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Chicken vs C.savignyi Translated Blat alignments

Chicken (Gallus gallus, Galgal4) and C.savignyi (Ciona savignyi, CSAV2.0) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl release 71. Chicken 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.

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

Chicken C.savignyi
Chunk size 1,000,000 25,000
Overlap 10,000 10,000
Group set size 100,000,000 10,000,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}

Results

Number of alignment blocks: 38,523

Genome coverage (bp) Coding exon coverage (bp)
Gallus gallus

Uncovered: 1,043,073,605 out of 1,046,932,099
Covered: 3,858,494 out of 1,046,932,099

Uncovered: 22,449,858 out of 25,934,237
Matches: 2,389,748 out of 25,934,237
Mismatches: 1,094,445 out of 25,934,237
Insertions: 186 out of 25,934,237

Ciona savignyi

Uncovered: 174,278,053 out of 176,989,013
Covered: 2,710,960 out of 176,989,013

Uncovered: 11,545,811 out of 13,806,906
Matches: 1,544,696 out of 13,806,906
Mismatches: 716,271 out of 13,806,906
Insertions: 128 out of 13,806,906