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Oryza sativa Japonica Group vs Oryza rufipogon LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Oryza rufipogon (Oryza rufipogon, OR_W1943) 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 GroupOryza rufipogon
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size10,100,000
Masking options{default_soft_masking => 1}

Statistics over 103,093 alignment blocks

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

Uncovered: 72,561,345 out of 375,049,285
Covered: 302,487,940 out of 375,049,285

Uncovered: 336,404 out of 34,818,902
Matches: 34,139,008 out of 34,818,902
Mismatches: 274,164 out of 34,818,902
Insertions: 69,326 out of 34,818,902
Identity over aligned base-pairs: 99.0%

Oryza rufipogon

Uncovered: 51,237,990 out of 338,040,714
Covered: 286,802,724 out of 338,040,714

Uncovered: 1,152,224 out of 42,763,723
Matches: 41,374,446 out of 42,763,723
Mismatches: 185,533 out of 42,763,723
Insertions: 51,520 out of 42,763,723
Identity over aligned base-pairs: 99.4%

Block size distribution

Size range All 103,093 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,141
6.8 kb
10 bp - 100 bp
17,599
987.8 kb
7,965
487.0 kb
100 bp - 1 kb
49,910
18.4 Mb
17,956
6.2 Mb
1 kb - 10 kb
25,467
92.3 Mb
4,463
10.2 Mb
10 kb - 100 kb
8,965
191.0 Mb
136
3.0 Mb
100 kb - 1 Mb
11
1.3 Mb
6
908.9 kb
10 Mb - 100 Mb
12
283.3 Mb