Ensembl Genomes HomeArchive plants HomeArchive plants Home ▼
More ▼
Search »

Oryza sativa Japonica Group vs Leersia perrieri LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Leersia perrieri (Leersia perrieri, Lperr_V1.4) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. 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
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 GroupLeersia perrieri
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size10,100,000
Masking options{default_soft_masking => 1}

Statistics over 260,363 alignment blocks

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

Uncovered: 229,629,610 out of 375,049,285
Covered: 145,419,675 out of 375,049,285

Uncovered: 1,823,238 out of 34,818,902
Matches: 28,271,909 out of 34,818,902
Mismatches: 3,998,005 out of 34,818,902
Insertions: 725,750 out of 34,818,902
Identity over aligned base-pairs: 85.7%

Leersia perrieri

Uncovered: 150,308,343 out of 266,687,832
Covered: 116,379,489 out of 266,687,832

Uncovered: 4,680,218 out of 36,898,596
Matches: 28,017,531 out of 36,898,596
Mismatches: 3,633,299 out of 36,898,596
Insertions: 567,548 out of 36,898,596
Identity over aligned base-pairs: 87.0%

Block size distribution

Size range All 260,363 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3,772
23.9 kb
10 bp - 100 bp
45,989
2.8 Mb
20,789
1.4 Mb
100 bp - 1 kb
165,943
61.4 Mb
63,161
19.6 Mb
1 kb - 10 kb
44,639
90.9 Mb
8,973
20.6 Mb
10 kb - 100 kb
20
221.7 kb
187
4.3 Mb
100 kb - 1 Mb
13
2.2 Mb
1 Mb - 10 Mb
9
63.1 Mb
10 Mb - 100 Mb
3
44.2 Mb