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 |
1,939,987 |
T→C |
100% |
P35P (CCA→CCG) |
ygfX ← |
hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,939,987 | 0 | T | C | 92.6%
| 22.5
/ ‑4.7
| 13 | P35P (CCA→CCG) | ygfX | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (1/0); new base C (12/0); total (13/0) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.87e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CCATCCATAACGGGGTGTAACTGAGTGGCCAGGGCATGAGTAAAATAACAGCGGCAACCAGCCCATGAATCA > minE/1939962‑1940033
|
ccatccatAACGGGGTGTAACTGAGCGGCCAGGGCATGAGTAAAATAACAGCGGCAAc > 1:1808130/1‑58 (MQ=255)
ccatccatAACGGGGTGTAACTGAGCGGCCAGGGCATGAGTAAAATAACAGCGGCAACCAGCCCATGa > 1:1117509/1‑68 (MQ=255)
ccatccatAACGGGGTGTAACTGAGCGGCCAGGGCATGAGTAAAATAACAGCGGCAACCAGCCCATGa > 1:1886790/1‑68 (MQ=255)
ccatccatAACGGGGTGTAACTGAGCGGCCAGGGCATGAGTAAAATAACAGCGGCAACCAGCCCATGa > 1:1912883/1‑68 (MQ=255)
ccatccatAACGGGGTGTAACTGAGCGGCCAGGGCATGAGTAAAATAACAGCGGCAACCAGCCCATGa > 1:216937/1‑68 (MQ=255)
ccatccatAACGGGGTGTAACTGAGCGGCCAGGGCATGAGTAAAATAACAGCGGCAACCAGCCCATGa > 1:2643735/1‑68 (MQ=255)
ccatccatAACGGGGTGTAACTGAGCGGCCAGGGCATGAGTAAAATAACAGCGGCAACCAGCCCATGa > 1:3312065/1‑68 (MQ=255)
ccatccatAACGGGGTGTAACTGAGCGGCCAGGGCATGAGTAAAATAACAGCGGCAACCAGCCCATGa > 1:469849/1‑68 (MQ=255)
ccatccatAACGGGGTGTAACTGAGCGGCCAGGGCATGAGTAAAATAACAGCGGCAACCAGCCCATGa > 1:588917/1‑68 (MQ=255)
ccatccatAACGGGGTGTAACTGAGCGGCCAGGGCATGAGTAAAATAACAGCGGCAACCAGCCCATGa > 1:712226/1‑68 (MQ=255)
ccatccatAACGGGGTGTAACTGAGCGGCCAGGGCATGAGTAAAATAACAGCGGCAACCAGCCCATGa > 1:763011/1‑68 (MQ=255)
ccatccatAACGGGGTGTAACTGAGCGGCCAGGGCATGAGTAAAATAACAGCGGCAACCAGCCCATGa > 1:778536/1‑68 (MQ=255)
catAACGGGGTGTAACTGAGTGGCCAGGGCATGAGTAAAATAACAGCGGCAACCAGCCCATGAATCa > 1:2879440/1‑67 (MQ=255)
|
CCATCCATAACGGGGTGTAACTGAGTGGCCAGGGCATGAGTAAAATAACAGCGGCAACCAGCCCATGAATCA > minE/1939962‑1940033
|
| 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
