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Oryza sativa Japonica Group vs Oryza sativa (Xian/Indica-3A var. Lima) LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Oryza sativa (Xian/Indica-3A var. Lima) (Oryza sativa Indica Group, Os127564RS1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 111. 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 GroupOryza sativa (Xian/Indica-3A var. Lima)
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 123,779 alignment blocks

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

Uncovered: 67,483,132 out of 375,049,285
Covered: 307,566,153 out of 375,049,285

Uncovered: 338,659 out of 34,818,902
Matches: 34,077,138 out of 34,818,902
Mismatches: 335,378 out of 34,818,902
Insertions: 67,727 out of 34,818,902
Identity over aligned base-pairs: 98.8%

Oryza sativa (Xian/Indica-3A var. Lima)

Uncovered: 89,732,914 out of 405,399,143
Covered: 315,666,229 out of 405,399,143

Uncovered: 300,161 out of 42,895,272
Matches: 41,941,680 out of 42,895,272
Mismatches: 551,086 out of 42,895,272
Insertions: 102,345 out of 42,895,272
Identity over aligned base-pairs: 98.5%

Block size distribution

Size range All 123,779 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,436
8.4 kb
10 bp - 100 bp
25,631
1.5 Mb
12,067
738.1 kb
100 bp - 1 kb
59,296
21.3 Mb
27,816
9.9 Mb
1 kb - 10 kb
28,130
100.4 Mb
8,181
18.8 Mb
10 kb - 100 kb
9,134
194.4 Mb
348
8.0 Mb
100 kb - 1 Mb
152
24.0 Mb
42
7.2 Mb
1 Mb - 10 Mb
2
4.9 Mb
10 Mb - 100 Mb
12
291.8 Mb