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 |
1,202,612 |
G→T |
67.3% |
A90A (GCG→GCT) |
yoaD → |
predicted phosphodiesterase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,202,612 | 0 | G | T | 67.3%
| 38.1
/ 37.6
| 52 | A90A (GCG→GCT) | yoaD | predicted phosphodiesterase |
| Reads supporting (aligned to +/- strand): ref base G (7/10); new base T (9/26); total (16/36) |
| Fisher's exact test for biased strand distribution p-value = 3.40e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.28e-01 |
AAGTCTTGCTTCCGCTGATTGGTCTGCCCTGCTCTGTCGCCCATTTGCCATTACGTAAACAGGCGGCAAAACTCCAAACTGTGCGATCCATTGGCCTGGTGCAAGACGGCACACTTTATT > minE/1202548‑1202667
|
aaGTCTTGCTTCCGCTGATTGGTCTGCCCTGCTCTGTCGCCCATTTGCCATTACGTAAACAGGCGGCaa < 1:2634786/69‑1 (MQ=255)
aaGTCTTGCTTCCGCTGATTGGTCTGCCCTGCTCTGTCGCCCATTTGCCATTACGTAAACAGGCGGCaa < 1:2697380/69‑1 (MQ=255)
aaGTCTTGCTTCCGCTGATTGGTCTGCCCTGCTCTGTCGCCCATTTGCCATTACGTAAACAGGCGGCaa < 1:1377379/69‑1 (MQ=255)
aaGTCTTGCTTCCGCTGATTGGTCTGCCCTGCTCTGTCGCCCATTTGCCATTACGTAAACAGGCGGCaa < 1:621840/69‑1 (MQ=255)
cTTGCTTCCGCTGATTGGTCTGCCCTGCTCTGTCGCCCATTTGCCATTACGTAAACAGGCGGCAAAAc > 1:2787484/1‑68 (MQ=255)
ttGCTTCCGCTGATTGGTCTGCCCTGCTCTGTCACCCATTTGCCATTACGTAAACAGTCTGCAAAACTc < 1:1901326/69‑1 (MQ=255)
ttGCTTCCGCTGATTGGTCTGCCCTGCTCTGTCACCCATTTGCCATTACGTAAACAGGCTGCAAAAccc < 1:1372970/69‑3 (MQ=255)
ttGCTTCCGCTGATTGGTCTGCCCTGCTCTGTCACCCATTTGCCATTACGTAAACAGGCTGCAAAACTc < 1:3227414/69‑1 (MQ=255)
ttGCTTCCGCTGATTGGTCTGCCCTGCTCTGTCACCCATTTGCCATTACGTAAACAGGCTGCAAAACTc < 1:2652269/69‑1 (MQ=255)
ttGCTTCCGCTGATTGGTCTGCCCTGCTCTGTCACCCATTTGCCATTACGTAAACAGGCTGCAAAACTc < 1:2885389/69‑1 (MQ=255)
ttGCTTCCGCTGATTGGTCTGCCCTGCTCTGTCACCCATTTGCCATTACGTAAACAGGCTGCAAAACTc < 1:2958477/69‑1 (MQ=255)
ttGCTTCCGCTGATTGGTCTGCCCTGCTCTGTCACCCATTTGCCATTACGTAAACAGGCTGCAAAACTc < 1:2960414/69‑1 (MQ=255)
ttGCTTCCGCTGATTGGTCTGCCCTGCTCTGTCACCCATTTGCCATTACGTAAACAGGCTGCAAAACTc < 1:3026839/69‑1 (MQ=255)
ttGCTTCCGCTGATTGGTCTGCCCTGCTCTGTCACCCATTTGCCATTACGTAAACAGGCTGCAAAACTc < 1:3097307/69‑1 (MQ=255)
ttGCTTCCGCTGATTGGTCTGCCCTGCTCTGTCACCCATTTGCCATTACGTAAACAGGCTGCAAAACTc < 1:3158035/69‑1 (MQ=255)
ttGCTTCCGCTGATTGGTCTGCCCTGCTCTGTCACCCATTTGCCATTACGTAAACAGGCTGCAAAACTc < 1:1220755/69‑1 (MQ=255)
ttGCTTCCGCTGATTGGTCTGCCCTGCTCTGTCACCCATTTGCCATTACGTAAACAGGCTGCAAAACTc < 1:323362/69‑1 (MQ=255)
ttGCTTCCGCTGATTGGTCTGCCCTGCTCTGTCACCCATTTGCCATTACGTAAACAGGCTGCAAAACTc < 1:3432097/69‑1 (MQ=255)
ttGCTTCCGCTGATTGGTCTGCCCTGCTCTGTCACCCATTTGCCATTACGTAAACAGGCTGCAAAACTc < 1:417772/69‑1 (MQ=255)
ttGCTTCCGCTGATTGGTCTGCCCTGCTCTGTCACCCATTTGCCATTACGTAAACAGGCTGCAAAACTc < 1:645866/69‑1 (MQ=255)
ttGCTTCCGCTGATTGGTCTGCCCTGCTCTGTCACCCATTTGCCATTACGTAAACAGGCTGCAAAACTc < 1:835322/69‑1 (MQ=255)
ttGCTTCCGCTGATTGGTCTGCCCTGCTCTGTCACCCATTTGCCATTACGTAAACAGGCTGCAAAACTc < 1:953058/69‑1 (MQ=255)
ttGCTTCCGCTGATTGGTCTGCCCTGCTCTGTCACCCATTTGCCATTACGTAAACAGGCTGCAAAACTc < 1:980682/69‑1 (MQ=255)
ttGCTTCCGCTGATTGGTCTGCCCTGCTCTGTCACCCATTTGCCATTACGTAAACAGGCTGCAAAACTc < 1:2589281/69‑1 (MQ=255)
ttGCTTCCGCTGATTGGTCTGCCCTGCTCTGTCACCCATTTGCCATTACGTAAACAGGCTGCAAAACTc < 1:1438002/69‑1 (MQ=255)
ttGCTTCCGCTGATTGGTCTGCCCTGCTCTGTCACCCATTTGCCATTACGTAAACAGGCTGCAAAACTc < 1:1501624/69‑1 (MQ=255)
ttGCTTCCGCTGATTGGTCTGCCCTGCTCTGTCACCCATTTGCCATTACGTAAACAGGCTGCAAAACTc < 1:2356869/69‑1 (MQ=255)
ttGCTTCCGCTGATTGGTCTGCCCTGCTCTGTCACCCATTTGCCATTACGTAAACAGGCTGCAAAACTc < 1:1596793/69‑1 (MQ=255)
ttGCTTCCGCTGATTGGTCTGCCCTGCTCTGTCACCCATTTGCCATTACGTAAACAGGCTGCAAAACTc < 1:1691619/69‑1 (MQ=255)
ttGCTTCCGCTGATTGGTCTGCCCTGCTCTGTCACCCATTTGCCATTACGTAAACAGGCTGCAAAACTc < 1:2258055/69‑1 (MQ=255)
tGCTTCCGCTGATTGGTCTGCCCTGCTCTGTCACCCATTTGCCATTACGTAAACAGGCTGCAAAACTc < 1:158955/68‑1 (MQ=255)
gCTTCCGCTGATTGGTCTGCCCTGCTCTGTCACCCATTTGCCATTACGTAAACAGGCTGCAAAACTcc > 1:2439774/1‑68 (MQ=255)
gCTTCCGCTGATTGGTCTGCCCTGCTCTGTCACCCATTTGCCATTACGTAAACAGGCTGCAAAACTcc > 1:847771/1‑68 (MQ=255)
gCTTCCGCTGATTGGTCTGCCCTGCTCTGTCACCCATTTGCCATTACGTAAACAGGCTGCAAAACTCCa > 1:3008970/1‑69 (MQ=255)
gCTTCCGCTGATTGGTCTGCCCTGCTCTGTCACCCATTTGCCATTACGTAAACAGGCTGCAAAACTCCa > 1:181076/1‑69 (MQ=255)
gCTTCCGCTGATTGGTCTGCCCTGCTCTGTCACCCATTTGCCATTACGTAAACAGGCTGCAAAACTCCa > 1:3151184/1‑69 (MQ=255)
gCTTCCGCTGATTGGTCTGCCCTGCTCTGTCACCCATTTGCCATTACGTAAACAGGCTGCAAAACTCCa > 1:2848548/1‑69 (MQ=255)
gCTTCCGCTGATTGGTCTGCCCTGCTCTGTCACCCATTTGCCATTACGTAAACAGGCTGCAAAACTCCa > 1:2778633/1‑69 (MQ=255)
gCTTCCGCTGATTGGTCTGCCCTGCTCTGTCACCCATTTGCCATTACGTAAACAGGCTGCAAAACTCCa > 1:3233924/1‑69 (MQ=255)
gCTCCCGCTGATTGGTCTGCCCTGCTCTGTCACCCATTTGCCATTACGTAAACAGGCTGCAAAACTCCa > 1:146271/1‑69 (MQ=255)
ccGCTGATTGGTCTGCCCTGCTCTGTCGCCCATTTGCCAATACGTAAACAGGCGGCaa < 1:1661192/58‑1 (MQ=255)
ggTCTGCCCTGCTCTGTCGCCCATTTGCCATTACGTAAACAGGCGGCAAAACTCCAAACTGTGCGATc < 1:271174/68‑1 (MQ=255)
ccATTTGCCATTACGTAAACAGGCGGCAAAACTCCAAACTGTGCGATCCATTGGCCTGGTGCAAGACgg < 1:2127476/69‑1 (MQ=255)
ccATTTGCCATTACGTAAACAGGCGGCAAAACTCCAAACTGTGCGATCCATTGGCCTGGTGCAAGACgg < 1:2282185/69‑1 (MQ=255)
ccATTTGCCATTACGTAAACAGGCGGCAAAACTCCAAACTGTGCGATCCATTGGCCTGGTGCAAGACgg < 1:2419795/69‑1 (MQ=255)
ccATTTGACATTACGTAAACAGGCGGCAAAACTCCAAACTGTGCGATCCATTGGCCTGGTGCAAGACgg < 1:1096545/69‑1 (MQ=255)
tACGTAAACAGGCGGCAAAACTCCAAACTGTGCGATCCATTGGCCTGGTGCAAGACGGCACACTTTAtt > 1:135231/1‑69 (MQ=255)
tACGTAAACAGGCGGCAAAACTCCAAACTGTGCGATCCATTGGCCTGGTGCAAGACGGCACACTTTAtt > 1:2768839/1‑69 (MQ=255)
tACGTAAACAGGCGGCAAAACTCCAAACTGTGCGATCCATTGGCCTGGTGCAAGACGGCACACTTTAtt > 1:1232555/1‑69 (MQ=255)
tACGTAAACAGGCGGCAAAACTCCAAACTGTGCGATCCATTGGCCTGGTGCAAGACGGCACACTTTAtt > 1:2981582/1‑69 (MQ=255)
tACGTAAACAGGCGGCAAAACTCCAAACTGTGCGATCCATTGGCCGGGTGCAAGACGGCACACTTTAtt > 1:888002/1‑69 (MQ=255)
tACGCAAACAGGCGGCAAAACTCCAAACTGTGCGATCCATTGGCCTGGTGCAAGACGGCACACTTTAtt > 1:123401/1‑69 (MQ=255)
|
AAGTCTTGCTTCCGCTGATTGGTCTGCCCTGCTCTGTCGCCCATTTGCCATTACGTAAACAGGCGGCAAAACTCCAAACTGTGCGATCCATTGGCCTGGTGCAAGACGGCACACTTTATT > minE/1202548‑1202667
|
| 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
