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 |
1,678,452 |
G→A |
68.0% |
D520D (GAC→GAT) |
pbpC ← |
fused transglycosylase and transpeptidase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,678,452 | 0 | G | A | 68.0%
| 62.6
/ 39.3
| 78 | D520D (GAC→GAT) | pbpC | fused transglycosylase and transpeptidase |
| Reads supporting (aligned to +/- strand): ref base G (17/8); new base A (47/6); total (64/14) |
| Fisher's exact test for biased strand distribution p-value = 5.39e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-01 |
CCGGTCTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCGTCACGATAGCCATAGCTGGTGCCCGTTTTCCATGCCAGTGGGGCGACGCGCGGCAAGGC > minE/1678394‑1678511
|
ccGGTCTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCGTCACGATAGc < 1:635492/69‑1 (MQ=255)
ccGGTCTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCGTCACGATAGc < 1:881197/69‑1 (MQ=255)
ctgTCTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAg > 1:465768/3‑67 (MQ=255)
cGGTCTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCGTCACGATAGc > 1:52160/1‑68 (MQ=255)
cGGTCTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCGTCACGATAGc > 1:3192956/1‑68 (MQ=255)
cGGTCTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCGTCACGATAGc < 1:93572/68‑1 (MQ=255)
cGGTCTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCGTCACGATAGc > 1:3046718/1‑68 (MQ=255)
cGGTCTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCGTCACGATAGc > 1:197584/1‑68 (MQ=255)
cGGTCTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAg > 1:687311/1‑67 (MQ=255)
cGGTCTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAg > 1:701214/1‑67 (MQ=255)
cGGTCTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAg > 1:454075/1‑67 (MQ=255)
cGGTCTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAg > 1:1968917/1‑67 (MQ=255)
cGGTCTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAg > 1:1972280/1‑67 (MQ=255)
cGGTCTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAg > 1:658030/1‑67 (MQ=255)
cGGTCTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAg > 1:2801753/1‑67 (MQ=255)
cGGTCTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAg > 1:553840/1‑67 (MQ=255)
cGGTCTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAg > 1:2192210/1‑67 (MQ=255)
cGGTCTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAg > 1:505163/1‑67 (MQ=255)
cGGTCTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAg > 1:172508/1‑67 (MQ=255)
cGGTCTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAg > 1:16721/1‑67 (MQ=255)
cGGTCTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAg > 1:829546/1‑67 (MQ=255)
cGGTCTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAg > 1:1548323/1‑67 (MQ=255)
cGGTCTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAg > 1:3091008/1‑67 (MQ=255)
cGGTCTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAg > 1:1482725/1‑67 (MQ=255)
cGGTCTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAg > 1:3395846/1‑67 (MQ=255)
cGGTCTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAg > 1:1329224/1‑67 (MQ=255)
cGGTCTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAg > 1:1266402/1‑67 (MQ=255)
cGGTCTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAg > 1:1216802/1‑67 (MQ=255)
cGGTCTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAg > 1:10958/1‑67 (MQ=255)
cGGTCTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAg > 1:3295918/1‑67 (MQ=255)
gTCTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCGTCACGATAGCCAt < 1:2848161/69‑1 (MQ=255)
cTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGGCCAGGCGTCACGATAGCCATAg > 1:2055272/1‑69 (MQ=255)
cTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCGTCACGATAGCCATAg > 1:238570/1‑69 (MQ=255)
cTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCGTCACGATAGCCATAg > 1:1301527/1‑69 (MQ=255)
cTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCGTCACGATAGCCATAg > 1:1339231/1‑69 (MQ=255)
cTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCGTCACGATAGCCATAg > 1:1903186/1‑69 (MQ=255)
cTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCGTCACGATAGCCATAg > 1:1872857/1‑69 (MQ=255)
cTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCGTCACGATAGCCATAg > 1:428710/1‑69 (MQ=255)
gATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCGTCACGATAGCCATAGCTGGTGCCCg < 1:2732165/68‑1 (MQ=255)
aTGACATAGCGAGCGTTACCCCCAATCGCCCAGGCATCACGATAGCCATAGCTGGTGCCCGTTTTCCAt > 1:3107847/1‑69 (MQ=255)
aTGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAGCCATa > 1:2672535/1‑50 (MQ=255)
aTGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAGCCATa > 1:915083/1‑50 (MQ=255)
aTGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAGCCATAGCTGGTGc > 1:2119397/1‑58 (MQ=255)
aTGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAGCCATAGCTGGTGCCCGTTTTCCAt > 1:35401/1‑69 (MQ=255)
aTGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAGCCATAGCTGGTGCCCGTTTTCCAt > 1:3420432/1‑69 (MQ=255)
aTGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAGCCATAGCTGGTGCCCGTTTTCCAt > 1:856189/1‑69 (MQ=255)
aTGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAGCCATAGCTGGTGCCCGTTTTCCAt > 1:941545/1‑69 (MQ=255)
aTGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAGCCATAGCTGGTGCCCGTTTTCCAt > 1:546985/1‑69 (MQ=255)
aTGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAGCCATAGCTGGTGCCCGTTTTCCAt > 1:3391137/1‑69 (MQ=255)
aTGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAGCCATAGCTGGTGCCCGTTTTCCAt > 1:52735/1‑69 (MQ=255)
aTGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAGCCATAGCTGGTGCCCGTTTTCCAt > 1:10557/1‑69 (MQ=255)
aTGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAGCCATAGCTGGTGCCCGTTTTCCAt > 1:2369824/1‑69 (MQ=255)
aTGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAGCCATAGCTGGTGCCCGTTTTCCAt > 1:1094632/1‑69 (MQ=255)
aTGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAGCCATAGCTGGTGCCCGTTTTCCAt > 1:1810712/1‑69 (MQ=255)
aTGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAGCCATAGCTGGTGCCCGTTTTCCAt > 1:1980917/1‑69 (MQ=255)
aTGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAGCCATAGCTGGTGCCCGTTTTCCAt > 1:2112903/1‑69 (MQ=255)
aTGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAGCCATAGCTGGTGCCCGTTTTCCAt > 1:2148334/1‑69 (MQ=255)
aTGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAGCCATAGCTGGTGCCCGTTTTCCAt > 1:3351367/1‑69 (MQ=255)
aTGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAGCCATAGCTGGTGCCCGTTTTCCAt > 1:238392/1‑69 (MQ=255)
aTGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAGCCATAGCTGGTGCCCGTTTTCCAt > 1:2728083/1‑69 (MQ=255)
aTGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAGCCATAGCTGGTGCCCGTTTTCCAt > 1:3183254/1‑69 (MQ=255)
aTGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAGCCATAGCTGGTGCCCGTTTTCCAt > 1:3032872/1‑69 (MQ=255)
aTGACATAGCGAGCGTTAACCCCAATCGCCCAGGCATCACGATAGCCATAGCTGGTGCCCGTTTTCCAt > 1:2983799/1‑69 (MQ=255)
aaCCCCAATCGCCCAGGCGTCACGATAGCCATAGCTGGTGCCCGtt > 1:2761095/1‑46 (MQ=255)
aaCCCCAATCGCCCAGGCGTCACGATAGCCATAGCTGGTGCCCGTTTTCCATGCCAGTGGGGCGAcgcg > 1:171393/1‑69 (MQ=255)
ccAATCGCCCAGGCGTCACGATAGCCATAGCTGGTGCCCGTTTTCCATGCCAGTGGGGCGACGCGCGGc < 1:2881047/69‑1 (MQ=255)
cAATCGCCCAGGCGTCACGATAGCCATAGCTGGTGCCCGTTTTCCATGCCAGTGGGGCGACGCGCGGc < 1:1627843/68‑1 (MQ=255)
cGCCCAGGCGTCACGATAGCCATAGCTGGTGCCCGTTTTCCATGCCAGTGGGGCGACGCGCGGCAAGGc > 1:3145353/1‑69 (MQ=255)
cGCCCAGGCGTCACGATAGCCATAGCTGGTGCCCGTTTTCCATGCCAGTGGGGCGACGCGCGGCAAGGc > 1:2683258/1‑69 (MQ=255)
cGCCCAGGCGTCACGATAGCCATAGCTGGTGCCCGTTTTCCATGCCAGTGGGGCGACGCGCGGCAAGGc > 1:871241/1‑69 (MQ=255)
cGCCCAGGCGTCACGATAGCCATAGCTGGTGCCCGTTTTCCATGCCAGTGGGGCGACGCGCGGCAAGGc > 1:1417462/1‑69 (MQ=255)
gCCCAGGCATCACGATAGCCATAGCTGGTGCCCGTTTTCCATGCCAGTGGGGCGACGCGCGGCAAGGc < 1:402861/68‑1 (MQ=255)
gCCCAGGCATCACGATAGCCATAGCTGGTGCCCGTTTTCCATGCCAGTGGGGCGACGCGCGGCAAGGc < 1:2940817/68‑1 (MQ=255)
gCCCAGGCATCACGATAGCCATAGCTGGTGCCCGTTTTCCATGCCAGTGGGGCGACGCGCGGCAAGGc < 1:3398498/68‑1 (MQ=255)
gCCCAGGCATCACGATAGCCATAGCTGGTGCCCGTTTTCCATGCCAGTGGGGCGACGCGCGGCAAGGc < 1:725224/68‑1 (MQ=255)
gCCCAGGCATCACGATAGCCATAGCTGGTGCCCGTTTTCCATGCCAGTGGGGCGACGCGCGGCAAGGc < 1:1667646/68‑1 (MQ=255)
gCCCAGGCATCACGATAGCCATAGCTGGTGCCCGTTTTCCATGCCAGTGGGGCGACGCGCGGCAAGGc < 1:1534101/68‑1 (MQ=255)
ccAGGCGTCACGATAGCCATAGCTGGTGCCCGTTTTCCATGCCAGTGGGGCGACGCGCGGc < 1:1542059/61‑1 (MQ=255)
|
CCGGTCTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCGTCACGATAGCCATAGCTGGTGCCCGTTTTCCATGCCAGTGGGGCGACGCGCGGCAAGGC > minE/1678394‑1678511
|
| 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
