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Sex hom index search. This page describes specialized PLINK input and output file formats which are identifiable by file extension. Jump to:. A text file with a header line, and then one line per set or polymorphic variant with the following fields:. As a result, if the QQ field is present, its values just increase linearly. Produced by --update-alleles when there is a mismatch between the loaded alleles for a variant and columns of the --update-alleles input file. A text file with no header line, and one line per mismatching variant with the following three fields:. A text file with a header line, and then one line per Sex hom typically with the following fields:. If --ci 0. A text file with a header line, and then usually one line per variant with the following fields:. A text file with a header line, and T lines per variant typically with the following nine fields where T is normally the number of terms, but the 'genotypic' and 'hethom' modifiers and the --tests flag can change this :. A text file with no header line, and one line per variant, each with at least Teens love sex tumblr fields. The first four are:. Subsequent fields are defined by the plugin function. Lines are permitted to contain different numbers of fields. In 'beagle' mode, one file pair is generated per autosome, while in 'beagle-nomap' mode, a single. Primary representation of genotype calls at biallelic variants. Must be accompanied by. The first three bytes should be 0x 6c, 0x1b, and 0x01 in that order. There are old versions of the. See the bottom Super rambo bros hacked the original. The first block corresponds to the first marker in the. The low-order two bits of a block's first byte store the first sample's genotype code. The next two bits store the second sample's genotype code, and so on for the 3rd and 4th samples. The second byte stores genotype codes for the 5th-8th samples, the third byte stores codes for the 9thth, etc. If N is not divisible by four, the extra high-order bits in the last byte of each block are always zero. Unix xxd :. Extended variant information file accompanying a. Produced by --write-cluster. Valid input for --within. With --clump-verbose, Mongole wiesbaden header line above is repeated for every clump, instead of just appearing once, and dashed line dividers are present between clumps. Also, each nonempty clump has its own subsection, with the different header line below, one line corresponding to the index variant with ' INDEX ' before the variant IDa blank line, and then one line for each other clump member with the following fields:. This is reported even for empty clumps. If --clump-range is used without --clump-verbose, region overlaps are reported in a separate. This has a header line, followed by one line per clump with the following seven fields:. Finally, if --clump-best is specified, a. This has a header line, followed by one line per clump with the following fields:. The other two files are also text files with no header line. A text file with a header line, and then one line per variant with the following fields where Topless punishment. A text file with a header line, and then one line per variant with the following five fields:. Produced by postprocessing the output of Birdsuite or a similar package. Must be accompanied by a. A text file with an optional header line, and one line per segmental call with the following eight fields:. Produced by --write-covar--make-bedand Sex hom when an input covariate table has been named with --covar. Valid input for --covar. A text file with a header line, and then one line per variant with the following eight fields:. A text file with a header line, and then one line per conflict with the following five fields:. If square, the upper-right triangle may be either zeroed out or the mirror-image of the lower-left triangle, depending on whether the 'square0' or 'square' modifier was used. When missing values are present, the affected raw Hamming distances are rescaled to be comparable to pairwise distances unaffected by missing data. Normally a tab-delimited text file with a header line, followed by one line per duplicate variant group with the following 4 columns:. Produced by --pca. Accompanied by an. The --pca 'header' modifier causes a header line to be Sex hom, and the 'tabs' modifier makes this file tab-delimited. With the 'var-wts' modifier, an. Produced by --epistasis and --fast-epistasis. The main report is normally a text file with a header line, followed by one line per variant pair clearing the --epi1 threshold with the following fields:. For two-set tests, if variant v 1 is in both sets but v 2 is only in set 1, the v 1 -v 2 test is only counted in the v 2 summary row. Sample information file accompanying a. Also generated by "--recode lgen" and "--recode rlist". In this case, -9 normally still designates a missing phenotype; use --missing-phenotype if this is problematic. If the 'verbose' modifier is present, a. This is a text file with a header line, and one line per relevant variant pair i. Produced by --freq. Valid input for --read-freq. Produced by " --freq case-control ". Not valid input for --read-freq. Produced by " --freq counts ". A text file with a header line, and then one line per variant with the following seven fields:. A text file with a header line, and then C lines per variant where C is the number of clusters with the following lines:. Produced by --freqx. A text file with a header line, and then one line per variant with the Sexy nude girl asian ten fields:. A text file with a header line, and then one line per autosomal diploid variant with the following five fields:. Should always be accompanied by a. Each line stores information for a single SNP. The first five fields are:. Each subsequent triplet of values then indicate Manga like overlord of homozygote A1, heterozygote, and homozygote A2 genotypes at this SNP, respectively, for one sample. If they add up to less than one, the remainder is a no-call probability weight. Since the PLINK 1 binary format cannot represent genotype probabilities, calls with uncertainty greater than 0. This behavior can be changed with --hard-call-threshold. We plan to remove this limitation in the future. Produced by --genome. Valid input for --read-genome. A text file with a header line, and one line per pair of distinct samples typically with the following 14 fields:. Produced by --make-grm-gz. Readable by --grm-gz. A text file with no header line, and one line per pair of samples not necessarily distinct with the following four fields:. Produced by --make-grm-bin. Readable by --grm-bin. These files contain single-precision 4-byte floating point values. Using 1-based matrix indices, the first value in each file is the 1, 1 relationship value. Produced by packages such as Birdsuite. Loaded with --gfile. A text file with no header line, and one line per variant call with the Rule34 fortnite seven fields:. A text file with one line per error sorted primarily by variant ID, secondarily by sample ID with the following three fields:. Produced when a flag in the --homozyg family is present. Accompanied by at least a. The second-to-last line Youporn woodman each pool describes the consensus match segment, while the last line describes the union of all segments in the pool. Pools are separated by blank lines, and sorted primarily by pool size largest first and secondarily by physical position. PLINK 1.{/INSERTKEYS}{/PARAGRAPH}.

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