In this section

Oryza sativa Japonica Group vs Oryza sativa (Geng/Japonica-trop1 var. Azucena) LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Oryza sativa (Geng/Japonica-trop1 var. Azucena) (Oryza sativa tropical japonica subgroup, AzucenaRS1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 111. 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)
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 GroupOryza sativa (Geng/Japonica-trop1 var. Azucena)
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 60,073 alignment blocks

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

Uncovered: 34,925,432 out of 375,049,285
Covered: 340,123,853 out of 375,049,285

Uncovered: 188,049 out of 34,818,902
Matches: 34,452,299 out of 34,818,902
Mismatches: 150,710 out of 34,818,902
Insertions: 27,844 out of 34,818,902
Identity over aligned base-pairs: 99.5%

Oryza sativa (Geng/Japonica-trop1 var. Azucena)

Uncovered: 41,276,679 out of 381,570,127
Covered: 340,293,448 out of 381,570,127

Uncovered: 149,284 out of 42,472,264
Matches: 42,010,748 out of 42,472,264
Mismatches: 267,245 out of 42,472,264
Insertions: 44,987 out of 42,472,264
Identity over aligned base-pairs: 99.3%

Block size distribution

Size range All 60,073 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
748
4.4 kb
10 bp - 100 bp
12,180
701.9 kb
6,085
370.9 kb
100 bp - 1 kb
28,644
10.2 Mb
13,750
4.9 Mb
1 kb - 10 kb
12,218
42.9 Mb
4,038
9.4 Mb
10 kb - 100 kb
5,472
166.4 Mb
233
4.9 Mb
100 kb - 1 Mb
811
137.9 Mb
10
2.5 Mb
1 Mb - 10 Mb
1
4.5 Mb
10 Mb - 100 Mb
12
331.6 Mb