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 |
680,673 |
A→G |
30.4% |
V125V (GTT→GTC) |
yccF ← |
conserved inner membrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 680,673 | 0 | A | G | 30.4%
| 60.4
/ 31.8
| 69 | V125V (GTT→GTC) | yccF | conserved inner membrane protein |
| Reads supporting (aligned to +/- strand): ref base A (20/28); new base G (2/19); total (22/47) |
| Fisher's exact test for biased strand distribution p-value = 1.07e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.11e-01 |
CGACGTGCATTGGCTTCACGCGCAGCTTGCGCTGTTTCTACCGATACCACGCGACGACCAACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAGGAATGCCAAT > minE/680614‑680732
|
cgacgTGCATTGGCTTCACGCGCAGCTTGCGCTGTTTCTACCGATACCACGCGACGACCAACCGGCCAt < 1:2779664/69‑1 (MQ=255)
cgacgTGCATTGGCTTCACGCGCAGCTTGCGCTGTTTCTACCGATACCACGCGACGACCAACCGGCCAt < 1:1073508/69‑1 (MQ=255)
cgacgTGCATTGGCTTCACGCGCAGCTTGCGCTGTTTCTACCGATACCACGCGACGACCAACCGGCCAt < 1:1087089/69‑1 (MQ=255)
cgacgTGCATTGGCTTCACGCGCAGCTTGCGCTGTTTCTACCGATACCACGCGACGACCAACCGGCCAt < 1:1101120/69‑1 (MQ=255)
cgacgTGCATTGGCTTCACGCGCAGCTTGCGCTGTTTCTACCGATACCACGCGACGACCAACCGGCCAt < 1:1198959/69‑1 (MQ=255)
cgacgTGCATTGGCTTCACGCGCAGCTTGCGCTGTTTCTACCGATACCACGCGACGACCAACCGGCCAt < 1:2863546/69‑1 (MQ=255)
cgacgTGCATTGGCTTCACGCGCAGCTTGCGCTGTTTCTACCGATACCACGCGACGACCAACCGGCCAt < 1:2345522/69‑1 (MQ=255)
cgacgTGCATTGGCTTCACGCGCAGCTTGCGCTGTTTCTACCGATACCACGCGACGACCAACCGGCCAt < 1:2520078/69‑1 (MQ=255)
cgacgTGCATTGGCTTCACGCGCAGCTTGCGCTGTTTCTACCGATACCACGCGACGACCAACCGCCCAt < 1:3314691/69‑1 (MQ=255)
gacgTGCATTGGCTTCACGCGCAGCTTGCGCTGTTTCTACCGATACCACGCGACGACCAACCGGCCAt < 1:3276724/68‑1 (MQ=255)
cATTGGCTTCACGCGCAGCTTGCGCTGTTTCTACCGCTACCACGCGACGACCAACCGGCCATAGTGc > 1:1012107/1‑67 (MQ=255)
cATTGGCTTCACGCGCAGCTTGCGCTGTTTCTACCGATACCCCGCGACGACCATCCGGCCATAGTGc > 1:1722556/1‑67 (MQ=255)
cACGCGCAGCTTGCGCTGTTTCTACCGATACCACGCGACGACCAACCGGCCATAGTGc > 1:692238/1‑58 (MQ=255)
cACGCGCAGCTTGCGCTGTTTCTACCGATACCACGCGACGACCAACCGGCCATAGTGc > 1:3102556/1‑58 (MQ=255)
cACGCGCAGCTTGCGCTGTTTCTACCGATACCACGCGACGACCAACCGGCCATAGTGc > 1:2830466/1‑58 (MQ=255)
cACGCGCAGCTTGCGCTGTTTCTACCGATACCACGCGACGACCAACCGGCCATAGTGc > 1:2330400/1‑58 (MQ=255)
cACGCGCAGCTTGCGCTGTTTCTACCGATACCACGCGACGACCAACCGGCCATAGTGc > 1:4078/1‑58 (MQ=255)
cACGCGCAGCTTGCGCTGTTTCTACCGATACCACGCGACGACCAACCGGCCATAGTGc > 1:2012388/1‑58 (MQ=255)
cACGCGCAGCTTGCGCTGTTTCTACCGATACCACGCGACGACCAACCGGCCATAGTGc > 1:1903539/1‑58 (MQ=255)
cACGCGCAGCTTGCGCTGTTTCTACCGATACCACGCGACGACCAACCGGCCATAGTGc > 1:1401855/1‑58 (MQ=255)
cACGCGCAGCTTGCGCTGTTTCTACCGATACCACGCGACGACCAACCGGCCATAGTGc > 1:1044644/1‑58 (MQ=255)
cACGCGCAGCTTGCGCTGTTTCTACCGATACCACGCGACGACCAACCGGCCATAGTGc > 1:1083791/1‑58 (MQ=255)
cACGCGCAGCTTGCGCTGTTTCTACCGATACCACGCGACGACCAACCGGCCATAGTGc > 1:933166/1‑58 (MQ=255)
cACGCGCAGCTTGCGCTGTTTCTACCGATACCACGCGACGACCAACCGGCCATAGTGc > 1:1627923/1‑58 (MQ=255)
cACGCGCAGCTTGCGCTGTTTCTACCGATACCACGCGACGACCAACCGGCCATAGTGc > 1:757359/1‑58 (MQ=255)
cACGCGCAGCTTGCGCTGTTTCTACCGATACCACGCGACGACCAACCGGCCATAGTGc > 1:771543/1‑58 (MQ=255)
cACGCGCAGCTTGCGCTGTTTCTACCGATACCACGCGACGACCAACCGGCCATAGTGCAATAGCGGCaa > 1:3193232/1‑69 (MQ=255)
cACGCGCAGCTTGCGCTGTTTCTACCGATACCACGCGACGACCAACCGGCCATAGTGCAATAGCGGCaa > 1:3301449/1‑69 (MQ=255)
cAGCTTGCGCTGTTTCTACCGATACCACGCGACGACCAACCGGCCATAGTGCAATAGCGGCAATTTTaa > 1:78705/1‑69 (MQ=255)
ttGCGCTGTTTCTACCGATACCACGCTACGACCAACCGGCCAt < 1:2841179/43‑1 (MQ=255)
gcTGTTTCTACCGATACCACGCGACGACCAACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGc < 1:2880691/68‑1 (MQ=255)
gcTGTTTCTACCGATACCACGCGACGACCAACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGc < 1:667475/68‑1 (MQ=255)
tCTACCGATACCACGCGACGACCAACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATGcc > 1:2357115/1‑68 (MQ=255)
gATACCACGCGACGACCAACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAgg < 1:2463033/68‑1 (MQ=255)
gATACCACGCGACGACCAACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAgg < 1:2617217/68‑1 (MQ=255)
ccACGCGACGACCAACCGGCCATAGTGCAATAGCGGCGATTTTAAAGTTCGCAATGCCGACAgg < 1:2965381/64‑1 (MQ=255)
ccACGCGACGACCAACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAgg < 1:158723/64‑1 (MQ=255)
ccACGCGACGACCAACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAgg < 1:1367840/64‑1 (MQ=255)
ccACGCGACGACCAACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAgg < 1:1306566/64‑1 (MQ=255)
ccACGCGACGACCAACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAgg < 1:2612564/64‑1 (MQ=255)
ccACGCGACGACCAACCGGCCATAGTCCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAgg < 1:1250746/64‑1 (MQ=255)
aCGCGACGACCAACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAGGAATGCCa < 1:71579/69‑1 (MQ=255)
aCGCGACGACCAACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAGGAATGCCa < 1:974698/69‑1 (MQ=255)
aCGCGACGACCAACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAGGAATGCCa < 1:2672217/69‑1 (MQ=255)
aCGCGACGACCAACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAGGAATGCCa < 1:1821078/69‑1 (MQ=255)
aCGCGACGACCAACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAGGAATGCCa < 1:189884/69‑1 (MQ=255)
aCGCGACGACCAACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAGGAATGCCa < 1:1968240/69‑1 (MQ=255)
aCGCGACGACCAACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAGGAATGCCa < 1:2319079/69‑1 (MQ=255)
gcgACGACCGACCGGGCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:2648430/69‑1 (MQ=255)
gcgACGACCGACCGGCCATAGTGCAGTAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:2831184/69‑1 (MQ=255)
gcgACGACCGACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:233199/69‑1 (MQ=255)
gcgACGACCGACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt > 1:1410835/1‑69 (MQ=255)
gcgACGACCGACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:1479843/69‑1 (MQ=255)
gcgACGACCGACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:843413/69‑1 (MQ=255)
gcgACGACCGACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:1662434/69‑1 (MQ=255)
gcgACGACCGACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:1694984/69‑1 (MQ=255)
gcgACGACCGACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:2321559/69‑1 (MQ=255)
gcgACGACCGACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:3434385/69‑1 (MQ=255)
gcgACGACCGACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:2776128/69‑1 (MQ=255)
gcgACGACCGACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:237531/69‑1 (MQ=255)
gcgACGACCGACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:2529724/69‑1 (MQ=255)
gcgACGACCGACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:2598150/69‑1 (MQ=255)
gcgACGACCGACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:2603918/69‑1 (MQ=255)
gcgACGACCGACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:304952/69‑1 (MQ=255)
gcgACGACCGACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:2650209/69‑1 (MQ=255)
gcgACGACCGACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:2841425/69‑1 (MQ=255)
gcgACGACCGACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:2696012/69‑1 (MQ=255)
gcgACGACCGACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt > 1:2730403/1‑69 (MQ=255)
cgacgaCCGACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:685974/68‑1 (MQ=255)
|
CGACGTGCATTGGCTTCACGCGCAGCTTGCGCTGTTTCTACCGATACCACGCGACGACCAACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAGGAATGCCAAT > minE/680614‑680732
|
| 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
