Pythium aphanidermatum vs Albugo laibachii Translated Blat results

Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444, pag1_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 aphanidermatum 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 aphanidermatumAlbugo 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 26,893 alignment blocks

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

Uncovered: 30,886,282 out of 35,876,849
Covered: 4,990,567 out of 35,876,849

Uncovered: 13,516,162 out of 18,015,574
Matches: 3,013,050 out of 18,015,574
Mismatches: 1,485,678 out of 18,015,574
Insertions: 684 out of 18,015,574
Identity over aligned base-pairs: 67.0%

Albugo laibachii

Uncovered: 28,308,402 out of 32,766,811
Covered: 4,458,409 out of 32,766,811

Uncovered: 11,706,825 out of 15,902,867
Matches: 2,820,094 out of 15,902,867
Mismatches: 1,374,707 out of 15,902,867
Insertions: 1,241 out of 15,902,867
Identity over aligned base-pairs: 67.2%