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 |
2,023,169 |
T→C |
28.5% |
G246G (GGA→GGG) |
ygiQ ← |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,023,169 | 0 | T | C | 28.5%
| 53.5
/ 22.1
| 56 | G246G (GGA→GGG) | ygiQ | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (17/23); new base C (6/10); total (23/33) |
| Fisher's exact test for biased strand distribution p-value = 7.73e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TGTTATCCGCGCACGGCAAATCTTCACCATACGGATGCGGGATTGGGTCGATTTTTCCAGGGGTATCAAGACGGGTGGAATCCACGCCGCTCCAGCCAGGCAGCGCCTCTTTCACGATAA > minE/2023114‑2023233
|
tGTTATCCGCGCACGGCAAATCTTCACCATACGGATGCGGGATTGGGTCGATTTTTCCAGGGGTATCaa < 1:9185/69‑1 (MQ=255)
tGTTATCCGCGCACGGCAAATCTTCACCATACGGATGCGGGATTGGGTCGATTTTTCCAGGGGTATCaa < 1:483896/69‑1 (MQ=255)
tGTTATCCGCGCACGGCAAATCTTCACCATACGGATGCGGGATTGGGTCGATTTTTCCAGGGGTATCaa < 1:3007426/69‑1 (MQ=255)
tGTTATCCGCGCACGGCAAATCTTCACCATACGGATGCGGGATTGGGTCGATTTTTCCAGGGGTATCaa < 1:2309829/69‑1 (MQ=255)
tGTTATCCGCGCACGGCAAATCTTCACCATACGGATGCGGGATTGGGTCGATTTTTCCAGGGGTATCaa < 1:185998/69‑1 (MQ=255)
gTTATCCGCGCACGGCAAATCTTCACCATACGGATGCGGGATTGGGTCGATTTTTCCAGGGGTATCaa < 1:238668/68‑1 (MQ=255)
aTCCGCGCACGGCAAATCTTCACCATACGGATGCGGGATTGGGTCGATTTTTCCAGGGGTATCAAGACg < 1:735356/69‑1 (MQ=255)
aTCCGCGCACGGCAAATCTTCACCATACGGATGCGGGATTGGGTCGATTTTTCCAGGGGTATCAAGACg < 1:2764204/69‑1 (MQ=255)
aTCCGCGCACGGCAAATCTTCACCATACGGATGCGGGATTGGGTCGATTTTTCCAGGGGTATCAAGACg < 1:2517064/69‑1 (MQ=255)
cGGCAAATCTTCACCATACGGATGCGGGATTGGGTCGATTTTTCCAGGGGTATCAAGACGGGTGGAATc < 1:1145868/69‑1 (MQ=255)
cGGCAAATCTTCACCATACGGATGCGGGATTGGGTCGATTTTTCCAGGGGTATCAAGACGGGTGGAATc < 1:1790401/69‑1 (MQ=255)
ggCATATCTTCACCATACGGATGCGGGATTGGGTCGATTTTTCCAGGGGTATCAAGACGGGTGGAATc < 1:1441901/68‑1 (MQ=255)
cAAATCTTCACCATACGGATGCGGGATTGGGTCGATTTTTCCAGGGGTATCaa < 1:1074611/53‑1 (MQ=255)
aaaTCTTCACCATACGGATGCGGGATTGGGTCGATTTTTCCAGGGGTATCAAGACg < 1:1712904/56‑1 (MQ=255)
aaTCTTCGCCATACGGATGCGGGATTGGGTCGATTTTCCCTGGGGTATCAAGACGGGTGGAATCCAcac < 1:488292/69‑3 (MQ=255)
aaTCTTCGCCATACGGATGCGGGATTGGGTCGATTTTCCCTGGGGTATCAAGACGGGTGGAATCCAcac < 1:1591362/69‑3 (MQ=255)
aaTCTTCGCCATACGGATGCGGGATTGGGTCGATTTTCCCTGGGGTATCAAGACGGGTGGAATCCAcac < 1:1714302/69‑3 (MQ=255)
aaTCTTCGCCATACGGATGCGGGATTGGGTCGATTTTCCCTGGGGTATCAAGACGGGTGGAATCCAcac < 1:2847823/69‑3 (MQ=255)
aaTCTTCGCCATACGGATGCGGGATTGGGTCGATTTTCCCTGGGGTATCAAGACGGGTGGAATCCAcac < 1:3282424/69‑3 (MQ=255)
aaTCTTCGCCATACGGATGCGGGATTGGGTCGATTTTCCCTGGGGTATCAAGACGGGTGGAATCCAcac < 1:1984730/69‑3 (MQ=255)
aTCTTCGCCATACGGATGCGGGATTGGGTCGATTTTCCCTGGGGTATCAAGACGGGTGGAATCCAcac < 1:2729898/68‑3 (MQ=255)
aTCTTCGCCATACGGATGCGGGATTGGGTCGATTTTCCCTGGGGTATCAAGACGGGTGGAATCCAcac < 1:815131/68‑3 (MQ=255)
tCTTCACCATACGGATGCGGGATTGGGTCGATTTTTCCAGGGGTATCAAGa > 1:3368074/1‑51 (MQ=255)
tCTTCACCATACGGATGCGGGATTGGGTCGATTTTTCCAGGGGTATCAAGACGGGTGGAATCCAcgccg > 1:580422/1‑69 (MQ=255)
tCTTCACCATACGGATGCGGGATTGGGTCGATTTTTCCAGGGGTATCAAGACGGGTGGAATCCAcgccg > 1:2205513/1‑69 (MQ=255)
tCTTCACCATACGGATGCGGGATTGGGTCGATTTTTCCAGGGGTATCAAGACGGGTGGAATCCAcgccg > 1:2849726/1‑69 (MQ=255)
tCTTCACCATACGGATGCGGGATTGGGTCGATTTTTCCAGGGGTATCAAGACGGGTGGAATCCAcgccg > 1:742739/1‑69 (MQ=255)
tCTTCACCATACGGATGCGGGATTGGGTCGATTTTTCCAGGGGTATCAAGACGGGTGGAATCCAcgccg > 1:156964/1‑69 (MQ=255)
cGGATGCGGGATTGGGTCGATTTTTCCAGGGGTATc > 1:2553086/1‑36 (MQ=255)
cGGATGCGGGATTGGGTCGATTTTTCCAGGGGTATc > 1:1549629/1‑36 (MQ=255)
cGGATGCGGGATTGGGTCGATTTTTCCAGGGGTATc > 1:2034274/1‑36 (MQ=255)
cGGATGCGGGATTGGGTCGATTTTTCCAGGGGTATc > 1:1180765/1‑36 (MQ=255)
cGGATGCGGGATTGGGTCGATTTTTCCAGGGGTATCaa > 1:27136/1‑38 (MQ=255)
cGGATGCGGGATTGGGTCGATTTTTCCAGGGGTATCAAGAc < 1:2252699/41‑1 (MQ=255)
cGGATGCGGGATTGGGTCGATTTTTCCAGGGGTATCAAGACGGGTGGa > 1:1876662/1‑48 (MQ=255)
cGGATGCGGGATTGGGTCGATTTTTCCAGGGGTATCAAGACGGGTGGAATCCACGCCGCTccagcca > 1:1335979/1‑67 (MQ=255)
cGGATGCGGGATTGGGTCGATTTTTCCAGGGGTATCAAGACGGGTGGAATCCACGCCGCTccagcca > 1:1719977/1‑67 (MQ=255)
cGGATGCGGGATTGGGTCGATTTTTCCAGGGGTATCAAGACGGGTGGAATCCACGCCGCTccagcca > 1:1558430/1‑67 (MQ=255)
gATTGGGTCGATTTTTCCAGGGGTATCAAGACGGGTGGAATCCACGCCGCTCCAGCCAGGCAGCGCctc > 1:2192304/1‑69 (MQ=255)
gATTGGGTCGATTTTTCCAGGGGTATCAAGACGGGTGGAATCCACGCCGCTCCAGCCAGGCAGCGCctc > 1:3406079/1‑69 (MQ=255)
gATTGGGTCGATTTTCCCTGGGGTATCAAGACGGGTGGAATCCAcac < 1:1513253/47‑3 (MQ=38)
ggTCGATTTTCCCTGGGGTATCAAGACGGGTGGAATCCAcac < 1:1426810/42‑3 (MQ=37)
gATTTTTCCAGGGGTATCAAGACGGGTGGAATCCACGCCGCTCCAGCCAGGCAGCGCCTCTTTCACGAt < 1:2635725/69‑1 (MQ=255)
gATTTTTCCAGGGGTATCAAGACGGGTGGAATCCACGCCGCTCCAGCCAGGCAGCGCCTCTTTCACGAt < 1:3257487/69‑1 (MQ=255)
gATTTTTCCAGGGGTATCAAGACGGGTGGAATCCACGCCGCTCCAGCCAGGCAGCGCCTCTTTCACGAt < 1:2887622/69‑1 (MQ=255)
gATTTTTCCAGGGGTATCAAGACGGGTGGAATCCACGCCGCTCCAGCCAGGCAGCGCCTCTTTCACGAt < 1:2883613/69‑1 (MQ=255)
gATTTTTCCAGGGGTATCAAGACGGGTGGAATCCACGCCGCTCCAGCCAGGCAGCGCCTCTTTCACGAt < 1:1359432/69‑1 (MQ=255)
gATTTTTCCAGGGGTATCAAGACGGGTGGAATCCACGCCGCTCCAGCCAGGCAGCGCCTCTTTCACGAt < 1:1770462/69‑1 (MQ=255)
gATTTTTCCAGGGGTATCAAGACGGGTGGAATCCACGCCGCTCCAGCCAGGCAGCGCCTCTTTCACGAt < 1:2252828/69‑1 (MQ=255)
gATTTTTCCAGGGGTATCAAGACGGGTGGAATCCACGCCGCTCCAGCCAGGCAGCGCCTCTTTCACGAt < 1:2047946/69‑1 (MQ=255)
gATTTTCCCTGGGGTATCAAGACGGGTGGAATCCACACCGCTCCAGCCAGGCAACGCCTCTTTTACGac > 1:2752343/1‑68 (MQ=255)
gATTTTCCCTGGGGTATCAAGACGGGTGGAATCCACACCGCTCCAGCCAGGCAACGCCTCTTTTACGAt > 1:1669257/1‑69 (MQ=255)
gATTTTCCCTGGGGTATCAAGACGGGTGGAATCCACACCGCTCCAGCCAGGCAACGCCTCTTTTACGAt > 1:813357/1‑69 (MQ=255)
gATTTTCCCTGGGGTATCAAGACGGGTGGAATCCACACCGCTCCAGCCAGGCAACGCCTCTTTTACGAt > 1:1389721/1‑69 (MQ=255)
gATTTTCCCTGGGGTATCAAGACGGGTGGAATCCACACCGCTCCAGCCAGGCAACGCCTCTTTTACGAt > 1:649188/1‑69 (MQ=255)
gATTTTCCCTGGGGTATCAAGACGGGTGGAATCCACACCGCTCCAGCCAGGCAACGCCTCTTTTACGAt > 1:798152/1‑69 (MQ=255)
tttttCCAGGGGTATCAAGACGGGTGGAATCCACGCCGCTCCAGCCAGGCAGCGCCTCTTTCACGATaa > 1:1258582/1‑69 (MQ=255)
tttttCCAGGGGTATCAAGACGGGTGGAATCCACGCCGCTCCAGCCAGGCAGCGCCTCTTTCACGATaa > 1:1223836/1‑69 (MQ=255)
tttttCCAGGGGTATCAAGACGGGTGGAATCCACGCCGCTCCAGCCAGGCAGCGCCTCTTTCACGATa < 1:178118/68‑1 (MQ=255)
tttttCCAGGGGTATCAAGACGGGTGGAATCCACGCCGCTCCAGCCAGGCAGCGCCTCTTTCACGATa < 1:2418023/68‑1 (MQ=255)
tttttCCAGGGGTATCAAGACGGGTGGAATCCACGCCGCTCCAGCCAGGCAGCGCCTCTTTCACGATa < 1:3300664/68‑1 (MQ=255)
tttttCCAGGGGTATCAAGACGGGTGGAATCCACGCCGCTCCAGCCAGGCAGCGCCTCTTTCACGATa < 1:920195/68‑1 (MQ=255)
|
TGTTATCCGCGCACGGCAAATCTTCACCATACGGATGCGGGATTGGGTCGATTTTTCCAGGGGTATCAAGACGGGTGGAATCCACGCCGCTCCAGCCAGGCAGCGCCTCTTTCACGATAA > minE/2023114‑2023233
|
| 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
