Guillardia theta CCMP2712 vs Entamoeba histolytica Translated Blat results

Guillardia theta CCMP2712 (Guillardia theta CCMP2712, Guith1) and Entamoeba histolytica (Entamoeba histolytica, JCVI-ESG2-1.0) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 76. Guillardia theta CCMP2712 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

ParameterGuillardia theta CCMP2712Entamoeba histolytica
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 1,590 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Guillardia theta CCMP2712

Uncovered: 87,046,076 out of 87,266,873
Covered: 220,797 out of 87,266,873

Uncovered: 30,430,893 out of 30,644,092
Matches: 133,496 out of 30,644,092
Mismatches: 79,587 out of 30,644,092
Insertions: 116 out of 30,644,092
Identity over aligned base-pairs: 62.6%

Entamoeba histolytica

Uncovered: 20,661,533 out of 20,835,395
Covered: 173,862 out of 20,835,395

Uncovered: 10,072,820 out of 10,244,611
Matches: 107,057 out of 10,244,611
Mismatches: 64,681 out of 10,244,611
Insertions: 53 out of 10,244,611
Identity over aligned base-pairs: 62.3%