Bigelowiella natans vs Hyaloperonospora arabidopsidis Translated Blat Results

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Bigelowiella natans (Bigelowiella natans CCMP2755, Bigna1) and Hyaloperonospora arabidopsidis (Hyaloperonospora arabidopsidis, HyaAraEmoy2_2.0) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 74. Bigelowiella natans 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: 6,247

Genome coverage (bp) Coding exon coverage (bp)
Bigelowiella natans CCMP2755

Uncovered: 94,008,486 out of 94,701,163
Covered: 692,677 out of 94,701,163

Uncovered: 28,151,572 out of 28,817,508
Matches: 444,495 out of 28,817,508
Mismatches: 221,392 out of 28,817,508
Insertions: 49 out of 28,817,508

Hyaloperonospora arabidopsidis

Uncovered: 78,347,873 out of 78,897,814
Covered: 549,941 out of 78,897,814

Uncovered: 12,663,853 out of 13,171,834
Matches: 337,568 out of 13,171,834
Mismatches: 170,388 out of 13,171,834
Insertions: 25 out of 13,171,834

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

Bigelowiella natans Hyaloperonospora arabidopsidis
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}