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 |
1,687,227 |
G→A |
100% |
S131S (AGC→AGT) |
sseB ← |
rhodanase‑like enzyme, sulfur transfer from thiosulfate |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,687,227 | 0 | G | A | 80.1%
| 23.2
/ 0.9
| 20 | S131S (AGC→AGT) | sseB | rhodanase‑like enzyme, sulfur transfer from thiosulfate |
| Reads supporting (aligned to +/- strand): ref base G (0/4); new base A (16/0); total (16/4) |
| Fisher's exact test for biased strand distribution p-value = 2.06e-04 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.75e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
ATTTGTGCTGGCGGCTCTGCGACTTCCGATAATATCAGCGATTCACCGCCTTCCAGGATTTCCTGGCTGCTCAGCGGATTTCCCTCTTCACCAATCAACAAACTGATTT > minE/1687159‑1687267
|
aTTTGTGCTGGCGGCTCTGCGACTTCCGATAATATCAGCGATTCACCGCCTTCCAGGATTTCCTGgctg < 1:1335555/69‑1 (MQ=255)
aTTTGTGCTGGCGGCTCTGCGACTTCCGATAATATCAGCGATTCACCGCCTTCCAGGATTTCCTGgctg < 1:534560/69‑1 (MQ=255)
aTTTGTGCTGGCGGCTCTGCGACTTCCGATAATATCAGCGATTCACCGCCTTCCAGGATTTCCTGgctg < 1:1994471/69‑1 (MQ=255)
aTTTGTGCTGGCGGCTCTGCGACTTCCGATAATATCAGCGATTCACCGCCTTCCAGGATTTCCTGgctg < 1:2056632/69‑1 (MQ=255)
aTTTGTGCTGGCGGCTCTGCGACTTCCGATAATATCAGCGATTCACCGCCTTCCAGGATTTCCTGgctg < 1:2678782/69‑1 (MQ=255)
aTTCACCGCCTTCCAGGATTTCCTGGCTGCTCAGCGGATTTGCCTCTTCACCAATCAACAAACTGAttt < 1:1244807/69‑1 (MQ=255)
aTTCACCGCCTTCCAGGATTTCCTGGCTGCTCAGCGGATTTCCCTCTTCACCAATCAACAAACTGAttt < 1:56674/69‑1 (MQ=255)
aTTCACCGCCTTCCAGGATTTCCTGGCTGCTCAGCGGATTTCCCTCTTCACCAATCAACAAACTGAttt < 1:3263548/69‑1 (MQ=255)
aTTCACCGCCTTCCAGGATTTCCTGGCTGCTCAGCGGATTTCCCTCTTCACCAATCAACAAACTGAttt < 1:3115155/69‑1 (MQ=255)
ccAGTACTTCCTGGCTACTCAGGGAATTCCCTTCTTCACCAATc > 1:223189/1‑44 (MQ=255)
ccAGTACTTCCTGGCTACTCAGCGAATTCCCTTCTTCACCAATc > 1:81742/1‑44 (MQ=255)
ccAGTACTTCCTGGCTACTCAGCGAATTCCCTTCTTCACCAATc > 1:3261280/1‑44 (MQ=255)
ccAGTACTTCCTGGCTACTCAGCGAATTCCCTTCTTCACCAATc > 1:3225919/1‑44 (MQ=255)
ccAGTACTTCCTGGCTACTCAGCGAATTCCCTTCTTCACCAATc > 1:2946256/1‑44 (MQ=255)
ccAGTACTTCCTGGCTACTCAGCGAATTCCCTTCTTCACCAATc > 1:2926496/1‑44 (MQ=255)
ccAGTACTTCCTGGCTACTCAGCGAATTCCCTTCTTCACCAATc > 1:2923367/1‑44 (MQ=255)
ccAGTACTTCCTGGCTACTCAGCGAATTCCCTTCTTCACCAATc > 1:2648455/1‑44 (MQ=255)
ccAGTACTTCCTGGCTACTCAGCGAATTCCCTTCTTCACCAATc > 1:2255422/1‑44 (MQ=255)
ccAGTACTTCCTGGCTACTCAGCGAATTCCCTTCTTCACCAATc > 1:2159651/1‑44 (MQ=255)
ccAGTACTTCCTGGCTACTCAGCGAATTCCCTTCTTCACCAATc > 1:2103404/1‑44 (MQ=255)
ccAGTACTTCCTGGCTACTCAGCGAATTCCCTTCTTCACCAATc > 1:1980290/1‑44 (MQ=255)
ccAGTACTTCCTGGCTACTCAGCGAATTCCCTTCTTCACCAATc > 1:1940686/1‑44 (MQ=255)
ccAGTACTTCCTGGCTACTCAGCGAATTCCCTTCTTCACCAATc > 1:185022/1‑44 (MQ=255)
ccAGTACTTCCTGGCTACTCAGCGAATTCCCTTCTTCACCAATc > 1:1686313/1‑44 (MQ=255)
ccAGTACTTCCTGGCTACTCAGCGAATTCCCTTCTTCACCAATc > 1:1531145/1‑44 (MQ=255)
|
ATTTGTGCTGGCGGCTCTGCGACTTCCGATAATATCAGCGATTCACCGCCTTCCAGGATTTCCTGGCTGCTCAGCGGATTTCCCTCTTCACCAATCAACAAACTGATTT > minE/1687159‑1687267
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
