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 |
2,971,396 |
T→C |
100% |
V71A (GTG→GCG) |
serB → |
3‑phosphoserine phosphatase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,971,396 | 0 | T | C | 97.8%
| 161.9
/ ‑3.7
| 45 | V71A (GTG→GCG) | serB | 3‑phosphoserine phosphatase |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base C (0/44); total (0/45) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.37e-01 |
| 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. |
TGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGTGGAAGATTATCAGGTGATT > minE/2971339‑2971415
|
tgtcccAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:1653848/64‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCTATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:1781161/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:376444/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:2022202/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:2067140/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:209987/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:212496/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:2154024/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:232551/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:248230/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:251700/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:1903513/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:399050/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:444226/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:485727/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:503003/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:540310/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:637627/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:774461/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:906463/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:963468/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:963638/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:1411516/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:1043598/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:1073561/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:1088683/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:1129626/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:1190409/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:1218118/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:124261/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:1327286/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:138643/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:1017722/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:1427132/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:1449645/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:1511008/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:1527803/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:1681942/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:170082/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:1750389/67‑1 (MQ=255)
tGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:1776389/67‑1 (MQ=255)
gACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:303298/66‑1 (MQ=255)
gACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:1684607/66‑1 (MQ=255)
cccAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGCGGAAGATTa < 1:590230/64‑1 (MQ=255)
ccAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGTGGAAGATTATCAGGTGAtt < 1:4553/67‑1 (MQ=255)
|
TGACCCAATACCAGAGCAAACTGGGTGCGGCGATGGTGATTGTTGCCGCCTGGTGCGTGGAAGATTATCAGGTGATT > minE/2971339‑2971415
|
| 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
