Pythium vexans vs Emiliania huxleyi Translated Blat results

Pythium vexans (Pythium vexans DAOM BR484, pve_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 vexans 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 vexansEmiliania 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 15,634 alignment blocks

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

Uncovered: 32,500,819 out of 33,844,883
Covered: 1,344,064 out of 33,844,883

Uncovered: 17,402,451 out of 18,608,353
Matches: 873,821 out of 18,608,353
Mismatches: 331,400 out of 18,608,353
Insertions: 681 out of 18,608,353
Identity over aligned base-pairs: 72.5%

Emiliania huxleyi

Uncovered: 166,569,999 out of 167,675,649
Covered: 1,105,650 out of 167,675,649

Uncovered: 38,782,964 out of 39,740,234
Matches: 694,106 out of 39,740,234
Mismatches: 262,860 out of 39,740,234
Insertions: 304 out of 39,740,234
Identity over aligned base-pairs: 72.5%