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Oryza sativa Indica Group vs Oryza rufipogon LastZ results

Oryza sativa Indica Group (Oryza sativa Indica Group, ASM465v1) and Oryza rufipogon (Oryza rufipogon, OR_W1943) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. Oryza sativa Indica 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 Indica GroupOryza rufipogon
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size10,100,000
Masking options{default_soft_masking => 1}

Statistics over 146,284 alignment blocks

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

Uncovered: 128,603,733 out of 427,004,890
Covered: 298,401,157 out of 427,004,890

Uncovered: 3,760,069 out of 45,465,969
Matches: 40,982,110 out of 45,465,969
Mismatches: 598,855 out of 45,465,969
Insertions: 124,935 out of 45,465,969
Identity over aligned base-pairs: 98.3%

Oryza rufipogon

Uncovered: 70,255,676 out of 338,040,714
Covered: 267,785,038 out of 338,040,714

Uncovered: 2,387,324 out of 42,763,723
Matches: 39,917,735 out of 42,763,723
Mismatches: 365,536 out of 42,763,723
Insertions: 93,128 out of 42,763,723
Identity over aligned base-pairs: 98.9%

Block size distribution

Size range All 146,284 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,449
8.8 kb
10 bp - 100 bp
23,713
1.3 Mb
11,217
680.7 kb
100 bp - 1 kb
70,368
27.7 Mb
27,961
10.6 Mb
1 kb - 10 kb
43,291
144.1 Mb
10,616
26.4 Mb
10 kb - 100 kb
7,463
127.5 Mb
696
14.4 Mb
100 kb - 1 Mb
15
3.9 Mb
10 Mb - 100 Mb
12
244.6 Mb