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 |
680,715 |
G→A |
30.0% |
G111G (GGC→GGT) |
yccF ← |
conserved inner membrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 680,715 | 0 | G | A | 30.0%
| 71.5
/ 31.6
| 73 | G111G (GGC→GGT) | yccF | conserved inner membrane protein |
| Reads supporting (aligned to +/- strand): ref base G (16/35); new base A (2/20); total (18/55) |
| Fisher's exact test for biased strand distribution p-value = 7.33e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.39e-01 |
TCTACCGATACCACGCGACGACCAACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAGGAATGCCAATGATTGAAATACATTGTGCGATGCCCGTTGCAATGTGCATCAGGCAT > minE/680650‑680778
|
tCTACCGATACCACGCGACGACCAACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATGcc > 1:2357115/1‑68 (MQ=255)
gATACCACGCGACGACCAACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAgg < 1:2617217/68‑1 (MQ=255)
gATACCACGCGACGACCAACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAgg < 1:2463033/68‑1 (MQ=255)
ccACGCGACGACCAACCGGCCATAGTGCAATAGCGGCGATTTTAAAGTTCGCAATGCCGACAgg < 1:2965381/64‑1 (MQ=255)
ccACGCGACGACCAACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAgg < 1:1306566/64‑1 (MQ=255)
ccACGCGACGACCAACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAgg < 1:2612564/64‑1 (MQ=255)
ccACGCGACGACCAACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAgg < 1:1367840/64‑1 (MQ=255)
ccACGCGACGACCAACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAgg < 1:158723/64‑1 (MQ=255)
ccACGCGACGACCAACCGGCCATAGTCCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAgg < 1:1250746/64‑1 (MQ=255)
aCGCGACGACCAACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAGGAATGCCa < 1:974698/69‑1 (MQ=255)
aCGCGACGACCAACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAGGAATGCCa < 1:71579/69‑1 (MQ=255)
aCGCGACGACCAACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAGGAATGCCa < 1:2672217/69‑1 (MQ=255)
aCGCGACGACCAACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAGGAATGCCa < 1:2319079/69‑1 (MQ=255)
aCGCGACGACCAACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAGGAATGCCa < 1:1968240/69‑1 (MQ=255)
aCGCGACGACCAACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAGGAATGCCa < 1:189884/69‑1 (MQ=255)
aCGCGACGACCAACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAGGAATGCCa < 1:1821078/69‑1 (MQ=255)
gcgACGACCGACCGGGCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:2648430/69‑1 (MQ=255)
gcgACGACCGACCGGCCATAGTGCAGTAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:2831184/69‑1 (MQ=255)
gcgACGACCGACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:233199/69‑1 (MQ=255)
gcgACGACCGACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt > 1:2730403/1‑69 (MQ=255)
gcgACGACCGACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:2776128/69‑1 (MQ=255)
gcgACGACCGACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:2696012/69‑1 (MQ=255)
gcgACGACCGACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:2650209/69‑1 (MQ=255)
gcgACGACCGACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:2841425/69‑1 (MQ=255)
gcgACGACCGACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:2603918/69‑1 (MQ=255)
gcgACGACCGACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:2598150/69‑1 (MQ=255)
gcgACGACCGACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:2529724/69‑1 (MQ=255)
gcgACGACCGACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:304952/69‑1 (MQ=255)
gcgACGACCGACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:237531/69‑1 (MQ=255)
gcgACGACCGACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt > 1:1410835/1‑69 (MQ=255)
gcgACGACCGACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:843413/69‑1 (MQ=255)
gcgACGACCGACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:1694984/69‑1 (MQ=255)
gcgACGACCGACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:1662434/69‑1 (MQ=255)
gcgACGACCGACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:3434385/69‑1 (MQ=255)
gcgACGACCGACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:2321559/69‑1 (MQ=255)
gcgACGACCGACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:1479843/69‑1 (MQ=255)
cgacgaCCGACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:685974/68‑1 (MQ=255)
gTGCAATAGCGGCAATTTTAAAGTTCTCAATGCCGACAGGAATGCCAATg < 1:2789679/50‑1 (MQ=255)
gTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACa > 1:34358/1‑38 (MQ=255)
gTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAGGa > 1:398893/1‑41 (MQ=255)
gTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAGGAATGCCAATg > 1:2999018/1‑50 (MQ=255)
gTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAGGAATGCCAATg > 1:3204939/1‑50 (MQ=255)
gTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAGGAATGCCAATg > 1:3119399/1‑50 (MQ=255)
gTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAGGAATGCCAATg > 1:3359016/1‑50 (MQ=255)
gTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAGGAATGCCAATg > 1:3418203/1‑50 (MQ=255)
gTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAGGAATGCCAATg < 1:3069680/50‑1 (MQ=255)
gTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAGGAATGCCAATg > 1:563111/1‑50 (MQ=255)
gTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAGGAATGCCAATg > 1:1232425/1‑50 (MQ=255)
gTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAGGAATGCCAATg > 1:806809/1‑50 (MQ=255)
gTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAGGAATGCCAATg > 1:1785591/1‑50 (MQ=255)
gTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAGGAATGCCAATg < 1:1633446/50‑1 (MQ=255)
gTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAGGAATGCCAATg < 1:161173/50‑1 (MQ=255)
gTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAGGAATGCCAATg < 1:2167186/50‑1 (MQ=255)
gTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAGGAATGCCAATg > 1:136486/1‑50 (MQ=255)
gTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAGGAATGCCAATg < 1:2497187/50‑1 (MQ=255)
gTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAGGAATGCCAATg > 1:887261/1‑50 (MQ=255)
gTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAGGAATGCCAATg > 1:1313910/1‑50 (MQ=255)
gTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAGGAATGCCAATg > 1:1165662/1‑50 (MQ=255)
tGCAATAGCGGCAATTTTAAAGTTCGCAATACCGACAGGAATGCCAAt < 1:1788915/48‑1 (MQ=255)
gCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAGGAATGCCAATGATTGAAATACATTGTGCGATg < 1:1908646/69‑1 (MQ=255)
gCAATTTTAAAGTTCGCAATGCCGACAGGAATGCCa < 1:2308322/36‑1 (MQ=255)
aGTTCGCAATGCCGACAGGAATGCCAATGATTGAAATACATTGTGCGATGCCCGTTGCAATGTGCATc < 1:1994316/68‑1 (MQ=255)
aGTTCGCAATGCCGACAGGAATGCCAATGATTGAAATACATTGTGCGATGCCCGTTGCAATGTGCATc < 1:3418014/68‑1 (MQ=255)
gTTCGCAATGCCGACAGGAATGCCAATGATTGAAATACATTGTGCGATGCCCGTTGCAATGTGCATCa < 1:743249/68‑1 (MQ=255)
gTTCGCAATGCCGACAGGAATGCCAATGATTGAAATACATTGTGCGATGCCCGTTGCAATGTGCATCa < 1:989511/68‑1 (MQ=255)
gTTCGCAATGCCGACAGGAATGCCAATGATTGAAATACATTGTGCGATGCCCGTTGCAATGTGCATCa < 1:3323706/68‑1 (MQ=255)
gTTCGCAATGCCGACAGGAATGCCAATGATTGAAATACATTGTGCGATGCCCGTTGCAATGTGCATCa < 1:1581368/68‑1 (MQ=255)
gTTCGCAATGCCGACAGGAATGCCAATGATTGAAATACATTGTGCGATGCCCGTTGCAATGTGCATCa < 1:133115/68‑1 (MQ=255)
gTTCGCAATGCCGACAGGAATGCCAATGATTGAAATACATTGTGCGATGCCCGTTGCAATGTGCATCa < 1:1141806/68‑1 (MQ=255)
ttCGCAATGCCGACAGGAATGCGAATGATTGAAATACATTGTGCGATGCCCGTTGCAATGTGCATCAgg < 1:2129513/69‑1 (MQ=255)
ttCGCAATGCCGACAGGAATGCCAATGATTGAAATACATTGTGCGATGCCCGTTGCAATGTGCATCAgg < 1:1784326/69‑1 (MQ=255)
ttCGCAATGCCGACAGGAATGCCAATGATTGAAATACATTGTGCGATGCCCGTTGCAATGTGCATCAgg < 1:105670/69‑1 (MQ=255)
aaTGCCGACAGGAATGCCAATGATTGAAATACATTGTGCGATGCCCGTTGCAATGTGCATCAGGCAt < 1:2727075/67‑1 (MQ=255)
|
TCTACCGATACCACGCGACGACCAACCGGCCATAGTGCAATAGCGGCAATTTTAAAGTTCGCAATGCCGACAGGAATGCCAATGATTGAAATACATTGTGCGATGCCCGTTGCAATGTGCATCAGGCAT > minE/680650‑680778
|
| 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
