onekg

This repository is designed to explore characteristics of 1000 Genome Data that is publicly available for use and analyses.

High-coverage PCR-free library

Index of CRAM files for high-coverage PCR-free library used for analysis on GRCh38 reference was downloaded from ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/1000genomes.high_coverage.GRCh38DH.alignment.index.

Discordant mappings

Table 1: Summary statistics of discordant mappings for 14 female samples of 1000 Genome (GRCh38) mapped.

Sample ID	# of discordants	# of discordants with mq20	# of reads mapped to the Y chromosome	Total # of reads	% of discordants	% of mq20 discordants	% of reads mapped to the Y chromosome
HG00268	21452730	9865992	1678244	788945768	2.72	45.99	0.21
HG00419	29959632	14656472	1692225	730182210	4.10	48.92	0.23
HG00759	24254366	9128952	1657402	793047110	3.06	37.64	0.21
HG01595	23405082	9045800	1777475	809779196	2.89	38.65	0.22
HG02568	33380642	17668340	1176896	416558544	8.01	52.93	0.28
HG02922	27371273	12264399	2058184	788768948	3.47	44.81	0.26
HG03052	29423416	13242420	1836908	724732312	4.06	45.01	0.25
HG03642	34143287	16482361	1561186	652081788	5.24	48.27	0.24
NA18525	24930157	8310473	1872109	773884178	3.22	33.34	0.24
NA18939	25968248	9814554	1690272	806242620	3.22	37.79	0.21
NA19017	26003479	11295761	1796170	787777536	3.30	43.44	0.23
NA19625	20655000	9079166	1760107	671389540	3.08	43.96	0.26
NA19648	37410954	20419118	1710430	602492930	6.21	54.58	0.28
NA20502	34411264	18535718	1520089	637337378	5.40	53.87	0.24
Average	28054966	12843538	1699121	713087147	4.14	44.94	0.24

1. Number of discordants:
   samtools view -F 1294 $cram | wc -l
2. Number of discordants with mapping quality of at least 20:
   samtools view -q 20 -F 1294 $cram | wc -l
3. Number of reads mapping to the Y chromosome:
   samtools view $cram chrY | wc -l
4. Total number of reads:

samtools flagstat $cram
## paired in sequencing number

5. % of discordants reads relative to the total number of reads
6. % of mq20 discordants is relative to the number of discordants
7. % of reads mapped to the Y chromosome is relative to the total number of reads.