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 |
2,279,686 |
G→A |
25.6% |
Q190Q (CAG→CAA) |
trmA → |
tRNA (uracil‑5‑)‑methyltransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,279,686 | 0 | G | A | 25.6%
| 84.3
/ 23.3
| 70 | Q190Q (CAG→CAA) | trmA | tRNA (uracil‑5‑)‑methyltransferase |
| Reads supporting (aligned to +/- strand): ref base G (30/22); new base A (8/10); total (38/32) |
| Fisher's exact test for biased strand distribution p-value = 4.14e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GATGAACGTCTGCCGGTCGCAGGGAAAGAGATGATCTACCGTCAGGTAGAAAACAGCTTTACCCAGCCGAACGCGGCGATGAATATTCAGATGCTGGAATGGGCGCTGGACGTAACCAAAGG > minE/2279621‑2279742
|
gATGAACGTCTGCCGGTCGCAGGGAAAGAGATGATCTACCGTCAGGTAGAAAACAGCTTTACCCAGCCg < 1:2110621/69‑1 (MQ=255)
cgAACGTCTGCTGATCGCGGGGAAAGAGATGATCTACCGTCAGGTAGAAAACAGCTTTACCCAACCg < 1:1343934/66‑1 (MQ=255)
cgAACGTCTGCCGATCGCGGGGAAAGATATGATCTACCGTCAGGTAGAAAACAGCTTTACCCAACCg < 1:759102/66‑1 (MQ=255)
cgAACGTCTGCCGATCGCGGGGAAAGATATGATCTACCGTCAGGTAGAAAACAGCTTTACCCAACCg < 1:3283211/66‑1 (MQ=255)
cgAACGTCTGCCGATCGCGGGGAAAGAGATGATCTACCGTCAGGTAGAAAACAGCTTTACCCAACCg < 1:2460577/66‑1 (MQ=255)
cgAACGTCTGCCGATCGCGGGGAAAGAGATGATCTACCGTCAGGTAGAAAACAGCTTTACCCAACCg < 1:2173323/66‑1 (MQ=255)
cgAACGTCTGCCGATCGCGGGGAAAGAGATGATCTACCGTCAGGTAGAAAACAGCTTTACCCAACCg < 1:1209287/66‑1 (MQ=255)
cgAACGTCTGCCGATCGCGGGGAAAGAGATGATCTACCGTCAGGTAGAAAACAGCTTTACCCAACCg < 1:3410884/66‑1 (MQ=255)
cgAACGTCTGCCGATCGCGGGGAAAGAGATGATCTACCGTCAGGTAGAAAACAGCTTTACCCAACCg < 1:50498/66‑1 (MQ=255)
cgAACGTCTGCCGATCGCGGGGAAAGAGATGATCTACCGTCAGGTAGAAAACAGCTTTACCCAACCg < 1:292582/66‑1 (MQ=255)
cgAACGTCTGCCGATCGCGGGGAAAGAGATGATCTACCGTCAGGTAGAAAACAGCTTTACCCAACCg < 1:1658936/66‑1 (MQ=255)
tCTGCCGGTCGCAGGGAAAGAGATGATCTACCGTCAGGTAGAAAACAGCTTTACCCAGCCGAACgcggc < 1:2680264/69‑1 (MQ=255)
tCTGCCGGTCGCAGGGAAAGAGATGATCTACCGTCAGGTAGAAAACAGCTTTACCCAGCCGAACgcggc < 1:2131855/69‑1 (MQ=255)
tCTGCCGGTCGCAGGGAAAGAGATGATCTACCGTCAGGTAGAAAACAGCTTTACCCAGCCGAACgcggc < 1:2066573/69‑1 (MQ=255)
tCTGCCGGTCGCAGGGAAAGAGATGATCTACCGTCAGGTAGAAAACAGCTTTACCCAGCCGAACgcggc < 1:1951421/69‑1 (MQ=255)
tCTGCCGGTCGCAGGGAAAGAGATGATCTACCGTCAGGTAGAAAACAGCTTTACCCAGCCGAACgcggc < 1:1744560/69‑1 (MQ=255)
tCTGCCGGTCGCAGGGAAAGAGATGATCTACCGTCAGGTAGAAAACAGCTTTACCCAGCCGAACgcggc < 1:1585579/69‑1 (MQ=255)
tCTGCCGGTCGCAGGGAAAGAGATGATCTACCGTCAGGTAGAAAACAGCTTTACCCAGCCGAACgcggc < 1:3274886/69‑1 (MQ=255)
tCTGCCGGTCGCAGGGAAAGAGATGATCTACCGTCAGGTAGAAAACAGCTTTACCCAGCCGAACgcggc < 1:3160311/69‑1 (MQ=255)
tCTGCCGGTCGCAGGGAAAGAGATGATCTACCGTCAGGTAGAAAACAGCTTTACCCAGCCGAACgcggc < 1:2725067/69‑1 (MQ=255)
gtGCCGGTCGCAGGGAAAGAGATGATCTACCGTCAGGTAGAAAACAGCTTTACCCAGCCGAACgcggc < 1:1252140/67‑1 (MQ=255)
cTGCCGGTCGCAGGGAAAGAGATGATCTACCGTCAGGTAGAAATCAGCTTTACCCAGCCGAACgcggc < 1:3410202/68‑1 (MQ=255)
cTGCCGGTCGCAGGGAAAGAGATGATCTACCGTCAGGTAGAAAACAGCTTTACCCAGCCGAACgcggc < 1:728304/68‑1 (MQ=255)
cTGCCGGTCGCAGGGAAAGAGATGATCTACAGTCAGGTAGAAAACAGCTTTACCCAGCCGAACgcggc < 1:2077560/68‑1 (MQ=255)
ccGGTCGCAGGGAAAGAGATGATCTACCGTCAGGTAGAAAACAGCTTTACCCAGCCTAACGCGGCGATg > 1:562083/1‑69 (MQ=255)
ggTCGCAGGGAAAGAGATGATCTACCGTCAGGTAGAAAACAGCTTTACCCAGCCGAACGCGGCGATGaa < 1:3277204/69‑1 (MQ=255)
gTCGCAGGGAAAGAGATGATCTACCGTCAGGTAGAAAACAGCTTTACCCAGCCGAACGCGGCGATGaa < 1:1207143/68‑1 (MQ=255)
cGCAGGGAAAGAGATGATCTACCGTCAGGTAGAAAACAGCTTTACCCAGCCGAACGCGGCGATGAata > 1:1998805/1‑68 (MQ=255)
cGCAGGGAAAGAGATGATCTACCGTCAGGTAGAAAACAGCTTTACCCAGCCGAACGCGGCGATGAata > 1:2108742/1‑68 (MQ=255)
aaaGAGATGATCTACCGTCAGGTAGAAAACAGCTTTACCCAGCCGAACGCGGCGATGAATATTCAGATg > 1:1518063/1‑69 (MQ=255)
aaaGAGATGATCTACCGTCAGGTAGAAAACAGCTTTACCCAGCCGAACGCGGCGATGAATATTCAGATg > 1:352996/1‑69 (MQ=255)
aaaGAGATGATCTACCGTCAGGTAGAAAACAGCTTTACCCAGCCGAACGCGGCGATGAATATTCAGATg > 1:2567977/1‑69 (MQ=255)
aaaGAGATGATCTACCGTCAGGTAGAAAACAGCTTTACCCAGCCGAACGCGGCGATGAATATTCAGATg > 1:532366/1‑69 (MQ=255)
aaaGAGATGATCTACCGTCAGGTAGAAAACAGCTTTACCCAGCCGAACGCGGCGATGAATATTCAGATg > 1:1692072/1‑69 (MQ=255)
aaGATATGATCTACCGTCAGGTAGAAAACAGCTTTACCCAGCCGAACgcggc < 1:2049488/52‑1 (MQ=255)
agaTGATCTACCGTCAGGTAGAAAACAGCTTTACCCAGCCGAACgcggc < 1:2188954/49‑1 (MQ=255)
agaTGATCTACCGTCAGGTAGAAAACAGCTTTACCCAGCCGAACGCGGCGATGAATATTCAGATGCTgg < 1:3123175/69‑1 (MQ=255)
gatgatCTACCGTCAGGTAGAAAACAGCTTTACCCAGCCGAACGCGGCGATGAATATTCAGATGCTGGa > 1:3154550/1‑69 (MQ=255)
gatgatCTACCGTCAGGTAGAAAACAGCTTTACCCAGCCGAACGCGGCGATGAATATTCAGATGCTGGa > 1:2360484/1‑69 (MQ=255)
gatgatCTACCGTCAGGTAGAAAACAGCTTTACCCAGCCGAACGCGGCGATGAATATTCAGATGCTGGa > 1:521489/1‑69 (MQ=255)
gatgatCTACCGTCAGGTAGAAAACAGCTTTACCCAGCCGAACGCGGCGATGAATATTCAGATGCTGGa > 1:525468/1‑69 (MQ=255)
tgatCTACCGTCAGGTAGAAAACAGCTTTACCCAGCCGAACgcggc < 1:1612206/46‑1 (MQ=255)
atCTACCGTCAGGTAGAAAACAGCTTTACCCAGCCGAACgcggc < 1:3335325/44‑1 (MQ=255)
cTACCGTCAGGTAGAAAACAGCTTTACCCAGCCGAACGCGGCGa > 1:2049906/1‑44 (MQ=255)
cTACCGTCAGGTAGAAAACAGCTTTACCCAGCCGAACGCGGCGa > 1:355993/1‑44 (MQ=255)
cTACCGTCAGGTAGAAAACAGCTTTACCCAGCCGAACGCGGCGa > 1:1282614/1‑44 (MQ=255)
cTACCGTCAGGTAGAAAACAGCTTTACCCAGCCGAACGCGGCGa > 1:1226695/1‑44 (MQ=255)
cTACCGTCAGGTAGAAAACAGCTTTACCCAGCCGAACGCGGCGa > 1:782045/1‑44 (MQ=255)
tACCGTCAGGTAGAAAACAGCTTTACCCAGCCGAACGCGGCGATGaa < 1:422703/47‑1 (MQ=255)
gTCAGGTAGAAAACAGCTTTACCCAGCCGAACGCGGCGATGAATATTCAGATGCTGGAATGGGCGCTgg > 1:2173639/1‑69 (MQ=255)
cAGGTAGAAAACAGCTTTACCCAGCCGAACGCGGCGAt > 1:435329/1‑38 (MQ=255)
cAGGTAGAAAACAGCTTTACCCAGCCGAACGCGGCGATg > 1:3001675/1‑39 (MQ=255)
cAGGTAGAAAACAGCTTTACCCAGCCGAACGCGGCGATg > 1:1555170/1‑39 (MQ=255)
cAGGTAGAAAACAGCTTTACCCAGCCGAACGCGGCGATg > 1:1965372/1‑39 (MQ=255)
cAGGTAGAAAACAGCTTTACCCAGCCGAACGCGGCGATg > 1:2074880/1‑39 (MQ=255)
cAGGTAGAAAACAGCTTTACCCAGCCGAACGCGGCGATg > 1:2099752/1‑39 (MQ=255)
aGAAAACAGCTTTACCCAGCCGAACGCGGCGATGAATATTCAGATGCTGGAATGGGCGCTGGACGTaa > 1:1921253/1‑68 (MQ=255)
aGAAAACAGCTTTACCCAGCCGAACGCGGCGATGAATATTCAGATGCTGGAATGGGCGCTGGACGTaa > 1:1097276/1‑68 (MQ=255)
aaaaCAGCTTTACCCAACCGAACGCGGCGATGAATATTCAGATGCTGGAATGGGCGCTGGACGTAAc > 1:372509/1‑67 (MQ=255)
aaaaCAGCTTTACCCAACCGAACGCGGCGATGAATATTCAGATGCTGGAATGGGCGCTGGACGTAAc > 1:393087/1‑67 (MQ=255)
aaaaCAGCTTTACCCAACCGAACGCGGCGATGAATATTCAGATGCTGGAATGGGCGCTGGACGTAAc > 1:398149/1‑67 (MQ=255)
aaaaCAGCTTTACCCAACCGAACGCGGCGATGAATATTCAGATGCTGGAATGGGCGCTGGACGTAAc > 1:1082312/1‑67 (MQ=255)
aaaaCAGCTTTACCCAACCGAACGCGGCGATGAATATTCAGATGCTGGAATGGGCGCTGGACGTAAc > 1:1828005/1‑67 (MQ=255)
aaaaCAGCTTTACCCAACCGAACGCGGCGATGAATATTCAGATGCTGGAATGGGCGCTGGACGTAAc > 1:301371/1‑67 (MQ=255)
aaaaCAGCTTTACCCAACCGAACGCGGCGATGAATATTCAGATGCTGGAATGGGCGCTGGACGTAAc > 1:668560/1‑67 (MQ=255)
aaaaCAGCTTTACCCAACCGAACGCGGCGATGAATATTCAGATGCTGGAATGGGCGCTGGACGTAAc > 1:1327371/1‑67 (MQ=255)
cAGCTTTACCCAGCCGAACGCGGCGATGAATATTCAGATGCTGGAATGGGCGCTGGACGt > 1:1545807/1‑60 (MQ=255)
cAGCTTTACCCAGCCGAACGCGGCGATGAATATTCAGATGCTGGAATGGGCGCTGGACGTAACCAAAgg > 1:2161245/1‑69 (MQ=255)
cAGCTTTACCCAGCCGAACGCGGCGATGAATATTCAGATGCTGGAATGGGCGCTGGACGTAACCAAAgg > 1:1675289/1‑69 (MQ=255)
cAGCTTTACCCAGCCGAACGCGGCGATGAATATTCAGATGCTGGAATGGGCGCTGGACGTAACCAAAgg > 1:1586493/1‑69 (MQ=255)
|
GATGAACGTCTGCCGGTCGCAGGGAAAGAGATGATCTACCGTCAGGTAGAAAACAGCTTTACCCAGCCGAACGCGGCGATGAATATTCAGATGCTGGAATGGGCGCTGGACGTAACCAAAGG > minE/2279621‑2279742
|
| 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
