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 |
413,105 |
G→A |
50.0% |
L360L (CTG→TTG) |
lnt ← |
apolipoprotein N‑acyltransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 413,105 | 0 | G | A | 50.0%
| ‑5.4
/ 55.9
| 62 | L360L (CTG→TTG) | lnt | apolipoprotein N‑acyltransferase |
| Reads supporting (aligned to +/- strand): ref base G (19/12); new base A (11/20); total (30/32) |
| Fisher's exact test for biased strand distribution p-value = 7.44e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.79e-01 |
TACCATTTGCCGACAGCGGCGGCTGGATATATGGCCCACGGCTGAACGACGACATCGGCAGATCAAAGAACGGTGCTAACGGACGCAGAATCGACTCCAGCGGGACAAACTCGCCAAACGGCACCAG > minE/413045‑413171
|
tACCATTTGCCGACAGCGGCGGCTGGATATATGGCCCACGGCTGAACGACGACATCGGCAGATCAAAg < 1:3072716/68‑1 (MQ=255)
tACCATTTGCCGACAGCGGCGGCTGGATATATGGCCCACGGCTGAACGACGACATCGGCAGATCAAAg < 1:1721012/68‑1 (MQ=255)
tACCATTTGCCCACAGCGGCGGCTGGATATATGGCCCACGGCTGAACGACGACATCGGCAGATCAAAg < 1:2635460/68‑1 (MQ=255)
ccATTTGCCGACAGCGGCGGCTGGATATATGGCCCACGGCTGAACGACGACATCGGCAGATCAAAGAAc > 1:1536832/1‑69 (MQ=255)
ccATTTGCCGACAGCGGCGGCTGGATATATGGCCCACGGCTGAACGACGACATCGGCAGATCAAAGAAc > 1:1436920/1‑69 (MQ=255)
ccATTTGCCGACAGCGGCGGCTGGATATATGGCCCACGGCTGAACGACGACATCGGCAGATCAAAGAAc > 1:1339300/1‑69 (MQ=255)
aGCGGCGGCTGGATATATGGCCCACGGCTGAACGACGACATCGGCAGATCAAAGAACGGTGCt > 1:1682644/1‑63 (MQ=255)
aGCGGCGGCTGGATATATGGCCCACGGCTGAACGACGACATCGGCAGATCAAAGAACGGTGCt > 1:1163170/1‑63 (MQ=255)
aGCGGCGGCTGGATATATGGCCCACGGCTGAACGACGACATCGGCAGATCAAAGAACGGTGCTAACGGa > 1:2050770/1‑69 (MQ=255)
aGCGGCGGCTGGATATATGGCCCACGGCTGAACGACGACATCGGCAGATCAAAGAACGGTGCTAACGGa > 1:608175/1‑69 (MQ=255)
aGCGGCGGCTGGATATATGGCCCACGGCTGAACGACGACATCGGCAGATCAAAGAACGGTGCTAACGGa > 1:1593153/1‑69 (MQ=255)
atatGGCCCACGGCTGAACGACGACATCGGCAGATCAAAGAACGGTGCTAACGGACg > 1:806745/1‑57 (MQ=255)
atatGGCCCACGGCTGAACGACGACATCGGCAGATCAAAGAACGGTGCTAACGGACGCAGAATCGAc > 1:350544/1‑67 (MQ=255)
atatGGCCCACGGCTGAACGACGACATCGGCAGATCAAAGAACGGTGCTAACGGACGCAGAATCGAc > 1:2646345/1‑67 (MQ=255)
atGGTCCGCGGCTGAATGAAGACATCGGCAAATCAAAGAACGGTGCt < 1:351491/47‑1 (MQ=255)
atGGTCCGCGGCTGAATGAAGACATCGGCAAATCAAAGAACGGTGCt < 1:945694/47‑1 (MQ=255)
atGGTCCGCGGCTGAATGAAGACATCGGCAAATCAAAGAACGGTGCt < 1:583354/47‑1 (MQ=255)
atGGTCCGCGGCTGAATGAAGACATCGGCAAATCAAAGAACGGTGCt < 1:3420669/47‑1 (MQ=255)
atGGTCCGCGGCTGAATGAAGACATCGGCAAATCAAAGAACGGTGCt < 1:60565/47‑1 (MQ=255)
atGGTCCGCGGCTGAATGAAGACATCGGCAAATCAAAGAACGGTGCt < 1:3383061/47‑1 (MQ=255)
atGGTCCGCGGCTGAATGAAGACATCGGCAAATCAAAGAACGGTGCt < 1:3362736/47‑1 (MQ=255)
atGGTCCGCGGCTGAATGAAGACATCGGCAAATCAAAGAACGGTGCt < 1:866392/47‑1 (MQ=255)
atGGTCCGCGGCTGAATGAAGACATCGGCAAATCAAAGAACGGTGCt < 1:2937674/47‑1 (MQ=255)
atGGTCCGCGGCTGAATGAAGACATCGGCAAATCAAAGAACGGTGCt < 1:267907/47‑1 (MQ=255)
atGGTCCGCGGCTGAATGAAGACATCGGCAAATCAAAGAACGGTGCt < 1:462443/47‑1 (MQ=255)
atGGTCCGCGGCTGAATGAAGACATCGGCAAATCAAAGAACGGTGCt < 1:478139/47‑1 (MQ=255)
atGGTCCGCGGCTGAATGAAGACATCGGCAAATCAAAGAACGGTGCt < 1:13825/47‑1 (MQ=255)
atGGTCCGCGGCTGAATGAAGACATCGGCAAATCAAAGAACGGTGCt < 1:1820306/47‑1 (MQ=255)
atGGTCCGCGGCTGAATGAAGACATCGGCAAATCAAAGAACGGTGCt < 1:1846753/47‑1 (MQ=255)
atGGTCCGCGGCTGAATGAAGACATCGGCAAATCAAAGAACGGTGCt < 1:2320419/47‑1 (MQ=255)
atGGTCCGCGGCTGAATGAAGACATCGGCAAATCAAAGAACGGTGCt < 1:2189286/47‑1 (MQ=255)
atGGTCCGCGGCTGAATGAAGACATCGGCAAATCAAAGAACGGTGCt < 1:2272132/47‑1 (MQ=255)
atGGTCCGCGGCTGAATGAAGACATCGGCAAATCAAAGAACGGTGCt < 1:2277951/47‑1 (MQ=255)
tGGTCCGCGGCTGAATGAAGACATCGGCAAATCAAAGAACGGTGCt < 1:2776181/46‑1 (MQ=255)
tGGCCCACGGCTGAACGACGACATCGGCAGATCAAAGAACGGTGCTAACgg > 1:1106052/1‑51 (MQ=255)
tGGCCCACGGCTGAACGACGACATCGGCAGATCAAAGAACGGTGCTAACGGACGCAGAATCGACTCCAg > 1:3382393/1‑69 (MQ=255)
ccgcGGCTGAATGAGGACATCGGCAAATCAAAGAACGGTGCTAACGGACGCAGTATCGACTCCAGTgg > 1:3195376/4‑68 (MQ=255)
ccgcGGCTGAATGAAGACATCGGCAAATCAAAGAACGGTGCTAACGGACGCAGTATCGACTCCAGTgg > 1:2639209/4‑68 (MQ=255)
ccgcGGCTGAATGAAGACATCGGCAAATCAAAGAACGGTGCTAACGGACGCAGTATCGACTCCAGTgg > 1:3094038/4‑68 (MQ=255)
ccgcGGCTGAATGAAGACATCGGCAAATCAAAGAACGGTGCTAACGGACGCAGTATCGACTCCAGTgg > 1:911651/4‑68 (MQ=255)
ccgcGGCTGAATGAAGACATCGGCAAATCAAAGAACGGTGCTAACGGACGCAGTATCGACTCCAGTgg > 1:3303627/4‑68 (MQ=255)
ccgcGGCTGAATGAAGACATCGGCAAATCAAAGAACGGTGCTAACGGACGCAGTATCGACTCCAGTgg > 1:2853679/4‑68 (MQ=255)
ccgcGGCTGAATGAAGACATCGGCAAATCAAAGAACGGTGCTAACGGACGCAGTATCGACTCCAGTgg > 1:775139/4‑68 (MQ=255)
ccgcGGCTGAATGAAGACATCGGCAAATCAAAGAACGGTGCTAACGGACGCAGTATCGACTCCAGTgg > 1:1187851/4‑68 (MQ=255)
ccgcGGCTGAATGAAGACATCGGCAAATCAAAGAACGGTGCTAACGGACGCAGTATCGACTCCAGTgg > 1:3046505/4‑68 (MQ=255)
ccgcGGCTGAATGAAGACATCGGCAAATCAAAGAACGGTGCTAACGGACGCAGTATCGACTCCAGTgg > 1:1711706/4‑68 (MQ=255)
ccgcGGCTGAATGAAGACATCGGCAAATCAAAGAACGGTGCTAACGGACGCAGTATCGACTCCAGTgg > 1:446005/4‑68 (MQ=255)
gCTGAACGACGACATCGGCAGATCAAAGAACGGTGCTAACGGACGCAGAATCGACTCCAGCGGGACaaa > 1:911544/1‑69 (MQ=255)
gacATCGGCAGATCAAAGAACGGTGCTAACGGACGCAGAATCGACTCCAGCGGGACAAACTCGCCaaa > 1:3393138/1‑68 (MQ=255)
gacATCGGCAGATCAAAGAACGGTGCTAACGGACGCAGAATCGACTCCAGCGGGACAAACTCGCCAAAc > 1:1164692/1‑69 (MQ=255)
ggCAGATCAAAGAACGGTGCTAACGGACGCAGAATCGACTCCAGCGGGACAAACTCGCCAAACgg > 1:2631455/1‑65 (MQ=255)
ggCAGATCAAAGAACGGTGCTAACGGACGCAGAATCGACTCCAGCGGGACAAACTCGCCAAACGGc > 1:2369359/1‑66 (MQ=255)
ggCAGATCAAAGAACGGTGCTAACGGACGCAGAATCGACTCCAGCGGGACAAACTCGCCAAACGGc > 1:1284739/1‑66 (MQ=255)
cAGATCAAAGAACGGTGCTAACGGACGCAGAATCGACTCCAGCGGGACAAACTCGCCAAACGGCACCa < 1:1358263/68‑1 (MQ=255)
cAGATCAAAGAACGGTGCTAACGGACGCAGAATCGACTCCAGCGGGACAAACTCGCCAAACGGCACCa < 1:3423198/68‑1 (MQ=255)
cAGATCAAAGAACGGTGCTAACGGACGCAGAATCGACTCCAGCGGGACAAACTCGCCAAACGGCACCa < 1:267541/68‑1 (MQ=255)
cAGATCAAAGAACGGTGCTAACGGACGCAGAATCGACTCCAGCGGGACAAACTCGCCAAACGGCACCa < 1:1178336/68‑1 (MQ=255)
cAGATCAAAGAACGGTGCTAACGGACGCAGAATCGACTCCAGCGGGACAAACTCGCCAAACGGCACCa < 1:231227/68‑1 (MQ=255)
cAGATCAAAGAACGGTGCTAACGGACGCAGAATCGACTCCAGCGGGACAAACTCGCCAAACGGCACCa < 1:3134752/68‑1 (MQ=255)
cAGATCAAAGAACGGTGCTAACGGACGCAGAATCGACTCCAGCGGGACAAACTCGCCAAACGGCACCAg < 1:1224223/69‑1 (MQ=255)
cAGATCAAAGAACGGTGCTAACGGACGCAGAATCGACTCCAGCGGGACAAACTCGCCAAACGGCACCAg < 1:2942222/69‑1 (MQ=255)
aGATCAAAGAACGGTGCTAACGGACGCAGAATCGACTCCAGCGGGACAAACTCGCCAAACGGCACCa < 1:3336997/67‑1 (MQ=255)
|
TACCATTTGCCGACAGCGGCGGCTGGATATATGGCCCACGGCTGAACGACGACATCGGCAGATCAAAGAACGGTGCTAACGGACGCAGAATCGACTCCAGCGGGACAAACTCGCCAAACGGCACCAG > minE/413045‑413171
|
| 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
