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Oryza sativa Japonica Group vs Oryza sativa (Xian/Indica-adm var. Minghui 63) LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Oryza sativa (Xian/Indica-adm var. Minghui 63) (Oryza sativa Indica Group, MH63RS2) 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-adm var. Minghui 63)
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 118,471 alignment blocks

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

Uncovered: 64,463,715 out of 375,049,285
Covered: 310,585,570 out of 375,049,285

Uncovered: 312,732 out of 34,818,902
Matches: 34,136,124 out of 34,818,902
Mismatches: 308,108 out of 34,818,902
Insertions: 61,938 out of 34,818,902
Identity over aligned base-pairs: 98.9%

Oryza sativa (Xian/Indica-adm var. Minghui 63)

Uncovered: 81,793,193 out of 395,765,488
Covered: 313,972,295 out of 395,765,488

Uncovered: 270,911 out of 42,271,986
Matches: 41,390,417 out of 42,271,986
Mismatches: 514,625 out of 42,271,986
Insertions: 96,033 out of 42,271,986
Identity over aligned base-pairs: 98.5%

Block size distribution

Size range All 118,471 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,389
8.0 kb
10 bp - 100 bp
24,632
1.4 Mb
11,852
724.3 kb
100 bp - 1 kb
56,815
20.6 Mb
26,828
9.7 Mb
1 kb - 10 kb
26,609
94.4 Mb
8,021
18.3 Mb
10 kb - 100 kb
8,838
191.9 Mb
350
6.6 Mb
100 kb - 1 Mb
188
31.4 Mb
17
3.2 Mb
1 Mb - 10 Mb
1
3.0 Mb
10 Mb - 100 Mb
12
298.2 Mb