Pythium irregulare vs Emiliania huxleyi Translated Blat results

Pythium irregulare (Pythium irregulare DAOM BR486, pir_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 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

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 irregulareEmiliania huxleyi
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 12,011 alignment blocks

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

Uncovered: 41,825,191 out of 42,968,084
Covered: 1,142,893 out of 42,968,084

Uncovered: 19,494,073 out of 20,543,058
Matches: 749,663 out of 20,543,058
Mismatches: 299,030 out of 20,543,058
Insertions: 292 out of 20,543,058
Identity over aligned base-pairs: 71.5%

Emiliania huxleyi

Uncovered: 166,739,552 out of 167,675,649
Covered: 936,097 out of 167,675,649

Uncovered: 38,901,363 out of 39,740,234
Matches: 599,668 out of 39,740,234
Mismatches: 239,063 out of 39,740,234
Insertions: 140 out of 39,740,234
Identity over aligned base-pairs: 71.5%