Pythium iwayamai vs Hyaloperonospora arabidopsidis Translated Blat results

Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_scaffolds_v1) and Hyaloperonospora arabidopsidis (Hyaloperonospora arabidopsidis, HyaAraEmoy2_2.0) 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 iwayamaiHyaloperonospora arabidopsidis
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 38,494 alignment blocks

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

Uncovered: 36,367,147 out of 43,199,174
Covered: 6,832,027 out of 43,199,174

Uncovered: 13,499,837 out of 19,552,457
Matches: 4,328,010 out of 19,552,457
Mismatches: 1,722,905 out of 19,552,457
Insertions: 1,705 out of 19,552,457
Identity over aligned base-pairs: 71.5%

Hyaloperonospora arabidopsidis

Uncovered: 72,888,041 out of 78,897,814
Covered: 6,009,773 out of 78,897,814

Uncovered: 7,994,587 out of 13,171,834
Matches: 3,724,479 out of 13,171,834
Mismatches: 1,450,822 out of 13,171,834
Insertions: 1,946 out of 13,171,834
Identity over aligned base-pairs: 71.9%