In this section

Oryza sativa Japonica Group vs Dioscorea rotundata LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Dioscorea rotundata (Dioscorea rotundata, TDr96_F1_v2_PseudoChromosome) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 102. 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 GroupDioscorea rotundata
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 155,456 alignment blocks

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

Uncovered: 338,196,771 out of 375,049,285
Covered: 36,852,514 out of 375,049,285

Uncovered: 12,398,143 out of 34,424,450
Matches: 14,525,809 out of 34,424,450
Mismatches: 6,898,237 out of 34,424,450
Insertions: 602,261 out of 34,424,450
Identity over aligned base-pairs: 65.9%

Dioscorea rotundata

Uncovered: 544,968,686 out of 584,153,202
Covered: 39,184,516 out of 584,153,202

Uncovered: 10,436,012 out of 29,758,230
Matches: 12,942,325 out of 29,758,230
Mismatches: 5,959,156 out of 29,758,230
Insertions: 420,737 out of 29,758,230
Identity over aligned base-pairs: 67.0%

Block size distribution

Size range All 155,456 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,124
5.5 kb
10 bp - 100 bp
24,003
1.7 Mb
6,332
454.3 kb
100 bp - 1 kb
120,072
39.8 Mb
37,825
14.6 Mb
1 kb - 10 kb
10,257
15.5 Mb
18,600
40.8 Mb
10 kb - 100 kb
77
1.0 Mb