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 |
1,679,847 |
G→A |
29.9% |
R55R (CGC→CGT) |
pbpC ← |
fused transglycosylase and transpeptidase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,679,847 | 0 | G | A | 29.9%
| 47.5
/ 19.8
| 50 | R55R (CGC→CGT) | pbpC | fused transglycosylase and transpeptidase |
| Reads supporting (aligned to +/- strand): ref base G (9/26); new base A (12/3); total (21/29) |
| Fisher's exact test for biased strand distribution p-value = 5.50e-04 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.53e-01 |
ACGTGGAGAAACATCTTCGATTGTTACCGGATAACGCCAGATGCCGTCAGCATCGGCGAAGCGCCAGAGCGGCGTACCATCCTGCGCCACGACCACTCGTGCGGGATTGACTTCATGCAGCGG > minE/1679787‑1679909
|
aCGTGGAGAAACATCTTCGATTGTTACTGGATAACGCCAGATGCCGTCAGCATCGGCGAAACGCCagag < 1:1013791/69‑1 (MQ=255)
aCGTGGAGAAACATCTTCGATTGTTACTGGATAACGCCAGATGCCGTCAGCATCGGCGAAACGCCagag < 1:1183915/69‑1 (MQ=255)
aCGTGGAGAAACATCTTCGATTGTTACTGGATAACGCCAGATGCCGTCAGCATCGGCGAAACGCCagag < 1:585360/69‑1 (MQ=255)
aCCGGATAACGCCAGATGCCGTCAGCATCGGCGAAGCGCCAGAGCGGCGTACCATCCTGCGCCACGAc < 1:1314839/68‑1 (MQ=255)
aCCGGATAACGCCAGATGCCGTCAGCATCGGCGAAGCGCCAGAGCGGCGTACCATCCTGCGCCACGAc < 1:910781/68‑1 (MQ=255)
aCCGGATAACGCCAGATGCCGTCAGCATCGGCGAAGCGCCAGAGCGGCGTACCATCCTGCGCCACGAc < 1:69460/68‑1 (MQ=255)
ctggATAACGCCAGATGCCGTCAGCATCGGCGAAACGCCAGAGTGGCGTACCAt > 1:1169010/3‑54 (MQ=38)
ctggATAACGCCAGATGCCGTCAGCATCGGCGAAACGCCAGAGTGGCGTACCAt > 1:2762369/3‑54 (MQ=38)
ctggATAACGCCAGATGCCGTCAGCATCGGCGAAACGCCAGAGTGGCGTACCATCCTGCGccaccacca > 1:65101/3‑69 (MQ=255)
ctggATAACGCCAGATGCCGTCAGCATCGGCGAAACGCCAGAGTGGCGTACCATCCTGCGccaccacca > 1:1790444/3‑69 (MQ=255)
ctggATAACGCCAGATGCCGTCAGCATCGGCGAAACGCCAGAGTGGCGTACCATCCTGCGccaccacca > 1:1876962/3‑69 (MQ=255)
ctggATAACGCCAGATGCCGTCAGCATCGGCGAAACGCCAGAGTGGCGTACCATCCTGCGccaccacca > 1:2915755/3‑69 (MQ=255)
ctggATAACGCCAGATGCCGTCAGCATCGGCGAAACGCCAGAGTGGCGTACCATCCTGCGccaccacca > 1:945285/3‑69 (MQ=255)
ctggATAACGCCAGATGCCGTCAGCATCGGCGAAACGCCAGAGTGGCGTACCATCCTGCGccaccacca > 1:2467055/3‑69 (MQ=255)
ctggATAACGCCAGATGCCGTCAGCATCGGCGAAACGCCAGAGTGGCGTACCATCCTGCGcc > 1:1343055/3‑62 (MQ=39)
ctggATAACGCCAGATGCCGTCAGCATCGGCGAAACGCCAGAGTGGCGTACCATCCTGCGCCaccacc > 1:3148372/3‑68 (MQ=255)
ctggATAACGCCAGATGCCGTCAGCATCGGCGAAACGCCAGAGTGGCGTACCATCCTGCGCCaccacc > 1:2615319/3‑68 (MQ=255)
ctggATAACGCCAGATGCCGTCAGCATCGGCGAAACGCCAGAGTGGCGTACCATCCTACGccaccacca > 1:2077950/3‑69 (MQ=255)
aGATGCCGTCAGCATCGGCGAAGCGCCAGAGCGGCGTACCATCCTGCGCCACGACCACTCGTg > 1:2660592/1‑63 (MQ=255)
aGATGCCGTCAGCATCGGCGAAGCGCCAGAGCGGCGTACCATCCTGCGCCACGACCACTCGTGCggg > 1:391637/1‑67 (MQ=255)
aGATGCCGTCAGCATCGGCGAAGCGCCAGAGCGGCGTACCATCCTGCGCCACGACCACTCGTGCGGGa > 1:1363845/1‑68 (MQ=255)
aGATGCCGTCAGCATCGGCGAAGCGCCAGAGCGGCGTACCATCCTGCGCCACGACCACTCGTGCGGGa > 1:3307787/1‑68 (MQ=255)
aGATGCCGTCAGCATCGGCGAAGCGCCAGAGCGGCGTACCATCCTGCGCCACGACCACTCGTGCGGGa > 1:3433260/1‑68 (MQ=255)
aGATGCCGTCAGCATCGGCGAAGCGCCAGAGCGGCGTACCATCCTGCGCCACGACCACTCGTGCGGGa > 1:1915854/1‑68 (MQ=255)
aGATGCCGTCAGCATCGGCGAAGCGCCAGAGCGGCGTACCATCCTGCGCCACGACCACTCGTGCGGGa > 1:751581/1‑68 (MQ=255)
aGATGCCGTCAGCATCGGCGAAGCGCCAGAGCGGCGTACCATCCTGCGCCACGACCACTCGTGCGGGa > 1:893258/1‑68 (MQ=255)
aGATGCCGTCAGCATCGGCGAAGCGCCAGAGCGGCGTACCATCCTGCGCCACGACCACTCGTGCGGGa > 1:2365515/1‑68 (MQ=255)
ccGTCAGCATCGGCGAAGCGCCAGAGCGGCGTACCATCCTGCGCCACGACCACTCGTGCGGGATTGACt < 1:2209589/69‑1 (MQ=255)
ccGTCAGCATCGGCGAAGCGCCAGAGCGGCGTACCATCCTGCGCCACGACCACTCGTGCGGGATTGACt < 1:2663726/69‑1 (MQ=255)
ccGTCAGCATCGGCGAAGCGCCAGAGCGGCGTACCATCCTGCGCCACGACCACTCGTGCGGGATTGACt < 1:2752940/69‑1 (MQ=255)
ccGTCAGCATCGGCGAAGCGCCAGAGCGGCGTACCATCCTGCGCCACGACCACTCGTGCGGGATTGACt < 1:1409724/69‑1 (MQ=255)
ccGTCAGCATCGGCGAAGCGCCAGAGCGGCGTACCATCCTGCGCCACGACCACTCGTGCGGGATTGACt < 1:1534050/69‑1 (MQ=255)
ccGTCAGCATCGGCGAAGCGCCAGAGCGGCGTACCATCCTGCGCCACGACCACTCGTGCGGGATTGACt < 1:3159159/69‑1 (MQ=255)
ccGTCAGCATCGGCGAAGCGCCAGAGCGGCGTACCATCCTGCGCCACGACCACTCGTGCGGGATTGACt < 1:2431300/69‑1 (MQ=255)
gTCAGCATCGGCGAAGCGCCAGAGCGGCGTACCATCCTGCGCCACGACCACTCGTGCGGGATTGACtt < 1:972870/68‑1 (MQ=255)
gTCAGCATCGGCGAAGCGCCAGAGCGGCGTACCATCCTGCGCCACGACCACTCGTGCGGGATTGACtt < 1:367347/68‑1 (MQ=255)
gTCAGCATCGGCGAAGCGCCAGAGCGGCGTACCATCCTGCGCCACGACCACTCGTGCGGGATTGACtt < 1:3224782/68‑1 (MQ=255)
gTCAGCATCGGCGAAGCGCCAGAGCGGCGTACCATCCTGCGCCACGACCACTCGTGCGGGATTGACtt < 1:2672010/68‑1 (MQ=255)
aTCGGCGAAGCGCCAGAGCGGCGTACCATCCTGCGCCACGACCACTCGTGCGGGATTGACtt < 1:3106685/62‑1 (MQ=255)
aTCGGCGAAGCGCCAGAGCGGCGTACCATCCTGCGCCACGACCACTCGTGCGGGATTGACtt < 1:571439/62‑1 (MQ=255)
aTCGGCGAAGCGCCAGAGCGGCGTACCATCCTGCGCCACGACCACTCGTGCGGGATTGACtt < 1:1913514/62‑1 (MQ=255)
aTCGGCGAAGCGCCAGAGCGGCGTACCATCCTGCGCCACGACCACTCGTGCGGGATTGACtt < 1:2612499/62‑1 (MQ=255)
aTCGGCGAAGCGCCAGAGCGGCGTACCATCCTGCGCCACGACCACTCGTGCGGGATTGACtt < 1:86819/62‑1 (MQ=255)
aTCGGCGAAGCGCCAGAGCGGCGTACCATCCTGCGCCACGACCACTCGTGCGGGATTGACtt < 1:2482072/62‑1 (MQ=255)
aTCGGCGAAGCGCCAGAGCGGCGTACCATCCTGCGCCACGACCACTCGTGCGGGATTGACtt < 1:1329388/62‑1 (MQ=255)
aTCGGCGAAGCGCCAGAGCGGCGTACCATCCTGCGCCACGACCACTCGTGCGGGATTGACtt < 1:2297204/62‑1 (MQ=255)
tCGGCGAAGCGCCAGAGCGGCGTACCATCCTGCGCCACGACCACTCGTGCGGGATTGACtt < 1:1883650/61‑1 (MQ=255)
ggCGAAGCGCCAGAGCGGCGTACCATCCTGCGCCACGACCACTCGTGCGGGATTGACTTCATGCAGCgg < 1:1751540/69‑1 (MQ=255)
ggCGAAGCGCCAGAGCGGCGTACCATCCTGCGCCACGACCACTCGTGCGGGATTGACTTCATGCAGCgg < 1:685693/69‑1 (MQ=255)
ggCGAAGCGCCAGAGCGGCGTACCATCCTGCGCCACGACCACTCGTGCGGGATTGACTTCATGCAGCgg < 1:1340985/69‑1 (MQ=255)
|
ACGTGGAGAAACATCTTCGATTGTTACCGGATAACGCCAGATGCCGTCAGCATCGGCGAAGCGCCAGAGCGGCGTACCATCCTGCGCCACGACCACTCGTGCGGGATTGACTTCATGCAGCGG > minE/1679787‑1679909
|
| 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
