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 F17 I0 R1
|
71 |
95.7 |
2922988 |
91.7% |
2680379 |
65.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,281,598:1 |
+G |
100% |
coding (3377/7104 nt) |
yeeJ → |
adhesin |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,281,598 | 1 | . | G | 85.0%
| 61.6
/ 4.9
| 20 | coding (3377/7104 nt) | yeeJ | adhesin |
| Reads supporting (aligned to +/- strand): ref base . (3/0); new base G (0/17); total (3/17) |
| Fisher's exact test for biased strand distribution p-value = 8.77e-04 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.83e-01 |
| 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. |
ACTCAGGCCAATGGGGAAGCGCATGTCACGCTGAAAGGTAAAAAAGC‑GGGCACGCATACGGTTACCGCAACGCTGGGTAATAACAATACCAGTGATTCGC > minE/1281552‑1281651
|
aCTCAGGCCAATGGGGAAGCGCATGTCACGCTGAAAGGTAAAAAAGC‑GGGCACGCATACGGTTACCGCAAc > 1:1144703/1‑71 (MQ=255)
aCTCAGGCCAATGGGGAAGCGCATGTCACGCTGAAAGGTAAAAAAGC‑GGGCACGCATACGGTTACCGCAAc > 1:1177989/1‑71 (MQ=255)
aCTCAGGCCAATGGGGAAGCGCATGTCACGCTGAAAGGTAAAAAAGC‑GGGCACGCATACGGTTACCGCAAc > 1:1314528/1‑71 (MQ=255)
cTGAAAGGTAAAAAAGCGGGGCACGCATACGGTTACCGCAACGCTGGGTAATAACAATACCAGTGATTCGc < 1:929920/71‑1 (MQ=255)
cTGAAAGGTAAAAAAGCGGGGCACGCATACGGTTACCGCAACGCTGGGTAATAACAATACCAGTGATTCGc < 1:1059301/71‑1 (MQ=255)
cTGAAAGGTAAAAAAGCGGGGCACGCATACGGTTACCGCAACGCTGGGTAATAACAATACCAGTGATTCGc < 1:87625/71‑1 (MQ=255)
cTGAAAGGTAAAAAAGCGGGGCACGCATACGGTTACCGCAACGCTGGGTAATAACAATACCAGTGATTCGc < 1:855229/71‑1 (MQ=255)
cTGAAAGGTAAAAAAGCGGGGCACGCATACGGTTACCGCAACGCTGGGTAATAACAATACCAGTGATTCGc < 1:709527/71‑1 (MQ=255)
cTGAAAGGTAAAAAAGCGGGGCACGCATACGGTTACCGCAACGCTGGGTAATAACAATACCAGTGATTCGc < 1:355872/71‑1 (MQ=255)
cTGAAAGGTAAAAAAGCGGGGCACGCATACGGTTACCGCAACGCTGGGTAATAACAATACCAGTGATTCGc < 1:303716/71‑1 (MQ=255)
cTGAAAGGTAAAAAAGCGGGGCACGCATACGGTTACCGCAACGCTGGGTAATAACAATACCAGTGATTCGc < 1:2655782/71‑1 (MQ=255)
cTGAAAGGTAAAAAAGCGGGGCACGCATACGGTTACCGCAACGCTGGGTAATAACAATACCAGTGATTCGc < 1:2277570/71‑1 (MQ=255)
cTGAAAGGTAAAAAAGCGGGGCACGCATACGGTTACCGCAACGCTGGGTAATAACAATACCAGTGATTCGc < 1:2253678/71‑1 (MQ=255)
cTGAAAGGTAAAAAAGCGGGGCACGCATACGGTTACCGCAACGCTGGGTAATAACAATACCAGTGATTCGc < 1:2074147/71‑1 (MQ=255)
cTGAAAGGTAAAAAAGCGGGGCACGCATACGGTTACCGCAACGCTGGGTAATAACAATACCAGTGATTCGc < 1:2025762/71‑1 (MQ=255)
cTGAAAGGTAAAAAAGCGGGGCACGCATACGGTTACCGCAACGCTGGGTAATAACAATACCAGTGATTCGc < 1:1931072/71‑1 (MQ=255)
cTGAAAGGTAAAAAAGCGGGGCACGCATACGGTTACCGCAACGCTGGGTAATAACAATACCAGTGATTCGc < 1:1656170/71‑1 (MQ=255)
cTGAAAGGTAAAAAAGCGGGGCACGCATACGGTTACCGCAACGCTGGGTAATAACAATACCAGTGATTCGc < 1:1284426/71‑1 (MQ=255)
cTGAAAGGTAAAAAAGCGGGGCACGCATACGGTTACCGCAACGCTGGGTAATAACAATACCAGTGATTCGc < 1:1255068/71‑1 (MQ=255)
cTGAAAGGTAAAAAAGCGGGGCACGCATACGGTTACCGCAACGCTGGGTAATAACAATACCAGTGATTCGc < 1:1224970/71‑1 (MQ=255)
|
ACTCAGGCCAATGGGGAAGCGCATGTCACGCTGAAAGGTAAAAAAGC‑GGGCACGCATACGGTTACCGCAACGCTGGGTAATAACAATACCAGTGATTCGC > minE/1281552‑1281651
|
| 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
