Bigelowiella natans vs Phytophthora infestans Translated Blat Results

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Bigelowiella natans (Bigelowiella natans CCMP2755, Bigna1) and Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) 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: 7,693

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

Uncovered: 93,857,797 out of 94,701,163
Covered: 843,366 out of 94,701,163

Uncovered: 28,005,586 out of 28,817,508
Matches: 543,827 out of 28,817,508
Mismatches: 268,022 out of 28,817,508
Insertions: 73 out of 28,817,508

Phytophthora infestans T30-4

Uncovered: 227,850,482 out of 228,543,505
Covered: 693,023 out of 228,543,505

Uncovered: 21,746,583 out of 22,421,425
Matches: 449,407 out of 22,421,425
Mismatches: 225,290 out of 22,421,425
Insertions: 145 out of 22,421,425

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 Phytophthora infestans
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}