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

2017-01-01_185233

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

2016-12-20_162158word:b w e ge

2016-12-20_162317

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. foo­bar