Pythium irregulare vs Albugo laibachii Translated Blat results

Pythium irregulare (Pythium irregulare DAOM BR486, pir_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 irregulare 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

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 irregulareAlbugo laibachii
Chunk size1,000,0001,000,000
Group set size100,000,000100,000,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 30,977 alignment blocks

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

Uncovered: 37,390,912 out of 42,968,084
Covered: 5,577,172 out of 42,968,084

Uncovered: 15,732,853 out of 20,543,058
Matches: 3,225,128 out of 20,543,058
Mismatches: 1,584,171 out of 20,543,058
Insertions: 906 out of 20,543,058
Identity over aligned base-pairs: 67.0%

Albugo laibachii

Uncovered: 27,912,829 out of 32,766,811
Covered: 4,853,982 out of 32,766,811

Uncovered: 11,501,928 out of 15,902,867
Matches: 2,961,061 out of 15,902,867
Mismatches: 1,438,398 out of 15,902,867
Insertions: 1,480 out of 15,902,867
Identity over aligned base-pairs: 67.3%