When you have a read, you must align it with a sequence in the reference genome. This is what alignment software does: it locates the read within the 3 billion bp genome. Allows you to identify nucleotide differences. Includes Bowtie, BWA, and STAR. The user can set criteria for alignements, allowing a certain number of gaps and mismatches between sequences and the reference genome. The more differences allowed, the more false positives and true positives. Output is in the .SAM format. Outcomes of a read are:

1. The read does not match anywhere in the genome. It may be because the reference genome is incomplete, or the read sequence has diverged from the reference genome (indels and SNPs). The software determines how much difference is accepted for a match.

2. The read matches to one site very well.

3. The read matches up equally well to more than one site. This is caused by genome repetition.

4. Paired ends match up at different sites: different fragments of the read match to separate sites, even on separate chromosomes. Caused by DNA fragmenting and moving around of the reference genome.

http://bowtie-bio.sourceforge.net/index.shtml

An alignment software. Outputs some optional fields for each alignment in the .SAM format, depending on the type of alignment, including edit distance.

http://bio-bwa.sourceforge.net/

An alignment software. Used in the study with Darwin's finches.

Traits must have two possibilities. Tests for an association between a trait and DNA sequences. Uses a contingency table. Gives a p value. The greater the deviation from the expected, given the null hypothesis, the more evidence for association. The Χ² statistic is larger the stronger the association.

Χ² = Σ ((observed - expected)² / expected)

Gallus gallus

Its ancestor is jungle fowl. It has 78 chromosomes, all of which  may have nucleotide differences with each other. Its genome is 1,200 Mbp.

Geospiza sp.

Famous because they are mentioned in Origin of the Species. Have been widely studied as a model of speciation and adaptive evolution. Illustrate young, adaptive radiation. One trait that has diverged is beak shape. Different beak shapes enable the birds to eat different foods. Lamichhaney et al (2015) discovered a likely gene contributing to beak evolution. There were 100 bp reads made, with 10x coverage, for 200 individuals. The reads were aligned using BWA alignment software, and GATK was used to identify SNPs and indels. Birds with blunt beaks should have different alleles than those with pointed beaks at alleles that contribute to beak shape; allele frequencies should differ at these loci. Blunt beak was the derived trait, and had little genetic diversity. The gene controlling beak shape was found to be ALX homeobox 1.

Novel trait

The trait which evolved from the acnestral trait. Loci for derived traits have less genetic diversity. In Darwin's finches, blunt beaks are the derived trait.

A function of allele frequencies between populations. Based on the frequency of heterozygotes expected, given a whole, random mating population, compared to the frequency of heterozygotes observed within subpopulations. If there is low diversity within a population, one expects a low frequency of heterozygotes. A value of 0 indicates no allelic differentiation between populations. A value of 1 indicates maximum allelic differentiation betwen populations.

F_ST = (H_T - H_S) / H_T

https://genome.ucsc.edu/index.html

A genome data browser for many organisms, including chickens is available. Allows you to investigate a region of a chromosome, and shows gene sequence and annotation with genes and protein coding sites. Genome sequence projects produce the DNA sequence of chromosomes, as completely as possible.

The distance between two genes can be measured in cM using this formula:

Distance = (# recombinant types / # gametes) x 100

A sequencing technology. The manufacturer includes in the output an estimate of the confidence that the sequence is correct. The raw data output is as follows:

1. Line 1 begins with an '@' character and sequence identifier.

2. Line 2 contains the nucleotide sequence. This is the read.

3. Line 3 begins with a '+' character and may be followed by the sequence identifier.

4. Line 4 encodes the quality values for the sequence in line 2. The quality symbols associated with each nucleotide is asci coded, and can be translated into Q scores.

Insertion/deletion event

Repeat number differences. A site in the DNA where there is a sequence present in one individual and absent in another. Can be very large, up to megabases, or they can be a few nucleotides.

The non-random association of alleles at two or more chromosomal sites within a population. Alleles that are very close together on a chromosome, and they are inherited together. Calculated using haplotype frequencies. D is not meaningful by itself, and is often expressed relative to the maximum possible D given haplotype frequencies. Haplotype frequencies can never be less than zero, so D can never be greater than (F_A x F_b) or (F_a x F_B), so the lesser of these values will give you the maximum value of D.

F_AB = (F_A + F_B) + D

F_Ab = (F_A + F_b) - D

F_aB = (F_a + F_B) - D

F_ab = (F_a + F_b) + D

Mendelian genes

Have a large effect on phenotype. Includes the gene controlling wrinkled vs. smooth peas in Mendel's experiments. Not typically the situation; it is rare.

www.ncbi.nlm.gov

A main source for molecular information. Has many databases that contain nucleotide/protein information and relevant literature. One main database is "nucleotide"; a collectioin of sequences from Genbank. It is a little confusing compared to other databases. A record consists of a feature table, summary, and sequence.

The further the value is from 1, the greater the association of allele differences to disease status. The value may be high, but the chances of being a case could still be low.

Odds ratio = [probability of being a case, given a genotype] / [probability of being  a case given another genotype]

Encoded in asci symbols in line 4 of Illumina FASTQ outputs. It is based on the p value.

Q = - 10 log₁₀ [probability that base pair is wrong]

Q-Q plot

Plots the theoretical or expected value of a statistic given the null hypothesis on the x axis. Plotted from small to large, with corresponding observed values on the y axis.

Quantitative genes

Have a small effect on phenotype. Many genes contribute to production of phenotype. More complex than Mendelian loci. They are the typical situation.

A ratio of estimated probabilities. The value can be high but have little real-world relevance.

Relative risk = [probability, given A] / [probability, given a]

First directory

Denoted by a / character alone.

The output of alignment software for sequence alignment. Each aligned sequence gets a single line of output. Information lcoated on the line:

1. Name of read.

2. Sum of all applicable flags.

3. Name of sequence where alignment occurs, indicating chromosome.

4. 1-based offset into the forward reference strand, where the leftmost character of alignment occurs.

5. Mapping quality.

6. CIGAR string.

7. Name of reference sequence where mate's alignment occurs.

8. 1-based offset into the forward reference strand whre the leftmost character of the mate's alignment occurs. Equal to 0 if there is no mate.

9. Inferred insert size. Size is negative if the mate's alignment occurs upstream of this alignment. Size is 0 if there is no mate.

10. Read sequence, reverse complemented if aligned to the reverse stand.

11. ASCII-encoded read quality. Encoded using Phred quality scale, offset by 33, similar to in FASTQ files.

12. Optional fields, often tab-separated. Includes edit distance in Bowtie.

https://github.com/alexdobin/STAR

An alignment software.

"Wobble"

A type of mutation where there is no change in amino acid sequence. In the GIT 264-1 sequencing, there were 6,462, and 253 of these were novel.

Output files of SNP detection software. A TAB-delimitated format with each data line consisting of the following fields:

1. CHROM: Chromosome name.

2. POS: The left-most position of the variant.

3. ID: Unique variatn identifier.

4. REFthe: Reference allele.

5. ALTthe: Alternate allele(s), comma separated.

6. QUAL: Variant/reference quality.

7. FILTER: Filters applied.

8. INFO: Information of variant, semicolon separated.

9. FORMAT: Format of genotype fields. Optionally colon separated.

10. SAMPLE: Sample genotypes and per-sample information.

Runs a block of code multiple times on different pieces of data. Evaluates a condition adn runs a block if the condition is true, like an if statement.

While (condition = true) {do this}