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Oryza sativa Japonica Group vs Oryza sativa (Xian/Indica-1A var. Zhenshan 97) LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Oryza sativa (Xian/Indica-1A var. Zhenshan 97) (Oryza sativa Indica Group, ZS97RS3) 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-1A var. Zhenshan 97)
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 114,346 alignment blocks

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

Uncovered: 64,487,423 out of 375,049,285
Covered: 310,561,862 out of 375,049,285

Uncovered: 298,033 out of 34,818,902
Matches: 34,153,663 out of 34,818,902
Mismatches: 306,129 out of 34,818,902
Insertions: 61,077 out of 34,818,902
Identity over aligned base-pairs: 98.9%

Oryza sativa (Xian/Indica-1A var. Zhenshan 97)

Uncovered: 79,036,417 out of 391,561,630
Covered: 312,525,213 out of 391,561,630

Uncovered: 227,005 out of 42,146,420
Matches: 41,340,369 out of 42,146,420
Mismatches: 486,366 out of 42,146,420
Insertions: 92,680 out of 42,146,420
Identity over aligned base-pairs: 98.6%

Block size distribution

Size range All 114,346 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,319
7.8 kb
10 bp - 100 bp
23,602
1.3 Mb
11,286
689.2 kb
100 bp - 1 kb
54,469
19.7 Mb
25,849
9.4 Mb
1 kb - 10 kb
25,960
93.0 Mb
7,587
17.4 Mb
10 kb - 100 kb
8,807
192.8 Mb
318
5.8 Mb
100 kb - 1 Mb
189
30.9 Mb
15
2.4 Mb
1 Mb - 10 Mb
1
3.2 Mb
10 Mb - 100 Mb
12
298.9 Mb