Pythium iwayamai vs Albugo laibachii Translated Blat results

Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_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 iwayamai 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 iwayamaiAlbugo 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 27,924 alignment blocks

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

Uncovered: 38,277,825 out of 43,199,174
Covered: 4,921,349 out of 43,199,174

Uncovered: 15,259,483 out of 19,552,457
Matches: 2,862,724 out of 19,552,457
Mismatches: 1,429,843 out of 19,552,457
Insertions: 407 out of 19,552,457
Identity over aligned base-pairs: 66.7%

Albugo laibachii

Uncovered: 28,383,846 out of 32,766,811
Covered: 4,382,965 out of 32,766,811

Uncovered: 11,893,477 out of 15,902,867
Matches: 2,685,098 out of 15,902,867
Mismatches: 1,323,319 out of 15,902,867
Insertions: 973 out of 15,902,867
Identity over aligned base-pairs: 67.0%