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 F3 I0 R1
|
328 |
90.1 |
2317887 |
85.2% |
1974839 |
62.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,541,194 |
A→T |
100% |
intergenic (‑296/+385) |
yfcV ← / ← sixA |
predicted fimbrial‑like adhesin protein/phosphohistidine phosphatase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,541,194 | 0 | A | T | 76.5%
| 28.7
/ 6.4
| 17 | intergenic (‑296/+385) | yfcV/sixA | predicted fimbrial‑like adhesin protein/phosphohistidine phosphatase |
| Reads supporting (aligned to +/- strand): ref base A (0/4); new base T (13/0); total (13/4) |
| Fisher's exact test for biased strand distribution p-value = 4.20e-04 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
ATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCC > minE/1541134‑1541256
|
aTCTTAAGGATCTTCTAAAAAAACACGTAATATATATTTAGAAAAAACAGGAAGCATATCAACaatg < 1:1716808/67‑1 (MQ=255)
aTCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACaatg < 1:1019397/67‑1 (MQ=255)
aTCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACaatg < 1:1191826/67‑1 (MQ=255)
aTCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACaatg < 1:1457899/67‑1 (MQ=255)
gatCTACAATGAATGCCAATAGCTTAAAAAACAAACAATGa > 1:1544901/2‑41 (MQ=255)
gatCTACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACa > 1:13089/2‑44 (MQ=255)
gatCTACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAAccc > 1:916221/2‑67 (MQ=255)
gatCTACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAAccc > 1:787634/2‑67 (MQ=255)
gatCTACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAAccc > 1:55329/2‑67 (MQ=255)
gatCTACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAAccc > 1:2139256/2‑67 (MQ=255)
gatCTACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAAccc > 1:1665731/2‑67 (MQ=255)
gatCTACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAAccc > 1:160601/2‑67 (MQ=255)
gatCTACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAAccc > 1:1547484/2‑67 (MQ=255)
gatCTACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAAccc > 1:144185/2‑67 (MQ=255)
gatCTACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAAccc > 1:1255290/2‑67 (MQ=255)
gatCTACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAAccc > 1:1132662/2‑67 (MQ=255)
gatCTACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAAccc > 1:1040637/2‑67 (MQ=255)
|
ATCTTAAGGATCTTCTAAAAAAACACGAAATATATATTTAGAAAAAACAGGAAGCATATCAACAATGAATGCCAATAGCTTAAAAAACAAACAATGAACATATAATGCGATTGGCATTAACCC > minE/1541134‑1541256
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
