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Arabidopsis thaliana vs Coffea canephora LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Coffea canephora (Coffea canephora str. DH200-94, AUK_PRJEB4211_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 98. Arabidopsis thaliana 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

ParameterArabidopsis thalianaCoffea 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 128,536 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 86,401,346 out of 119,667,750
Covered: 33,266,404 out of 119,667,750

Uncovered: 9,533,609 out of 33,775,569
Matches: 16,105,174 out of 33,775,569
Mismatches: 7,671,052 out of 33,775,569
Insertions: 465,734 out of 33,775,569
Identity over aligned base-pairs: 66.4%

Coffea canephora

Uncovered: 533,444,799 out of 568,611,505
Covered: 35,166,706 out of 568,611,505

Uncovered: 9,216,946 out of 30,830,841
Matches: 14,344,990 out of 30,830,841
Mismatches: 6,709,828 out of 30,830,841
Insertions: 559,077 out of 30,830,841
Identity over aligned base-pairs: 66.4%

Block size distribution

Size range All 128,536 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,107
5.9 kb
10 bp - 100 bp
19,278
1.3 Mb
3,893
273.2 kb
100 bp - 1 kb
99,747
33.5 Mb
24,170
9.7 Mb
1 kb - 10 kb
8,381
12.7 Mb
14,556
32.9 Mb
10 kb - 100 kb
22
716.2 kb
277
5.4 Mb
100 kb - 1 Mb
1
131.3 kb
1
131.3 kb