IBD vs IBS

Pedigree,_recombination_and_resulting_IBD_segments,_schematic_representation

The origin of IBD segments is depicted via a pedigree of 12 individuals. Each box (male) and circle (female) represents an individual with two homologous chromosomes as bars. The top row shows three couples with their chromosomes colored differently. Due to crossing over, offspring inherit recombinant chromosomes of their parents. The first order cousins in the bottom row share one IBD segment (borders marked by grey lines). Both have inherited this IBD segment from the same individual, namely their grandfather (orange colored chromosome in the top row). Diagram courtesy of Gklambauer, Wikimedia Commons.

The IBS (identity by state) definition refers to the fact that at some point two individuals, even if they are not related to each other, present the same allele at a specific locus. Because of their un-relatedness this similarity probably arose from a similar mutational event. On the other side, with IBD two individuals happen to share the same allele because of their coancestry.

Variety of Formulae

1. Nucleotide Diversity

Screenshot from 2016-12-30 20-44-52

where xi and xj are the respective frequencies of the ith and jth sequences, πij is the number of nucleotide differences per nucleotide site between the ith and jth sequences, and n is the number of sequences in the sample.

2. variance

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3. the average k-mer coverage

如果k=L, 根据公式,那么Ckmer=0。但是这明显是错的,实际应该是1,因为,每个k-mer(reads),至少被覆盖了一次。而在k=L的极端情况下,只会存在少量频率大于1的k-mer。因为reads之间,除了PCR duplication会生成完全相同的reads,一般情况下,两条reads完全相同的概率是非常小的。

4.

Timeline of genus Bos

bos_species

source:http://www.timetree.org/

TimeTree is a public knowledge-base for information on the tree-of-life and its evolutionary timescale. For those interested in published summaries of relationships and divergence times of major groups of organisms, see publications from Hedges and Kumar (2009) and Hedges et al. (2015). For reviews of the history and methods of time estimation, and other useful information, see RESOURCES. TimeTree is jointly directed by Blair Hedges and Sudhir Kumar (Temple University). We encourage suggestions for improvement of this resource (see CONTACT). Current staff members include: Glen Stecher, Bremen Braun, and Michael Suleski (Software and Database Developers), and Julie Marin, and Sarah Hanson (Data Research and Assembly). Previously we have been assisted by Brooke Gattens, Michael McCutchan, Kelly Boccia, Wayne Parkhurst, Tina Dennison, Mandy Hippenstiel, Audrie Kapinus, Lainey Lee, Jaclyn McKay, Molly Oberholtzer, Davide Pisani, Kathy Plavnik, Prachi Shaw, Lidsay Stork, Vinod Swarna, Graziela Valente, Curtis Williams, and Lin-Wei Wu. We continue to receive helpful feedback from our colleagues in the evolutionary biology community. This project has been supported, in part, by grants from the National Science Foundation, NASA Astrobiology Institute, and Science Foundation of Arizona.

Bos taurus (Cattle)

Bos taurus (cow) is an agriculturally important animal; beef and milk production are the largest manufacturing industries in the United States. The cow is an important model organism for health research in obesity, female health, and infectious diseases. Cow is also used in studies of endocrinology, physiology and reproductive techniques. The cow genome will be useful for comparative genomics, representing a non-primate, non-rodent eutherian genome. The B. taurus genome is estimated to be 3000 MB, organized in 29 pairs of autosomes and two sex chromosomes. Bovine chromosomes are acrocentric.

cow

 Screenshot from 2016-12-28 17-15-04

Sus scrofa (Pig)

The pig (Sus scrofa) is a member of the artiodactyls, or cloven-hoofed mammals, which are an evolutionary clade distinct from the primates and rodents. Pigs exist in both feral and domesticated populations that have distinct phenotypes and karyotypes. The haploid genome of the domesticated pig is estimated to be 2800 Mb. The diploid genome is organized in 18 pairs of autosomes and two sex chromosomes.Sus scrofa is an important model organism for health research due to parallels with humans. Swine are omnivores and their digestive physiology is similar to humans. Similarities between humans and pigs also exist in renal function, vascular structure, and respiratory rates. Pigs are used as model organism in many areas of medical research including obesity, cardiovascular disease, endocrinology, alcoholism, diabetes, nephropathy, and organ transplantation. Pigs are also agriculturally important, as pork is a leading source of protein worldwide.

k7974-18_pig_usda_2

Screenshot from 2016-12-24 17-18-44

VIM Tips

  1. Quick Move

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WORD:B W E gE

2. S-LEFT/RIGHT: 在命令行模式下,shift+方向键可以快速跳跃一个单词,但是在putty,x-shell都会失效。

3. :verbose set tabstop
当我们发现vim的实际值与我们在vimrc中的设定值不一致时,可以使用这个命令去查看值的设置来源。

4.