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Oryza sativa Japonica Group vs Vigna angularis LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Vigna angularis (Vigna angularis, Vigan1.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 93. Oryza sativa Japonica Group was used as the reference species. After running LastZ, the raw LastZ 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
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)3000
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Chunking parameters

ParameterOryza sativa Japonica GroupVigna angularis
Chunk size50,000,000100,100,000
Overlap0100,000
Group set size0100,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 149,005 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Oryza sativa Japonica Group

Uncovered: 342,676,222 out of 375,049,285
Covered: 32,373,063 out of 375,049,285

Uncovered: 14,305,021 out of 34,403,043
Matches: 13,004,823 out of 34,403,043
Mismatches: 6,575,119 out of 34,403,043
Insertions: 518,080 out of 34,403,043
Identity over aligned base-pairs: 64.7%

Vigna angularis

Uncovered: 433,220,647 out of 466,744,453
Covered: 33,523,806 out of 466,744,453

Uncovered: 17,005,442 out of 37,822,470
Matches: 13,600,080 out of 37,822,470
Mismatches: 6,779,830 out of 37,822,470
Insertions: 437,118 out of 37,822,470
Identity over aligned base-pairs: 65.3%

Block size distribution

Size range All 149,005 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,077
5.1 kb
10 bp - 100 bp
23,794
1.7 Mb
5,678
408.0 kb
100 bp - 1 kb
116,817
37.2 Mb
36,036
14.0 Mb
1 kb - 10 kb
7,317
10.6 Mb
16,984
34.7 Mb
10 kb - 100 kb
35
423.9 kb