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Human vs White-tufted-ear marmoset LastZ results

Human (Homo sapiens, GRCh38) and White-tufted-ear marmoset (Callithrix jacchus, mCalJac1.pat.X) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 105. Human 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
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

ParameterHumanWhite-tufted-ear marmoset
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size10,100,000
Masking options

Statistics over 1,799,693 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Human

Uncovered: 750,484,870 out of 3,099,750,718
Covered: 2,349,265,848 out of 3,099,750,718

Uncovered: 428,221 out of 38,571,754
Matches: 35,546,640 out of 38,571,754
Mismatches: 2,402,114 out of 38,571,754
Insertions: 194,779 out of 38,571,754
Identity over aligned base-pairs: 93.2%

White-tufted-ear marmoset

Uncovered: 631,424,251 out of 2,829,711,198
Covered: 2,198,286,947 out of 2,829,711,198

Uncovered: 3,504,430 out of 36,931,356
Matches: 31,468,593 out of 36,931,356
Mismatches: 1,876,021 out of 36,931,356
Insertions: 82,312 out of 36,931,356
Identity over aligned base-pairs: 94.1%

Block size distribution

Size range All 1,799,693 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
74,224
498.6 kb
10 bp - 100 bp
297,952
13.8 Mb
49,509
3.2 Mb
100 bp - 1 kb
749,556
317.7 Mb
129,308
39.5 Mb
1 kb - 10 kb
661,925
1.9 Gb
20,786
55.1 Mb
10 kb - 100 kb
16,014
216.6 Mb
2,766
76.0 Mb
100 kb - 1 Mb
22
2.7 Mb
347
86.8 Mb
1 Mb - 10 Mb
48
169.0 Mb
10 Mb - 100 Mb
55
1.6 Gb
100 Mb - 1 Gb
4
464.8 Mb