Pythium iwayamai vs Emiliania huxleyi Translated Blat results

Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_scaffolds_v1) and Emiliania huxleyi (Emiliania huxleyi CCMP1516, Emiliana_huxleyi_CCMP1516_main_genome_assembly_v1.0) 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

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 iwayamaiEmiliania huxleyi
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 12,379 alignment blocks

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

Uncovered: 42,056,377 out of 43,199,174
Covered: 1,142,797 out of 43,199,174

Uncovered: 18,534,498 out of 19,552,457
Matches: 738,004 out of 19,552,457
Mismatches: 279,705 out of 19,552,457
Insertions: 250 out of 19,552,457
Identity over aligned base-pairs: 72.5%

Emiliania huxleyi

Uncovered: 166,741,387 out of 167,675,649
Covered: 934,262 out of 167,675,649

Uncovered: 38,911,743 out of 39,740,234
Matches: 601,520 out of 39,740,234
Mismatches: 226,707 out of 39,740,234
Insertions: 264 out of 39,740,234
Identity over aligned base-pairs: 72.6%