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 |
267,480 |
G→A |
100% |
V389V (GTC→GTT) |
dxs ← |
1‑deoxyxylulose‑5‑phosphate synthase, thiamine‑requiring, FAD‑requiring |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 267,480 | 0 | G | A | 88.3%
| 92.6
/ 2.6
| 52 | V389V (GTC→GTT) | dxs | 1‑deoxyxylulose‑5‑phosphate synthase, thiamine‑requiring, FAD‑requiring |
| Reads supporting (aligned to +/- strand): ref base G (0/6); new base A (37/8); total (38/14) |
| Fisher's exact test for biased strand distribution p-value = 1.67e-04 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.95e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
AATCGCCACGTCATGCAGCACCTGATCATAGGCGCGTTGCAGGAAAGTGGAGTAAATCGCGACAATGGGTTTGTACCCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTCGGCAATT > minE/267420‑267546
|
aaTCGCCACGTCATGCAGCACCTGATCATAGGCGCGTTGCAGGAAAGTGGAGTAAATCGCGACAATgg < 1:1099099/68‑1 (MQ=255)
aaTCGCCACGTCATGCAGCACCTGATCATAGGCGCGTTGCAGGAAAGTGGAGTAAATCGCGACAATgg < 1:1969040/68‑1 (MQ=255)
aaTCGCCACGTCATGCAGCACCTGATCATAGGCGCGTTGCAGGAAAGTGGAGTAAATCGCGACAATgg < 1:470047/68‑1 (MQ=255)
aaTCGCCACGTCATGCAGCACCTGATCATAGGCGCGTTGCAGGAAAGTGGAGTAAATCGCGACAATgg < 1:46182/68‑1 (MQ=255)
tCGCCACGTCATGCAGCACCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAAt > 1:1607685/1‑64 (MQ=255)
tCGCCACGTCATGCAGCACCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATg > 1:3306147/1‑65 (MQ=255)
tCGCCACGTCATGCAGCACCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATg > 1:3282900/1‑65 (MQ=255)
tCGCCACGTCATGCAGCACCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATg > 1:1461589/1‑65 (MQ=255)
tCGCCACGTCATGCAGCACCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATg > 1:328034/1‑65 (MQ=255)
tCGCCACGTCATGCAGCACCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATg > 1:313625/1‑65 (MQ=255)
tCGCCACGTCATGCAGCACCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATg > 1:1684524/1‑65 (MQ=255)
tCGCCACGTCATGCAGCACCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATg > 1:1689191/1‑65 (MQ=255)
tCGCCACGTCATGCAGCACCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATg > 1:2832444/1‑65 (MQ=255)
tCGCCACGTCATGCAGCACCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATg > 1:280863/1‑65 (MQ=255)
tCGCCACGTCATGCAGCACCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATg > 1:263637/1‑65 (MQ=255)
tCGCCACGTCATGCAGCACCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATg > 1:2041280/1‑65 (MQ=255)
gCCACGTCATGCAGCACCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCTCAACa > 1:1565067/1‑60 (MQ=255)
gCCACGTCATGCAGCACCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCTACAATGGGtt > 1:2306560/1‑67 (MQ=255)
gCCACGTCATGCAGCACCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGtt > 1:3419236/1‑67 (MQ=255)
gCCACGTCATGCAGCACCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGtt > 1:1427720/1‑67 (MQ=255)
gCCACGTCATGCAGCACCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGtt > 1:92928/1‑67 (MQ=255)
gCCACGTCATGCAGCACCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGtt > 1:2293556/1‑67 (MQ=255)
gCCACGTCATGCAGCACCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGtt > 1:3190060/1‑67 (MQ=255)
gCCACGTCATGCAGCACCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGtt > 1:1650724/1‑67 (MQ=255)
gCCACGTCATGCAGCACCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGtt > 1:506181/1‑67 (MQ=255)
gCCACGTCATGCAGCACCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGtt > 1:1874212/1‑67 (MQ=255)
gCCACGTCATGCAGCACCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGtt > 1:2669036/1‑67 (MQ=255)
gCCACGTCATGCAGCACCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGtt > 1:784107/1‑67 (MQ=255)
gCCACGTCATGCAGCACCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGtt > 1:2825784/1‑67 (MQ=255)
gCCACGTCATGCAGCACCTGATAATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGtt > 1:869655/1‑67 (MQ=255)
caCCTGATCATAGGCGCGTTGCAGGAAAGTGGAGTAAATCGCGACAATGGGTTTGTACCCACCAATCGc < 1:20259/69‑1 (MQ=255)
caCCTGATCATAGGCGCGTTGCAGGAAAGTGGAGTAAATCGCGACAATGGGTTTGTACCCACCAATCGc < 1:823779/69‑1 (MQ=255)
aCCTGATCATAGGCGCGTTTCAGGAAGGTGGAGTAGATCGCAACAATGGGTTTGTAGCCTCCAATc > 1:1432310/1‑66 (MQ=255)
aCCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGTTTGTAGcctcc > 1:396958/1‑62 (MQ=255)
aCCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGTTTGTAGCCTCCAATc > 1:1875378/1‑66 (MQ=255)
aCCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGTTTGTAGCCTCCAATc > 1:1897281/1‑66 (MQ=255)
aCCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGTTTGTAGCCTCCAATc > 1:717394/1‑66 (MQ=255)
aCCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGTTTGTAGCCTCCAATc > 1:2337692/1‑66 (MQ=255)
aCCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGTTTGTAGCCTCCAATc > 1:2208084/1‑66 (MQ=255)
aCCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGTTTGTAGCCTCCAATc > 1:1475585/1‑66 (MQ=255)
aCCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGTTTGTAGCCTCCAATc > 1:193886/1‑66 (MQ=255)
aCCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGTTTGTAGCCTCCAATc > 1:1270586/1‑66 (MQ=255)
aCCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGTTTGTAGCCTCCAATc > 1:432012/1‑66 (MQ=255)
aCCTGATCATAGGCGCGTTGCAGGAAGGTGGAGTAGATCCCAACAATGGGTTTGTAGCCTCCAATc > 1:2351589/1‑66 (MQ=255)
cgcgTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGTTTGTAGCCTCCAATCGCCAGACCCgcagca < 1:1226057/68‑1 (MQ=255)
cgcgTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGTTTGTAGCCTCCAATCGCCAGACCCgcagca < 1:90811/68‑1 (MQ=255)
cgcgTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGTTTGTAGCCTCCAATCGCCAGACCCgcagca < 1:3206777/68‑1 (MQ=255)
cgcgTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGTTTGTAGCCTCCAATCGCCAGACCCgcagca < 1:3110022/68‑1 (MQ=255)
cgcgTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGTTTGTAGCCTCCAATCGCCAGACCCgcagca < 1:2321842/68‑1 (MQ=255)
cgcgTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGTTTGTAGCCTCCAATCGCCAGACCCgcagca < 1:200264/68‑1 (MQ=255)
cgcgTTGCAGGAAGGTGGAGTAGATCGCAACAATGGGTTTGTAGCCTCCAATCGCCAGACCCgcagca < 1:157190/68‑1 (MQ=255)
gcgTTGCAGGAAGGTGGAGTAGATCGCAACAATCGGTTTGTAGCCTCCAATCGCCAGACCCgcagca < 1:2828582/67‑1 (MQ=255)
gcgACAATGGGTTTGTACCCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTc > 1:941351/1‑62 (MQ=255)
gcgACAATGGGTTTGTACCCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTCGGCAAtt > 1:336637/1‑69 (MQ=255)
gcgACAATGGGTTTGTACCCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTCGGCAAtt > 1:3047174/1‑69 (MQ=255)
gcgACAATGGGTTTGTACCCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTCGGCAAtt > 1:2825384/1‑69 (MQ=255)
|
AATCGCCACGTCATGCAGCACCTGATCATAGGCGCGTTGCAGGAAAGTGGAGTAAATCGCGACAATGGGTTTGTACCCACCAATCGCCAGACCCGCAGCAAAGGTCACCGCGTGTTGCTCGGCAATT > minE/267420‑267546
|
| 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
