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Arabidopsis thaliana vs Manihot esculenta LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Manihot esculenta (Manihot esculenta, Manihot_esculenta_v6) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 91. 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 thalianaManihot esculenta
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 151,801 alignment blocks

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

Uncovered: 80,973,383 out of 119,667,750
Covered: 38,694,367 out of 119,667,750

Uncovered: 7,421,507 out of 33,775,569
Matches: 17,742,499 out of 33,775,569
Mismatches: 8,048,240 out of 33,775,569
Insertions: 563,323 out of 33,775,569
Identity over aligned base-pairs: 67.3%

Manihot esculenta

Uncovered: 533,737,641 out of 582,117,524
Covered: 48,379,883 out of 582,117,524

Uncovered: 8,222,757 out of 38,679,430
Matches: 20,650,995 out of 38,679,430
Mismatches: 8,948,826 out of 38,679,430
Insertions: 856,852 out of 38,679,430
Identity over aligned base-pairs: 67.8%

Block size distribution

Size range All 151,801 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,534
8.3 kb
10 bp - 100 bp
21,679
1.4 Mb
4,255
298.9 kb
100 bp - 1 kb
115,175
41.0 Mb
24,796
9.9 Mb
1 kb - 10 kb
13,385
20.7 Mb
17,728
43.2 Mb
10 kb - 100 kb
28
311.2 kb
523
9.3 Mb
100 kb - 1 Mb
6
731.7 kb