGGTTGCTGCGATGAAAGAAGATGGCGTGAATATCTGGGGTGACGGTAGCACCTa > 1:406478/1‑68 (MQ=255)
aCTGGTACCATGCTGGTTGCTGCGATGAAAGAAGATGGCGTGAATATCTGGGGTGACGGTAGCACCTa > 1:2177696/1‑68 (MQ=255)
|
TCATAACACCACCGGCGGCCTGACCTATTTCAACACGACGCCGCTGGGCCGCGCCGTGACTGGTACCATGCTGGTTGCTGCGATGAAAGAAGATGGCGTGAATATCTGGGGTGACGGTAGCACCTA > minE/2143999‑2144124
|
| 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
