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 |
1,555,457 |
T→C |
35.2% |
Y212Y (TAT→TAC) |
dsdA → |
D‑serine ammonia‑lyase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,555,457 | 0 | T | C | 35.2%
| 43.3
/ 38.9
| 68 | Y212Y (TAT→TAC) | dsdA | D‑serine ammonia‑lyase |
| Reads supporting (aligned to +/- strand): ref base T (15/29); new base C (11/13); total (26/42) |
| Fisher's exact test for biased strand distribution p-value = 4.35e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.37e-01 |
GATGCCCGGGCATGGAAAAAAGCGAAACTGCGCAGCCATGGCGTTACGGTCGTGGAATATGAGCAAGATTATGGTGTTGCCGTCGAGGAAGGACGTAAAGCAGCGCAGTCTGACCCG > minE/1555398‑1555514
|
gATGCCCGGGCATGGAAAAAAGCGAAACTGCGCAGCCATGGCGTTACGGTCGTGGAATATGAGCaa < 1:1871845/66‑1 (MQ=255)
gATGCCCGGGCATGGAAAAAAGCGAAACTGCGCAGCCATGGCGTTACGGTCGTGGAATATGAGCaa < 1:1642431/66‑1 (MQ=255)
gATGCCCGGGCATGGAAAAAAGCGAAACTGCGCAGCCATGGCGTTACGGTCGTGGAATATGAGCaa < 1:158635/66‑1 (MQ=255)
gATGCCCGGGCATGGAAAAAAGCGAAACTGCGCAGCCATGGCGTTACGGTCGTGGAATATGAGCaa < 1:2752062/66‑1 (MQ=255)
gATGCCCGGGCATGGAAAAAAGCGAAACTGCGCAGCCATGGCGTTACGGTCGTGGAATATGAGCaa < 1:2992732/66‑1 (MQ=255)
gATGCCCGGGCATGGAAAAAAGCGAAACTGCGCAGCCATGGCGTTACGGTCGTGGAATATGAGCAAGAt < 1:387520/69‑1 (MQ=255)
gATGCCCGGGCATGGAAAAAACCGAAACTGCGCAGCCATGGCGGTACGGGCGTGGAATATGAGCaa < 1:1038347/66‑1 (MQ=255)
gCCCGGGCATGGAAAAAAGCGAAACTGCGCAGCCATGGCGTTACGGTCGTGGAATATGAGCAAGATTa > 1:488565/1‑68 (MQ=255)
gCCCGGGCATGGAAAAAAGCGAAACTGCGCAGCCATGGCGTTACGGTCGTGGAATATGAGCAAGATTAt > 1:901999/1‑69 (MQ=255)
gCCCGGGCATGGAAAAAAGCGAAACTGCGCAGCCATGGCGTTACGGTCGTGGAATATGAGCAAGATTAt > 1:2144680/1‑69 (MQ=255)
ggCATGGAAAAAAGCGAAACTGCGCAGCCATGGCGTTACGGTCGTGGAATATGAG‑‑‑GATTATGGTGTTGc < 1:3046230/69‑1 (MQ=255)
cATGGAAAAAAGCGAAACTGCGCAGACATGGCGTTACGGTCGTGGAATATGAGCAAGATTa > 1:1911257/1‑61 (MQ=255)
aTGGAAAAAAGCGAAACTGCGCAGCCATGGCGTTACGGTCGTGGAATATGAGCAAGATTATGGTGTTGc < 1:2697161/69‑1 (MQ=255)
aTGGAAAAAAGCGAAACTGCGCAGCCATGGCGTTACGGTCGTGGAATATGAGCAAGATTATGGTGTTGc < 1:239706/69‑1 (MQ=255)
aTGGAAAAAAGCGAAACTGCGCAGCCATGGCGTTACGGTCGTGGAATATGAGCAAGATTATGGTGTTGc < 1:1037882/69‑1 (MQ=255)
aTGGAAAAAAGCGAAACTGCGCAGCCATGGCGTTACGGTCGTGGAATATGAGCAAGATTATGGTGTTGc < 1:3067367/69‑1 (MQ=255)
aTGGAAAAAAGCGAAACTGCGCAGCCATGGCGTTACGGTCGTGGAATATGAGCAAGATTATGGTGTTGc < 1:67140/69‑1 (MQ=255)
aTGGAAAAAAGCGAAACTGCGCAGCCATGGCGTTACGGTCGTGGAATATGAGCAAGATTATGGTGTTGc < 1:3149260/69‑1 (MQ=255)
aTGGAAAAAAGCGAAACTGCGCAGCCATGGCGTTACGGTCGTGGAATATGAGCAAGATTATGGTGTTGc < 1:2068380/69‑1 (MQ=255)
aTGGAAAAAAGCGAAACTGCGCAGCCATGGCGTTACGGTCGTGGAATATGAGCAAGATTATGGTGTTGc < 1:714632/69‑1 (MQ=255)
aTGGAAAAAAGCGAAACTGCGCAGCCATGGCGTTACGGTCGTGGAATATGAGCAAGATTATGGTGTTGc < 1:19058/69‑1 (MQ=255)
aTGGAAAAAAGCGAAACTGCGCAGCCATGGCGTTACGGTCGTGGAATATGAGCAAGATTATGGTGTTGc < 1:328296/69‑1 (MQ=255)
aTGGAAAAAAGCGAAACTGCGCAGCCATGGCGTTACGGTCGTGGAATATGAGCAAGATTATGGTGTTGc < 1:1666320/69‑1 (MQ=255)
gAAAAAAGCGAAACTGCGCAGCCATGGCGTTACGGTCGTGGAATATGAGCAAGATTATGGTGTTGcc > 1:1341385/1‑67 (MQ=255)
gAAAAAAGCGAAACTGCGCAGCCATGGCGTTACGGTCGTGGAATATGAGCAAGATTATGGTGTTGCCg > 1:2000923/1‑68 (MQ=255)
gAAAAAAGCGAAACTGCGCAGCCATGGCGTTACGGTCGTGGAATATGAGCAAGATTATGGTGTTGCCg > 1:2550577/1‑68 (MQ=255)
gAAAAAAGCGAAACTGCGCAGCCATGGCGTTACGGTCGTGGAATATGAGCAAGATTATGGTGTTGCCg > 1:1259636/1‑68 (MQ=255)
gAAAAAAGCGAAACTGCGCAGCCATGGCGTTACGGTCGTGGAATATGAGCAAGATTATGGTGTTGCCg > 1:1168801/1‑68 (MQ=255)
gAAAAAAGCGAAAATGCGCAGCCATGGCGTTACGGTCGTGGAATATGAGCAAGATTATGGTGTTGCCg > 1:2165391/1‑68 (MQ=255)
cTGCGCAGCCATGGCGTTACGGTCGTGGAATATGAGCAAGATTATGGTGTTGc < 1:3236282/53‑1 (MQ=255)
gcgcAGTCATGGCGTTACTGTCGTGGAATACGAGCAAGATTATGGTGTTGCCGTCGAGGAAGGACGTaa < 1:2257959/69‑1 (MQ=255)
gcgcAGTCATGGCGTTACTGTCGTGGAATACGAGCAAGATTATGGTGTTGCCGTCGAGGAAGGACGTaa < 1:2741611/69‑1 (MQ=255)
gcgcAGTCATGGCGTTACTGTCGTGGAATACGAGCAAGATTATGGTGTTGCCGTCGAGGAAGGACGTaa < 1:1290792/69‑1 (MQ=255)
gcgcAGTCATGGCGTTACTGTCGTGGAATACGAGCAAGATTATGGTGTTGCCGTCGAGGAAGGACGTaa < 1:299554/69‑1 (MQ=255)
gcgcAGTCATGGCGTTACTGTCGTGGAATACGAGCAAGATTATGGTGTTGCCGTCGAGGAAGGACGTaa < 1:1383325/69‑1 (MQ=255)
gcgcAGTCATGGCGTTACTGTCGTGGAATACGAGCAAGATTATGGTGTTGCCGTCGAGGAAGGACGTaa < 1:1393704/69‑1 (MQ=255)
gcgcAGTCATGGCGTTACTGTCGTGGAATACGAGCAAGATTATGGTGTTGCCGTCGAGGAAGGACGTaa < 1:2189599/69‑1 (MQ=255)
gcgcAGTCATGGCGTTACTGTCGTGGAATACGAGCAAGATTATGGTGTTGCCGTCGAGGAAGGACGTaa < 1:3114285/69‑1 (MQ=255)
gcgcAGTCATGGCGTTACTGTCGTGGAATACGAGCAAGATTATGGTGTTGCCGTCGAGGAAGGACGTaa < 1:853970/69‑1 (MQ=255)
gcgcAGTCATGGCGTTACTGTCGTGGAATACGAGCAAGATTATGGTGTTGCCGTCGAGGAAGGACGTaa < 1:829275/69‑1 (MQ=255)
gcgcAGTCATGGCGTTACTGTCGTGGAATACGAGCAAGATTATGGTGTTGCCGTCGAGGAAGGACGTaa < 1:927714/69‑1 (MQ=255)
gcAGTCATGGCGTTACTGTCGTGGAATACGAGCAAGATTATGGTGTTGCCGTCGAGGAAGGACGTaa < 1:2076072/67‑1 (MQ=255)
ttACGGTCGTGGAATATGAGCAAGATTATGGTGTTGCCGTCGAGGTAGGACGTAAAGCAGCGCAGTCTg < 1:2455727/69‑1 (MQ=255)
ttACGGTCGTGGAATATGAGCAAGATTATGGTGTTGCCGTCGAGGAAGGACGTAAAGCAGCGCAGTCTg < 1:2736375/69‑1 (MQ=255)
ttACGGTCGTGGAATATGAGCAAGATTATGGTGTTGCCGTCGAGGAAGGACGTAAAGCAGCGCAGTCTg < 1:1808936/69‑1 (MQ=255)
ttACGGTCGTGGAATATGAGCAAGATTATGGTGTTGCCGTCGAGGAAGGACGTAAAGCAGCGCAGTCTg < 1:1570605/69‑1 (MQ=255)
ttACGGTCGTGGAATATGAGCAAGATTATGGTGTTGCCGTCGAGGAAGGACGTAAAGCAGCGCAGTCTg < 1:3136851/69‑1 (MQ=255)
aCGGTCGTGGAATATGAGCAAGATTATGGTGTTGCCGt > 1:2758296/1‑38 (MQ=255)
aCGGTCGTGGAATATGAGCAAGATTATGGTGTTGCCGTCGAGGAAGGCCGTAAAGCAGCGCAGTCTGAc > 1:791326/1‑69 (MQ=255)
aCGGTCGTGGAATATGAGCAAGATTATGGTGTTGCCGTCGAGGAAGGACGTAAAGCAGCGCAGTCTGa > 1:1614469/1‑68 (MQ=255)
aCGGTCGTGGAATATGAGCAAGATTATGGTGTTGCCGTCGAGGAAGGACGTAAAGCAGCGCAGTCTGAc > 1:122361/1‑69 (MQ=255)
aCGGTCGTGGAATATGAGCAAGATTATGGTGGTGCCGTCGAGGAAGGACGTAAAGCAGCGCAGTCTGa > 1:1350087/1‑68 (MQ=255)
gTCGTGGAATATGAGCAAGATTATGGTGTTGCCGTCGAGGAAGGACGTAAAGCAGCGCAGTCTGACCCg < 1:505596/69‑1 (MQ=255)
gTCGTGGAATATGAGCAAGATTATGGTGTTGCCGTCGAGGAAGGACGTAAAGCAGCGCAGTCTGACCCg < 1:23243/69‑1 (MQ=255)
gTCGTGGAATATGAGCAAGATTATGGTGTTGCCGTCGAGGAAGGACGTAAAGCAGCGCAGTCTGACCCg < 1:2348917/69‑1 (MQ=255)
gTCGTGGAATATGAGCAAGATTATGGTGTTGCCGTCGAGGAAGGACGTAAAGCAGCGCAGTCTGACCCg < 1:1930693/69‑1 (MQ=255)
gTCGTGGAATACGAGCAAGATTATGGTGTTGCCGTCGAGGAAGGACGTaa < 1:1748632/50‑1 (MQ=255)
ggAATACGAGCAAGATTATGGTGTTGCCGTCGAGGAAGGACGTAAagcc > 1:2289879/1‑48 (MQ=255)
ggAATACGAGCAAGATTATGGTGTTGCCGTCGAGGAAGGACGTAAAGCCgcgc > 1:1211643/1‑53 (MQ=255)
ggAATACGAGCAAGATTATGGTGTTGCCGTCGAGGAAGGACGTAAAGCCGCGCa > 1:3284487/1‑54 (MQ=255)
ggAATACGAGCAAGATTATGGTGTTGCCGTCGAGGAAGGACGTAAAGCCGCGCa > 1:3308961/1‑54 (MQ=255)
ggAATACGAGCAAGATTATGGTGTTGCCGTCGAGGAAGGACGTAAAGCCGCGCa > 1:3556/1‑54 (MQ=255)
ggAATACGAGCAAGATTATGGTGTTGCCGTCGAGGAAGGACGTAAAGCCGCGCa > 1:2529948/1‑54 (MQ=255)
ggAATACGAGCAAGATTATGGTGTTGCCGTCGAGGAAGGACGTAAAGCCGCGCa > 1:2186027/1‑54 (MQ=255)
ggAATACGAGCAAGATTATGGTGTTGCCGTCGAGGAAGGACGTAAAGCCGCGCa > 1:1792823/1‑54 (MQ=255)
ggAATACGAGCAAGATTATGGTGTTGCCGTCGAGGAAGGACGTAAAGCCGCGCa > 1:1664743/1‑54 (MQ=255)
ggAATACGAGCAAGATTATGGTGTTGCCGTCGAGGAAGGACGTAAAGCCGCGCa > 1:1168051/1‑54 (MQ=255)
ggAATACGAGCAAGATTATGGTGTTGCCGTCGAGGAAGGACGTAAAGCCGCGCa > 1:975527/1‑54 (MQ=255)
|
GATGCCCGGGCATGGAAAAAAGCGAAACTGCGCAGCCATGGCGTTACGGTCGTGGAATATGAGCAAGATTATGGTGTTGCCGTCGAGGAAGGACGTAAAGCAGCGCAGTCTGACCCG > minE/1555398‑1555514
|
| 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
