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Oryza sativa Japonica Group vs Chlamydomonas reinhardtii LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Chlamydomonas reinhardtii (Chlamydomonas reinhardtii, Chlamydomonas_reinhardtii_v5.5) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 93. 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)3000
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 GroupChlamydomonas reinhardtii
Chunk size50,000,000100,100,000
Overlap0100,000
Group set size0100,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 21,592 alignment blocks

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

Uncovered: 372,441,909 out of 375,049,285
Covered: 2,607,376 out of 375,049,285

Uncovered: 32,229,621 out of 34,403,043
Matches: 1,458,062 out of 34,403,043
Mismatches: 670,839 out of 34,403,043
Insertions: 44,521 out of 34,403,043
Identity over aligned base-pairs: 67.1%

Chlamydomonas reinhardtii

Uncovered: 109,446,095 out of 111,098,438
Covered: 1,652,343 out of 111,098,438

Uncovered: 37,692,140 out of 39,157,072
Matches: 977,248 out of 39,157,072
Mismatches: 451,364 out of 39,157,072
Insertions: 36,320 out of 39,157,072
Identity over aligned base-pairs: 66.7%

Block size distribution

Size range All 21,592 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
112
646.0 bp
10 bp - 100 bp
8,711
622.6 kb
1,879
133.7 kb
100 bp - 1 kb
12,734
2.4 Mb
6,200
2.1 Mb
1 kb - 10 kb
35
41.8 kb
536
795.4 kb