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Oryza sativa Japonica Group vs Vigna radiata LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Vigna radiata (Vigna radiata var. radiata, Vradiata_ver6) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 94. 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
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
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 radiata
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 155,870 alignment blocks

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

Uncovered: 341,429,803 out of 375,049,285
Covered: 33,619,482 out of 375,049,285

Uncovered: 14,180,833 out of 34,818,902
Matches: 13,266,349 out of 34,818,902
Mismatches: 6,843,051 out of 34,818,902
Insertions: 528,669 out of 34,818,902
Identity over aligned base-pairs: 64.3%

Vigna radiata

Uncovered: 427,352,416 out of 463,085,359
Covered: 35,732,943 out of 463,085,359

Uncovered: 9,215,768 out of 28,307,530
Matches: 12,495,813 out of 28,307,530
Mismatches: 6,196,959 out of 28,307,530
Insertions: 398,990 out of 28,307,530
Identity over aligned base-pairs: 65.5%

Block size distribution

Size range All 155,870 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,081
5.3 kb
10 bp - 100 bp
26,170
1.8 Mb
7,429
523.0 kb
100 bp - 1 kb
120,542
38.4 Mb
37,198
14.3 Mb
1 kb - 10 kb
8,075
12.1 Mb
17,997
37.0 Mb
10 kb - 100 kb
2
21.8 kb
47
594.4 kb