Pythium vexans vs Albugo laibachii Translated Blat results

Pythium vexans (Pythium vexans DAOM BR484, pve_scaffolds_v1) and Albugo laibachii (Albugo laibachii, ENA1) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 75. Pythium vexans was used as the reference species. After running Translated Blat, the raw Translated Blat alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

Configuration parameters

ParameterValue
Minimum score (minScore)30
Database type (t)dnax
Query type (q)dnax
Mask out repeats (mask)lower
Mask out repeats on query (qMask)lower

Chunking parameters

ParameterPythium vexansAlbugo laibachii
Chunk size1,000,0001,000,000
Overlap10,00010,000
Group set size100,000,000100,000,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 26,933 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Pythium vexans

Uncovered: 28,951,200 out of 33,844,883
Covered: 4,893,683 out of 33,844,883

Uncovered: 14,163,901 out of 18,608,353
Matches: 2,949,210 out of 18,608,353
Mismatches: 1,494,566 out of 18,608,353
Insertions: 676 out of 18,608,353
Identity over aligned base-pairs: 66.4%

Albugo laibachii

Uncovered: 28,458,977 out of 32,766,811
Covered: 4,307,834 out of 32,766,811

Uncovered: 11,855,053 out of 15,902,867
Matches: 2,697,683 out of 15,902,867
Mismatches: 1,349,196 out of 15,902,867
Insertions: 935 out of 15,902,867
Identity over aligned base-pairs: 66.6%