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Triticum aestivum vs Saccharum spontaneum LastZ results

Triticum aestivum (Triticum aestivum, IWGSC) and Saccharum spontaneum (Saccharum spontaneum, Sspon.HiC_chr_asm) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 107. Triticum aestivum 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

ParameterTriticum aestivumSaccharum spontaneum
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 2,480,931 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Triticum aestivum

Uncovered: 13,998,543,575 out of 14,547,261,565
Covered: 548,717,990 out of 14,547,261,565

Uncovered: 11,489,926 out of 133,674,966
Matches: 93,331,780 out of 133,674,966
Mismatches: 26,023,910 out of 133,674,966
Insertions: 2,829,350 out of 133,674,966
Identity over aligned base-pairs: 76.4%

Saccharum spontaneum

Uncovered: 2,279,792,049 out of 2,900,240,836
Covered: 620,448,787 out of 2,900,240,836

Uncovered: 6,853,482 out of 62,027,027
Matches: 42,534,731 out of 62,027,027
Mismatches: 11,082,348 out of 62,027,027
Insertions: 1,556,466 out of 62,027,027
Identity over aligned base-pairs: 77.1%

Block size distribution

Size range All 2,480,931 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
19,965
101.7 kb
10 bp - 100 bp
469,646
30.1 Mb
298,144
19.8 Mb
100 bp - 1 kb
1,698,909
583.1 Mb
989,734
317.0 Mb
1 kb - 10 kb
292,401
524.1 Mb
285,659
746.0 Mb
10 kb - 100 kb
10
233.3 kb
4,107
54.8 Mb
100 kb - 1 Mb
1
110.3 kb