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Oryza sativa Japonica Group vs Oryza sativa (Xian/Indica-1B2 var. PR106) LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Oryza sativa (Xian/Indica-1B2 var. PR106) (Oryza sativa Indica Group, Os127742RS1) 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-1B2 var. PR106)
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 115,505 alignment blocks

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

Uncovered: 65,254,583 out of 375,049,285
Covered: 309,794,702 out of 375,049,285

Uncovered: 308,992 out of 34,818,902
Matches: 34,142,276 out of 34,818,902
Mismatches: 305,922 out of 34,818,902
Insertions: 61,712 out of 34,818,902
Identity over aligned base-pairs: 98.9%

Oryza sativa (Xian/Indica-1B2 var. PR106)

Uncovered: 82,298,778 out of 394,601,903
Covered: 312,303,125 out of 394,601,903

Uncovered: 264,289 out of 42,333,327
Matches: 41,461,843 out of 42,333,327
Mismatches: 511,300 out of 42,333,327
Insertions: 95,895 out of 42,333,327
Identity over aligned base-pairs: 98.6%

Block size distribution

Size range All 115,505 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,324
7.7 kb
10 bp - 100 bp
23,978
1.4 Mb
11,460
700.5 kb
100 bp - 1 kb
54,840
19.7 Mb
25,801
9.2 Mb
1 kb - 10 kb
26,369
94.1 Mb
7,646
17.7 Mb
10 kb - 100 kb
8,813
192.2 Mb
342
6.4 Mb
100 kb - 1 Mb
181
29.7 Mb
19
3.0 Mb
1 Mb - 10 Mb
1
3.2 Mb
10 Mb - 100 Mb
12
296.7 Mb