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 |
626,273 |
T→C |
31.6% |
S62S (AGT→AGC) |
ycaQ → |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 626,273 | 0 | T | C | 31.6%
| 66.4
/ 39.3
| 79 | S62S (AGT→AGC) | ycaQ | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (37/17); new base C (20/5); total (57/22) |
| Fisher's exact test for biased strand distribution p-value = 4.19e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.60e-01 |
TGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTCTCTGGCGCGTGGCGAATTAATGGAATAC > minE/626209‑626339
|
tGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCGTAGTCCATATCTGGTGCTTTTCAgtcgtc > 1:3257880/1‑69 (MQ=255)
tGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCGTAGTCCATATCTGGTGCTTTTCAgtcgtc > 1:133103/1‑69 (MQ=255)
tGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCGTAGTCCATATCTGGTGCTTTTCAgtcgt > 1:564396/1‑68 (MQ=255)
tCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCt > 1:966354/1‑68 (MQ=255)
tCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCt > 1:2862215/1‑68 (MQ=255)
tCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCt > 1:3436353/1‑68 (MQ=255)
aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAgccg > 1:1685817/1‑55 (MQ=255)
aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTAt > 1:1746876/1‑68 (MQ=255)
aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc > 1:594451/1‑69 (MQ=255)
aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc > 1:3017598/1‑69 (MQ=255)
aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc > 1:2997019/1‑69 (MQ=255)
aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc > 1:2234190/1‑69 (MQ=255)
aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc > 1:3362860/1‑69 (MQ=255)
aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc > 1:1819781/1‑69 (MQ=255)
aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc > 1:3420740/1‑69 (MQ=255)
aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc > 1:2237045/1‑69 (MQ=255)
aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc > 1:2307125/1‑69 (MQ=255)
aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc > 1:1731285/1‑69 (MQ=255)
aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc > 1:1093865/1‑69 (MQ=255)
aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc > 1:2738872/1‑69 (MQ=255)
aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc > 1:484176/1‑69 (MQ=255)
aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc > 1:1523200/1‑69 (MQ=255)
aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc > 1:516147/1‑69 (MQ=255)
aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc > 1:2577171/1‑69 (MQ=255)
aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc > 1:1393987/1‑69 (MQ=255)
aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc > 1:131070/1‑69 (MQ=255)
aaaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTCTCAGCCGTCTGGGAGATTATc > 1:2102096/1‑69 (MQ=255)
aaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGTGAGATTATc < 1:3004942/68‑1 (MQ=255)
aaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc < 1:2498651/68‑1 (MQ=255)
aaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc < 1:5181/68‑1 (MQ=255)
aaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc < 1:533575/68‑1 (MQ=255)
aaTCGATACCATCAATATTGTTGTCCGTAGCCCATATCTGGTGCTTTTCAGCCGTCTGGGAGATTATc < 1:885545/68‑1 (MQ=255)
tCGATACCATCAATATTGTTGCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTg > 1:3360344/1‑69 (MQ=255)
tCGATACCATCAATATTGTTGCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTg > 1:867053/1‑69 (MQ=255)
tCGATACCATCAATATTGTTGCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTg > 1:1427952/1‑69 (MQ=255)
aaTATTGTTGCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTg > 1:3272872/1‑69 (MQ=255)
aaTATTGTTGCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTg > 1:2216587/1‑69 (MQ=255)
aaTATTGTTGCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTg > 1:757102/1‑69 (MQ=255)
aaTATTGTTGCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTg > 1:349397/1‑69 (MQ=255)
ttgttgCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATg > 1:3293259/1‑69 (MQ=255)
ttgttgCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATg > 1:3324505/1‑69 (MQ=255)
ttgttgCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATg > 1:1306717/1‑69 (MQ=255)
ttgttgCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATg > 1:2808472/1‑69 (MQ=255)
ttgttgCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATg > 1:1653515/1‑69 (MQ=255)
ttgttgCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATg > 1:1066277/1‑69 (MQ=255)
ttgttgCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATg > 1:2730976/1‑69 (MQ=255)
gttgCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGa < 1:2574915/68‑1 (MQ=255)
gttgCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGa < 1:1999733/68‑1 (MQ=255)
gttgCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGa < 1:2149632/68‑1 (MQ=255)
gCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGtc < 1:3352669/68‑1 (MQ=255)
gCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGtc < 1:3325009/68‑1 (MQ=255)
gCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGtc < 1:1357729/68‑1 (MQ=255)
gCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGtc < 1:2382793/68‑1 (MQ=255)
cGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTctct < 1:1269484/68‑1 (MQ=255)
cATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTCTCTGGCGCGt > 1:1410443/1‑68 (MQ=255)
cATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTCTCTGGCGCGTg > 1:2634035/1‑69 (MQ=255)
cATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTCTCTGGCGCGTg > 1:412140/1‑69 (MQ=255)
cATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTCTCTGGCGCGTg > 1:3068812/1‑69 (MQ=255)
cATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTCTCTGGCGCGTg > 1:1731875/1‑69 (MQ=255)
cATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTCTCTGGCGCGTg > 1:1770403/1‑69 (MQ=255)
cATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTCTCTGGCGCGTg > 1:3215624/1‑69 (MQ=255)
cATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTCTCTGGCGCGTg > 1:461938/1‑69 (MQ=255)
cATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTCTCTGGCGCGTg > 1:2120053/1‑69 (MQ=255)
cATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTCTCTGGCGCGTg > 1:1334499/1‑69 (MQ=255)
cATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTCTCTGGCGAGTg > 1:1914437/1‑69 (MQ=255)
tatCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTCTCTGGCGCGTgg > 1:1988987/1‑68 (MQ=255)
tatCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTCTCTGGCGCGTgg > 1:3243071/1‑68 (MQ=255)
tCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTCTCTGGCGCGTGGCGa > 1:1634396/1‑69 (MQ=255)
tCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTCTCTGGCGCGTGGCGa > 1:1544706/1‑69 (MQ=255)
tCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTCTCTGGCGCGTGGCGa > 1:1435371/1‑69 (MQ=255)
tCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTCTCTGGCGCGTGGCGa > 1:3215951/1‑69 (MQ=255)
tCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTCTCTGGCGCGTGGCGa > 1:1276587/1‑69 (MQ=255)
tCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTCTCTGGCGCGTGGCGa > 1:236781/1‑69 (MQ=255)
tCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTCTCTGGCGCGTGGCGa > 1:269730/1‑69 (MQ=255)
gCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTCTCTGGCGCGTGGCGAAtt < 1:3135630/66‑1 (MQ=255)
gCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTCTCTGGCGCGTGGCGAAtt < 1:2152586/66‑1 (MQ=255)
gCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTCTCTGGCGCGTGGCGAAtt < 1:2320527/66‑1 (MQ=255)
gCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTCTCTGGCGCGTGGCGAAtt < 1:2618148/66‑1 (MQ=255)
tttCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTCTCTGGCGCGTGGCGAATTAATgg < 1:3340818/68‑1 (MQ=255)
tttCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTCTCTGGCGCGTGGCGAATTAATgg < 1:2035335/68‑1 (MQ=255)
tttCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTCTCTGGCGCGTGGCGAATTAATgg < 1:2193294/68‑1 (MQ=255)
cAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTCTCTGGCGCGTGGCGAATTAATGGAAt < 1:402954/68‑1 (MQ=255)
cAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTCTCTGGCGCGTGGCGAATTAATGGAAt < 1:3118812/68‑1 (MQ=255)
gtcgtcTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTCTCTGGCGCGTGGCGAATTAATGGAATAc < 1:1376260/68‑1 (MQ=255)
gtcgtcTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTCTCTGGCGCGTGGCGAATTAATGGAATAc < 1:1876373/68‑1 (MQ=255)
gtcgtcTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTCTCTGGCGCGTGGCGAATTAATGGAATAc < 1:1348143/68‑1 (MQ=255)
gtcgtcTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTCTCTGGCGCGTGGCGAATTAATGGAATAc < 1:956212/68‑1 (MQ=255)
gtcgtcTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTCTCTGGCGCGTGGCGAATTAATGGAATAc < 1:1066632/68‑1 (MQ=255)
|
TGTCCTTGCTGCAAATCGATACCATCAATATTGTTGCCCGTAGTCCATATCTGGTGCTTTTCAGTCGTCTGGGAAATTATCCTGCCCAGTGGCTGGATGAGTCTCTGGCGCGTGGCGAATTAATGGAATAC > minE/626209‑626339
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
