Phytophthora kernoviae vs Bigelowiella natans Translated Blat Results

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Phytophthora kernoviae (Phytophthora kernoviae 00238/432, PhyKer238_432v1) 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 74. Phytophthora kernoviae 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: 7,693

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora kernoviae 00238/432

Uncovered: 42,324,169 out of 43,208,681
Covered: 884,512 out of 43,208,681

Uncovered: 10,846,990 out of 11,508,642
Matches: 440,724 out of 11,508,642
Mismatches: 220,817 out of 11,508,642
Insertions: 111 out of 11,508,642

Bigelowiella natans CCMP2755

Uncovered: 94,011,635 out of 94,701,163
Covered: 689,528 out of 94,701,163

Uncovered: 28,151,904 out of 28,817,508
Matches: 440,967 out of 28,817,508
Mismatches: 224,537 out of 28,817,508
Insertions: 100 out of 28,817,508

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

Phytophthora kernoviae Bigelowiella natans
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}