Arabidopsis thaliana vs Glycine max BlastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Glycine max (Glycine max, V1.0) 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 Plants release 76. Arabidopsis thaliana 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.

Results

Number of alignment blocks: 106,030

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 83,347,681 out of 119,667,750
Covered: 36,320,069 out of 119,667,750

Uncovered: 7,927,504 out of 33,462,323
Matches: 17,292,574 out of 33,462,323
Mismatches: 7,669,050 out of 33,462,323
Insertions: 573,195 out of 33,462,323

Glycine max

Uncovered: 942,590,215 out of 973,344,380
Covered: 30,754,165 out of 973,344,380

Uncovered: 44,019,136 out of 64,476,920
Matches: 13,835,778 out of 64,476,920
Mismatches: 6,063,013 out of 64,476,920
Insertions: 558,993 out of 64,476,920

Configuration parameters

ParameterValue
Gap open penalty (O)
Gap extend penalty (E)
HSP threshold (K)
Threshold for gapped extension (L)
Threshold for alignments between gapped alignment blocks (H)
Masking count (M)
Seed and Transition value (T)
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91
Other parameters (other)