Pythium iwayamai vs Bigelowiella natans Translated Blat results

Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_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 iwayamai 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 iwayamaiBigelowiella 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 6,897 alignment blocks

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

Uncovered: 42,434,453 out of 43,199,174
Covered: 764,721 out of 43,199,174

Uncovered: 18,854,255 out of 19,552,457
Matches: 469,092 out of 19,552,457
Mismatches: 228,990 out of 19,552,457
Insertions: 120 out of 19,552,457
Identity over aligned base-pairs: 67.2%

Bigelowiella natans

Uncovered: 94,077,019 out of 94,701,163
Covered: 624,144 out of 94,701,163

Uncovered: 28,215,688 out of 28,817,508
Matches: 404,190 out of 28,817,508
Mismatches: 197,597 out of 28,817,508
Insertions: 33 out of 28,817,508
Identity over aligned base-pairs: 67.2%