Emiliania huxleyi vs Phytophthora ramorum Translated Blat Results

Back to all analyses

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 are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Results

Number of alignment blocks: 18,044

Genome coverage (bp) Coding exon coverage (bp)
Emiliania huxleyi CCMP1516

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

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

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

Emiliania huxleyi Phytophthora ramorum
Chunk size 1,000,000 1,000,000
Overlap 10,000 10,000
Group set size 100,000,000 100,000,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}