Human vs Chimpanzee BlastZ alignments

Human (Homo sapiens, GRCh37) and Chimpanzee (Pan troglodytes, CHIMP2.1) were aligned using the BlastZ alignment algorithm (Schwartz S et al., Genome Res.;13(1):103-7, Kent WJ et al., Proc Natl Acad Sci U S A., 2003;100(20):11484-9) in Ensembl release 55. Human was used as the reference species. After running BlastZ , the raw BlastZ 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.

Full list of pairwise alignments

Configuration parameters

Gap open penalty (O) 600
Gap extend penalty (E) 150
HSP threshold (K) 4500
Threshold for gapped extension (L) 2200
Threshold for alignments between gapped alignment blocks (H) 2000
Masking count (M) 50
Seed and Transition value (T) 2
Scoring matrix (Q)
A C G T
90 -330 -236 -356
-330 100 -318 -236
-236 -318 100 -330
-356 -236 -330 90

Results

Number of alignment blocks: 692174

Genome coverage(bp) Coding exon coverage (bp)
Human
2,263,640,977 out of 3,098,825,702 34,385,806 out of 35,483,623
Chimpanzee
2,220,936,942 out of 3,350,413,343 31,889,779 out of 32,180,345