Phytophthora kernoviae vs Emiliania huxleyi Translated Blat results

Phytophthora kernoviae (Phytophthora kernoviae 00238/432, PhyKer238_432v1) 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 76. Phytophthora kernoviae 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

ParameterPhytophthora kernoviaeEmiliania 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 9,213 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora kernoviae

Uncovered: 42,183,604 out of 43,208,681
Covered: 1,025,077 out of 43,208,681

Uncovered: 10,725,631 out of 11,508,642
Matches: 538,103 out of 11,508,642
Mismatches: 244,746 out of 11,508,642
Insertions: 162 out of 11,508,642
Identity over aligned base-pairs: 68.7%

Emiliania huxleyi

Uncovered: 166,858,024 out of 167,675,649
Covered: 817,625 out of 167,675,649

Uncovered: 38,984,336 out of 39,740,234
Matches: 513,638 out of 39,740,234
Mismatches: 242,197 out of 39,740,234
Insertions: 63 out of 39,740,234
Identity over aligned base-pairs: 68.0%