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Oryza sativa Japonica Group vs Oryza sativa (Xian/Indica-3B2 var. Liu Xu) LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Oryza sativa (Xian/Indica-3B2 var. Liu Xu) (Oryza sativa Indica Group, Os125827RS1) 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-3B2 var. Liu Xu)
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 142,835 alignment blocks

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

Uncovered: 63,795,304 out of 375,049,285
Covered: 311,253,981 out of 375,049,285

Uncovered: 313,638 out of 34,818,902
Matches: 34,141,368 out of 34,818,902
Mismatches: 295,727 out of 34,818,902
Insertions: 68,169 out of 34,818,902
Identity over aligned base-pairs: 98.9%

Oryza sativa (Xian/Indica-3B2 var. Liu Xu)

Uncovered: 114,938,583 out of 490,154,521
Covered: 375,215,938 out of 490,154,521

Uncovered: 604,626 out of 50,008,342
Matches: 48,649,004 out of 50,008,342
Mismatches: 634,757 out of 50,008,342
Insertions: 119,955 out of 50,008,342
Identity over aligned base-pairs: 98.5%

Block size distribution

Size range All 142,835 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,708
10.1 kb
10 bp - 100 bp
29,760
1.7 Mb
13,286
810.4 kb
100 bp - 1 kb
65,615
23.7 Mb
29,563
10.5 Mb
1 kb - 10 kb
34,786
126.6 Mb
8,560
19.9 Mb
10 kb - 100 kb
10,833
227.1 Mb
680
27.2 Mb
100 kb - 1 Mb
133
21.6 Mb
245
42.6 Mb
1 Mb - 10 Mb
2
4.3 Mb
10 Mb - 100 Mb
12
295.4 Mb