Pythium irregulare vs Emiliania huxleyi Translated Blat Results

Back to all analyses

Pythium irregulare (Pythium irregulare DAOM BR486, pir_scaffolds_v1) 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 74. Pythium irregulare 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: 12,011

Genome coverage (bp) Coding exon coverage (bp)
Pythium irregulare DAOM BR486

Uncovered: 41,825,191 out of 42,968,084
Covered: 1,142,893 out of 42,968,084

Uncovered: 19,494,073 out of 20,543,058
Matches: 749,663 out of 20,543,058
Mismatches: 299,030 out of 20,543,058
Insertions: 292 out of 20,543,058

Emiliania huxleyi CCMP1516

Uncovered: 166,739,552 out of 167,675,649
Covered: 936,097 out of 167,675,649

Uncovered: 38,901,363 out of 39,740,234
Matches: 599,668 out of 39,740,234
Mismatches: 239,063 out of 39,740,234
Insertions: 140 out of 39,740,234

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

Pythium irregulare Emiliania huxleyi
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}