Pythium vexans vs Bigelowiella natans Translated Blat results

Pythium vexans (Pythium vexans DAOM BR484, pve_scaffolds_v1) and Bigelowiella natans (Bigelowiella natans CCMP2755, Bigna1) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 75. Pythium vexans 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

ParameterPythium vexansBigelowiella natans
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 7,452 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Pythium vexans

Uncovered: 33,009,880 out of 33,844,883
Covered: 835,003 out of 33,844,883

Uncovered: 17,831,936 out of 18,608,353
Matches: 519,589 out of 18,608,353
Mismatches: 256,695 out of 18,608,353
Insertions: 133 out of 18,608,353
Identity over aligned base-pairs: 66.9%

Bigelowiella natans

Uncovered: 94,033,656 out of 94,701,163
Covered: 667,507 out of 94,701,163

Uncovered: 28,172,269 out of 28,817,508
Matches: 431,962 out of 28,817,508
Mismatches: 213,229 out of 28,817,508
Insertions: 48 out of 28,817,508
Identity over aligned base-pairs: 66.9%