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Oryza sativa Japonica Group vs Rosa chinensis LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Rosa chinensis (Rosa chinensis, RchiOBHm-V2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 101. 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 GroupRosa chinensis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 178,143 alignment blocks

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

Uncovered: 340,842,864 out of 375,049,285
Covered: 34,206,421 out of 375,049,285

Uncovered: 13,459,335 out of 34,424,450
Matches: 13,639,399 out of 34,424,450
Mismatches: 6,786,360 out of 34,424,450
Insertions: 539,356 out of 34,424,450
Identity over aligned base-pairs: 65.1%

Rosa chinensis

Uncovered: 474,252,490 out of 515,588,973
Covered: 41,336,483 out of 515,588,973

Uncovered: 18,337,818 out of 43,773,732
Matches: 16,506,520 out of 43,773,732
Mismatches: 8,318,927 out of 43,773,732
Insertions: 610,467 out of 43,773,732
Identity over aligned base-pairs: 64.9%

Block size distribution

Size range All 178,143 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,274
6.4 kb
10 bp - 100 bp
30,877
2.2 Mb
8,719
637.8 kb
100 bp - 1 kb
136,893
42.8 Mb
48,369
17.6 Mb
1 kb - 10 kb
9,099
13.4 Mb
19,211
39.4 Mb
10 kb - 100 kb
54
725.1 kb