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 F8 I0 R1
|
82 |
77.9 |
2158605 |
86.8% |
1873669 |
62.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,847,650:1 |
+T |
100% |
coding (285/315 nt) |
yjeO → |
conserved inner membrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,847,650 | 1 | . | T | 97.7%
| 159.0
/ ‑3.2
| 44 | coding (285/315 nt) | yjeO | conserved inner membrane protein |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base T (43/0); total (44/0) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. |
CGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAG‑T‑TTTTTCTGCGCTATCAGTTTTGTTTGTGAGCCGGATTGGTTCATCCGGCACACAAACTTACAAAC > minE/2847611‑2847716
|
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCTGTT‑TTTTTCTGCGCTATCAGTtttgttt > 1:1529213/1‑67 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATc > 1:401352/1‑57 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATc > 1:1389685/1‑57 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCTGTtttgtt > 1:1887106/1‑66 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAg > 1:1144137/1‑59 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAGttt > 1:2022352/1‑62 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAGTtttgttt > 1:311169/1‑67 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAGTtttgttt > 1:1088432/1‑67 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAGTtttgttt > 1:1811512/1‑67 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAGTtttgttt > 1:189168/1‑67 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAGTtttgttt > 1:1963359/1‑67 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAGTtttgttt > 1:2094441/1‑67 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAGTtttgttt > 1:243251/1‑67 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAGTtttgttt > 1:260593/1‑67 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAGTtttgttt > 1:1786654/1‑67 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAGTtttgttt > 1:378262/1‑67 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAGTtttgttt > 1:473128/1‑67 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAGTtttgttt > 1:503964/1‑67 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAGTtttgttt > 1:761697/1‑67 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAGTtttgttt > 1:784409/1‑67 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAGTtttgttt > 1:928490/1‑67 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAGTtttgttt > 1:949548/1‑67 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAGTtttgttt > 1:1440997/1‑67 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAGTtttgttt > 1:1099296/1‑67 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAGTtttgttt > 1:110555/1‑67 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAGTtttgttt > 1:1158921/1‑67 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAGTtttgttt > 1:1198085/1‑67 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAGTtttgttt > 1:1237915/1‑67 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAGTtttgttt > 1:1386497/1‑67 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAGTtttgttt > 1:1404772/1‑67 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAGTtttgttt > 1:1456645/1‑67 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAGTtttgttt > 1:1530720/1‑67 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAGTtttgttt > 1:1630764/1‑67 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAGTtttgttt > 1:1691948/1‑67 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAGTtttgttt > 1:1696562/1‑67 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAGTtttgttt > 1:173791/1‑67 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAGTtttgtt > 1:2054802/1‑66 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAGTtttgtt > 1:178513/1‑66 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAGTtttgtt > 1:1565872/1‑66 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAGTtttgtt > 1:1976028/1‑66 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAGTtttgtt > 1:1384032/1‑66 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAGTtttgtt > 1:1299453/1‑66 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAGTT‑TTTTTCTGCGCTATCAGTtttgt > 1:282040/1‑65 (MQ=255)
cGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAG‑TCTTTTTCTGCGCTATCAGTtttgttt > 1:817001/1‑67 (MQ=255)
g‑T‑TTTTTCTGCGCTATCAGTTTTGTTTGTGAGCCGGATCGGTTCATCCGGCACacaaacttacaaac < 1:1968836/67‑1 (MQ=255)
|
CGCCACCGCGCTGGCTATTTTCGGCTACTGGCTGTGGCAG‑T‑TTTTTCTGCGCTATCAGTTTTGTTTGTGAGCCGGATTGGTTCATCCGGCACACAAACTTACAAAC > minE/2847611‑2847716
|
| 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
