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Oryza sativa Japonica Group vs Oryza sativa (circum-Aus2 var. Natel Boro) LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Oryza sativa (circum-Aus2 var. Natel Boro) (Oryza sativa aus subgroup, Os127652RS1) 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 (circum-Aus2 var. Natel Boro)
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 124,948 alignment blocks

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

Uncovered: 70,124,755 out of 375,049,285
Covered: 304,924,530 out of 375,049,285

Uncovered: 340,154 out of 34,818,902
Matches: 34,077,309 out of 34,818,902
Mismatches: 331,183 out of 34,818,902
Insertions: 70,256 out of 34,818,902
Identity over aligned base-pairs: 98.8%

Oryza sativa (circum-Aus2 var. Natel Boro)

Uncovered: 78,985,637 out of 384,203,823
Covered: 305,218,186 out of 384,203,823

Uncovered: 318,006 out of 41,781,302
Matches: 40,842,824 out of 41,781,302
Mismatches: 518,539 out of 41,781,302
Insertions: 101,933 out of 41,781,302
Identity over aligned base-pairs: 98.5%

Block size distribution

Size range All 124,948 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,417
8.5 kb
10 bp - 100 bp
25,859
1.5 Mb
12,431
761.2 kb
100 bp - 1 kb
58,495
20.9 Mb
27,519
9.6 Mb
1 kb - 10 kb
30,028
109.0 Mb
7,546
17.6 Mb
10 kb - 100 kb
9,073
187.4 Mb
305
5.8 Mb
100 kb - 1 Mb
76
11.4 Mb
21
4.7 Mb
1 Mb - 10 Mb
2
4.3 Mb
10 Mb - 100 Mb
12
287.4 Mb