population genetics lab
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Population Genetics Lab
Lab Instructor: Hari Chhetri PhD student
Department of Biology Area of Research: Association genetics (Populus) Office: Life Sciences Building, Room # 5206. Office Hour: T, W, F – 11:30 AM – 12:30 PM or by appointment. Email ID: harichhetri@gmail.com Tel. #: 304-293-6181
Probability and Popula/on Gene/cs
Popula/on gene/cs is a study of probability Sampling alleles from popula/on each genera/on
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Probability
Frequen'st Approach • Determine how o;en you
expect event A to occur given a LONG series of trials
Bayesian Approach • Determine the plausibility
of event A given what you already know (prior).
Probability Measure of chance. P(E) = # of favorable outcome / Total # of possible outcome It lies between 0 (impossible event) and 1 (certain event). Ex. What is the probability of geGng a head in one toss of a balanced coin.
Total possible outcomes = 2 ( H, T) # of Heads = 1 (H) P(H) = 1/ 2 = 0.5 = 50 %
Sample-‐ point method : 1. Define sample space (S): Collec/on of all possible outcomes of a random expt. Ex. S (Coin tossed twice)
2. Assign probabili'es to all sample points Ex. P(HH) = ¼ ; P(HT) = ¼ ; P(TH) = ¼ ; P(TT) = ¼
Outcome 1 2 3 4
First Toss H H T T
Second Toss H T H T
Shorthand HH HT TH TT
Sample-‐ point method : 3.Determine event of interest and add their probabili'es. Ex. Find the probability of geXng exactly one head in two tosses of a balanced coin.
i. S (Coin tossed twice) { HH, HT, TH, TT}. ii. P(HT) = ¼ ; P(TH) = ¼
iii. P(HT) + P (TH) = ¼ + ¼ = 2/4 = ½ . If all sample points have equal probabili'es then –
P(A) = na / N where, na = # of points cons/tu/ng event A and N= Total # of sample points.
Sample-‐ point method : Example: Use the Sample Point Method to find the probability of geXng exactly two heads in three tosses of a balanced coin. 1. The sample space of this experiment is:
2. Assuming that the coin is fair, each of these 8 outcomes has a probability of 1/8. 3. The probability of geXng two heads is the sum of the probabili/es of outcomes 2, 3, and 4 (HHT, HTH, and THH), or 1/8 + 1/8 + 1/8 = 3/8 = 0.375. In above example, find the probability of geGng at least two heads. Solu'on: 1/8 + 1/8 + 1/8+ 1/8 = 1/2
Outcome Toss 1 Toss 2 Toss 3 Shorthand Probabilities 1 Head Head Head HHH 1/8 2 Head Head Tail HHT 1/8 3 Head Tail Head HTH 1/8 4 Tail Head Head THH 1/8 5 Tail Tail Head TTH 1/8 6 Tail Head Tail THT 1/8 7 Head Tail Tail HTT 1/8 8 Tail Tail Tail TTT 1/8
Problem 1: The game of “craps” consists of rolling a pair of balanced dice (i.e., for each die geGng 1, 2, 3, 4, 5, and 6 all have equal probabili'es) and adding up the resul'ng numbers. A roll of “2” is commonly called “snake eyes” and causes an instant loss when rolled in the opening round. Using the Sample-‐Point Method, find the exact probability of a roll of snaked eyes. (Time : 10 minutes)
Probability
For large sample space: Use fundamental coun'ng methods. 1. mn rule : If there are “m” elements from one group and “n” elements from another group, then we can have “mn” possible pairs, with one element from each group.
mn= 6*6= 36 .
Second die 1 2 3 4 5 6
Firs
t die
1 2 3 4 5 6
For large sample space : Use fundamental coun'ng methods. 2. Permuta'on: Ordered set of “r” elements, chosen without replacement, from “n” available elements. Remember: 0! = 1 (By defini/on)
n! = n*(n-‐1)*(n-‐2)*…………*2*1. Example: How many trinucleo'de sequences can be formed without repea'ng a nucleo'de , where ATC is different from CAT? Solu'on: n = 4 ( A, T, C and G) r = 3
= 24.
)!(!rnnPnr −
=
)!34(!4−
=nrP
For large sample space : Use fundamental coun'ng principle. 3. Combina'on: Unordered set of “r” elements, chosen without replacement, from “n” available elements. Example: How many trinucleo/de sequences, can be formed without repea/ng a nucleo/de , where ATC is same as CAT. Solu'on: n = 4 ( A, T, C and G) r = 3
= 4.
)!(!!rnr
nC nr −=
)!34(!3!4−
=nrC
For large sample space : Use fundamental coun'ng principle. Problem 2: There are 36 computer workstations in this lab. If there are 18 students in the class, how many distinct ways could students be arranged, with one student per workstation? ( 10 minutes). Problem 3: A local fraternity is organizing a raffle in which 30 tickets are to be sold - one per customer. (10 minutes). a. What is the total number of distinct ways in which winners can be chosen if prizes are awarded as follows: b. If holders of the first four tickets drawn each receive a $30 prize?
Order of Drawing Prize
First $100
Second $50
Third $25
Fourth 10$
Laws of Probability 1. Additive law of probability:
B)P(A - P(B) P(A) B)(A P ∩+=∪
P(B) P(A) B)P(A then 0, B)P(A events, exclusivemutually For usly.simaltaneo B andA event of occurrence ofy ProbabilitB)P(A
B.or A event of occurrence ofy ProbabilitB)P(AWhere,
+=∪=∩
=∩
=∪
B)(A Pfor diagramVenn ∪ B)(A Pfor diagramVenn ∩
A B
A and B are Mutually Exclusive
Laws of Probability 1. Additive law of probability:
Example: From a pack of 52 cards, one card is drawn at random. Find the probability that the card is “Heart” or “Ace”. Four suits are : Spades, Diamonds, Clubs and Hearts. Each suit has 13 cards: Ace,2,3,4,5,6,7,8,9,10,Jack, Queen and King. There are four of each type, like 4 Aces,4 Jacks, 4 Queens, 4 Kings etc. Solution:
5216
521
524
5213 A)P(H
521 A)P(H ;
524 P(A) ;
5213 P(H)
A)P(H - P(A) P(H) A)(H P
=−+=∪
=∩==
∩+=∪
Laws of Probability 2. Multiplicative law of probability:
P(B) P(A) B)(A P ×=∩ (If A and B are independent events)
B)|P(A P(B) A)|P(B P(A) B)(A P ×=×=∩(If A and B are dependent events)
\
Example: A pond consists of 50 salmon and 25 trout. Two fish are drawn one by one. Find the probability that both fish are Salmon. a.)with replacement and b.)without replacement
11149
22298
7449
7550
A)|P(B P(A) B)P(A :treplacemen Without :(b) Case
94
7550
7550
P(B) P(A) B)P(A :treplacemen With :(a) Case
Salmon. isdrawn fish second that Prob. : P(B) Salmon. isdrawn fish first that Prob. :P(A) Let,
:Solution
==×=
×=∩
=
×=
×=∩
Problem 4. An inexperienced spelunker is preparing for the explora'on of a big cave in a rural area of Mexico. He is planning to use two independent light sources and from reading their technical specifica'ons, he has concluded that each source is expected to malfunc'on with probability of 0.01. What is the probability that: a) At least one of his light sources malfunc'ons? b) Neither of his light sources malfunc'on? (Time : 15 minutes)
Problem 5. GRADUATE STUDENTS ONLY: In street craps, the opening toss wins if a 7 or 11 is rolled, and the “pass” bets will pay off. Meanwhile if 2, 3, or 12 is rolled, only “don’t pass” bets will win. a) Is it safest to bet “pass” or “don’t pass” on the opening roll? Show the exact probability of each outcome. b) If the shooter rolls 7 three 'mes in a row, is it safest to bet “pass” or “don’t pass” on the next roll? Defend your answer.
(Time: 5 minutes)
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