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Arabidopsis thaliana vs Papaver somniferum LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Papaver somniferum (Papaver somniferum, ASM357369v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 103. 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 thalianaPapaver somniferum
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options

Statistics over 280,999 alignment blocks

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

Uncovered: 86,878,877 out of 119,667,750
Covered: 32,788,873 out of 119,667,750

Uncovered: 11,329,074 out of 33,775,569
Matches: 14,945,809 out of 33,775,569
Mismatches: 6,982,876 out of 33,775,569
Insertions: 517,810 out of 33,775,569
Identity over aligned base-pairs: 66.6%

Papaver somniferum

Uncovered: 2,626,834,422 out of 2,715,377,404
Covered: 88,542,982 out of 2,715,377,404

Uncovered: 16,579,056 out of 47,183,124
Matches: 20,293,138 out of 47,183,124
Mismatches: 9,458,779 out of 47,183,124
Insertions: 852,151 out of 47,183,124
Identity over aligned base-pairs: 66.3%

Block size distribution

Size range All 280,999 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,778
10.4 kb
10 bp - 100 bp
49,319
3.4 Mb
20,009
1.4 Mb
100 bp - 1 kb
209,774
70.9 Mb
79,080
28.6 Mb
1 kb - 10 kb
20,128
29.7 Mb
34,522
72.4 Mb
10 kb - 100 kb
112
1.4 Mb