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Mouse vs Upper Galilee mountains blind mole rat LastZ results

Mouse (Mus musculus, GRCm39) and Upper Galilee mountains blind mole rat (Nannospalax galili, S.galili_v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 103. Mouse 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)3000
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

ParameterMouseUpper Galilee mountains blind mole rat
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options

Statistics over 2,222,096 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Mouse

Uncovered: 1,328,107,346 out of 2,728,222,451
Covered: 1,400,115,105 out of 2,728,222,451

Uncovered: 596,823 out of 36,014,121
Matches: 30,088,444 out of 36,014,121
Mismatches: 5,083,731 out of 36,014,121
Insertions: 245,123 out of 36,014,121
Identity over aligned base-pairs: 85.0%

Upper Galilee mountains blind mole rat

Uncovered: 1,748,140,267 out of 3,061,408,210
Covered: 1,313,267,943 out of 3,061,408,210

Uncovered: 669,865 out of 29,132,429
Matches: 24,802,687 out of 29,132,429
Mismatches: 3,526,784 out of 29,132,429
Insertions: 133,093 out of 29,132,429
Identity over aligned base-pairs: 87.1%

Block size distribution

Size range All 2,222,096 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
54,109
354.5 kb
10 bp - 100 bp
244,392
12.9 Mb
32,862
2.3 Mb
100 bp - 1 kb
1,446,991
636.6 Mb
151,398
54.1 Mb
1 kb - 10 kb
476,129
854.6 Mb
36,683
90.8 Mb
10 kb - 100 kb
472
6.3 Mb
1,864
42.4 Mb
100 kb - 1 Mb
3
414.2 kb
807
340.7 Mb
1 Mb - 10 Mb
456
980.9 Mb