Emiliania huxleyi vs Phytophthora ramorum Translated Blat results

Emiliania huxleyi (Emiliania huxleyi CCMP1516, Emiliana_huxleyi_CCMP1516_main_genome_assembly_v1.0) and Phytophthora ramorum (Phytophthora ramorum, ASM14973v1) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 74. Emiliania huxleyi 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

ParameterEmiliania huxleyiPhytophthora ramorum
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 18,044 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Emiliania huxleyi

Uncovered: 165,884,183 out of 167,675,649
Covered: 1,791,466 out of 167,675,649

Uncovered: 38,162,959 out of 39,740,234
Matches: 1,123,760 out of 39,740,234
Mismatches: 453,236 out of 39,740,234
Insertions: 279 out of 39,740,234
Identity over aligned base-pairs: 71.2%

Phytophthora ramorum

Uncovered: 65,648,717 out of 66,652,401
Covered: 1,003,684 out of 66,652,401

Uncovered: 21,411,382 out of 22,377,278
Matches: 681,188 out of 22,377,278
Mismatches: 284,472 out of 22,377,278
Insertions: 236 out of 22,377,278
Identity over aligned base-pairs: 70.5%