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Oryza sativa Japonica Group vs Coffea canephora LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Coffea canephora (Coffea canephora str. DH200-94, AUK_PRJEB4211_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 98. 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 GroupCoffea canephora
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 133,289 alignment blocks

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

Uncovered: 342,625,991 out of 375,049,285
Covered: 32,423,294 out of 375,049,285

Uncovered: 14,773,187 out of 34,424,450
Matches: 12,634,853 out of 34,424,450
Mismatches: 6,589,682 out of 34,424,450
Insertions: 426,728 out of 34,424,450
Identity over aligned base-pairs: 64.3%

Coffea canephora

Uncovered: 538,200,691 out of 568,611,505
Covered: 30,410,814 out of 568,611,505

Uncovered: 11,467,833 out of 30,830,841
Matches: 12,504,343 out of 30,830,841
Mismatches: 6,432,482 out of 30,830,841
Insertions: 426,183 out of 30,830,841
Identity over aligned base-pairs: 64.6%

Block size distribution

Size range All 133,289 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
854
4.2 kb
10 bp - 100 bp
21,227
1.5 Mb
4,836
350.2 kb
100 bp - 1 kb
104,265
33.0 Mb
30,391
12.1 Mb
1 kb - 10 kb
6,910
10.7 Mb
15,501
31.9 Mb
10 kb - 100 kb
33
1.1 Mb
76
1.8 Mb
100 kb - 1 Mb
1
109.1 kb