Emiliania huxleyi vs Leishmania major Translated Blat Results

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Emiliania huxleyi (Emiliania huxleyi CCMP1516, Emiliana_huxleyi_CCMP1516_main_genome_assembly_v1.0) and Leishmania major (Leishmania major strain Friedlin, ASM272v2) 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: 11,493

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

Uncovered: 166,679,186 out of 167,675,649
Covered: 996,463 out of 167,675,649

Uncovered: 38,896,017 out of 39,740,234
Matches: 604,949 out of 39,740,234
Mismatches: 239,006 out of 39,740,234
Insertions: 262 out of 39,740,234

Leishmania major strain Friedlin

Uncovered: 32,319,067 out of 32,855,095
Covered: 536,028 out of 32,855,095

Uncovered: 15,218,766 out of 15,726,087
Matches: 362,382 out of 15,726,087
Mismatches: 144,778 out of 15,726,087
Insertions: 161 out of 15,726,087

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 Leishmania major
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}