Emiliania huxleyi vs Pythium ultimum Translated Blat results

Emiliania huxleyi (Emiliania huxleyi CCMP1516, Emiliana_huxleyi_CCMP1516_main_genome_assembly_v1.0) and Pythium ultimum (Pythium ultimum DAOM BR144, pug) 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 huxleyiPythium ultimum
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 18,345 alignment blocks

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

Uncovered: 165,895,361 out of 167,675,649
Covered: 1,780,288 out of 167,675,649

Uncovered: 38,171,651 out of 39,740,234
Matches: 1,114,099 out of 39,740,234
Mismatches: 454,183 out of 39,740,234
Insertions: 301 out of 39,740,234
Identity over aligned base-pairs: 71.0%

Pythium ultimum

Uncovered: 43,929,885 out of 44,913,582
Covered: 983,697 out of 44,913,582

Uncovered: 18,938,927 out of 19,826,256
Matches: 624,234 out of 19,826,256
Mismatches: 262,873 out of 19,826,256
Insertions: 222 out of 19,826,256
Identity over aligned base-pairs: 70.3%