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Oryza rufipogon vs Leersia perrieri LastZ results

Oryza rufipogon (Oryza rufipogon, OR_W1943) and Leersia perrieri (Leersia perrieri, Lperr_V1.4) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. Oryza rufipogon 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 rufipogonLeersia perrieri
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size10,100,000
Masking options{default_soft_masking => 1}

Statistics over 253,725 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Oryza rufipogon

Uncovered: 198,926,311 out of 338,040,714
Covered: 139,114,403 out of 338,040,714

Uncovered: 3,702,688 out of 42,763,723
Matches: 32,951,500 out of 42,763,723
Mismatches: 5,128,370 out of 42,763,723
Insertions: 981,165 out of 42,763,723
Identity over aligned base-pairs: 84.4%

Leersia perrieri

Uncovered: 150,785,574 out of 266,687,832
Covered: 115,902,258 out of 266,687,832

Uncovered: 4,755,711 out of 36,898,596
Matches: 27,935,917 out of 36,898,596
Mismatches: 3,628,224 out of 36,898,596
Insertions: 578,744 out of 36,898,596
Identity over aligned base-pairs: 86.9%

Block size distribution

Size range All 253,725 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3,700
23.4 kb
10 bp - 100 bp
46,382
2.8 Mb
21,085
1.4 Mb
100 bp - 1 kb
161,246
59.1 Mb
58,949
17.8 Mb
1 kb - 10 kb
42,378
86.4 Mb
7,146
16.4 Mb
10 kb - 100 kb
19
209.7 kb
196
4.7 Mb
100 kb - 1 Mb
13
2.1 Mb
1 Mb - 10 Mb
9
62.4 Mb
10 Mb - 100 Mb
3
43.7 Mb