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Oryza sativa Japonica Group vs Zea mays LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Zea mays (Zea mays, Zm-B73-REFERENCE-NAM-5.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 104. 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 GroupZea mays
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 275,837 alignment blocks

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

Uncovered: 307,110,444 out of 375,049,285
Covered: 67,938,841 out of 375,049,285

Uncovered: 4,567,050 out of 34,818,902
Matches: 23,295,145 out of 34,818,902
Mismatches: 6,169,823 out of 34,818,902
Insertions: 786,884 out of 34,818,902
Identity over aligned base-pairs: 77.0%

Zea mays

Uncovered: 2,081,386,120 out of 2,182,075,994
Covered: 100,689,874 out of 2,182,075,994

Uncovered: 5,652,343 out of 43,681,835
Matches: 29,890,254 out of 43,681,835
Mismatches: 7,238,675 out of 43,681,835
Insertions: 900,563 out of 43,681,835
Identity over aligned base-pairs: 78.6%

Block size distribution

Size range All 275,837 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,187
11.7 kb
10 bp - 100 bp
43,008
2.8 Mb
18,673
1.3 Mb
100 bp - 1 kb
201,544
72.5 Mb
91,854
31.9 Mb
1 kb - 10 kb
29,026
48.5 Mb
23,262
56.3 Mb
10 kb - 100 kb
72
1.2 Mb
898
18.7 Mb
100 kb - 1 Mb
35
8.9 Mb
1 Mb - 10 Mb
6
7.9 Mb