BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472635.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 15,731,340 number of mapped reads = 15,608,224 (99.22%) number of supplementary alignments = 76,582 (0.49%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,825,702 number of mapped paired reads (second in pair) = 7,782,522 number of mapped paired reads (both in pair) = 15,524,904 number of mapped paired reads (singletons) = 83,320 number of mapped bases = 1,535,825,458 bp number of sequenced bases = 1,535,626,033 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,660,943 duplication rate = 49.78% >>>>>>> Insert size mean insert size = 24,424.7499 std insert size = 1,468,756.1793 median insert size = 213 >>>>>>> Mapping quality mean mapping quality = 54.7137 >>>>>>> ACTG content number of A's = 417,573,383 bp (27.19%) number of C's = 351,290,138 bp (22.88%) number of T's = 419,202,033 bp (27.3%) number of G's = 347,280,439 bp (22.61%) number of N's = 280,040 bp (0.02%) GC percentage = 45.49% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 9,360,862 number of insertions = 94,325 mapped reads with insertion percentage = 0.6% number of deletions = 83,224 mapped reads with deletion percentage = 0.52% homopolymer indels = 46.08% >>>>>>> Coverage mean coverageData = 0.4961X std coverageData = 22.1627X There is a 3.14% of reference with a coverageData >= 1X There is a 1.44% of reference with a coverageData >= 2X There is a 0.7% of reference with a coverageData >= 3X There is a 0.54% of reference with a coverageData >= 4X There is a 0.42% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.35% of reference with a coverageData >= 7X There is a 0.33% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.3% of reference with a coverageData >= 10X There is a 0.29% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.26% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.24% of reference with a coverageData >= 18X There is a 0.23% of reference with a coverageData >= 19X There is a 0.23% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.22% of reference with a coverageData >= 22X There is a 0.21% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 243139419 0.9754816979974545 33.483785597108415 chr2 243199373 108558557 0.44637679637438865 19.55604532701897 chr3 198022430 115242184 0.5819653056474461 17.13971422752666 chr4 191154276 41116425 0.21509550223192497 11.64012336144448 chr5 180915260 72344952 0.3998830833839003 16.58019087213878 chr6 171115067 134332674 0.785042932543164 27.701623236851518 chr7 159138663 98949042 0.6217787691228749 27.16484861765448 chr8 146364022 86857746 0.5934364525730237 20.137408461065057 chr9 141213431 76893669 0.5445209315819258 15.847512255727183 chr10 135534747 36317826 0.2679595218486666 14.63897398974041 chr11 135006516 40214865 0.29787351152739916 12.646690166391924 chr12 133851895 34281344 0.2561139982366331 12.821527809222626 chr13 115169878 85674858 0.7438998763200912 41.96748887145119 chr14 107349540 18481631 0.1721631131349049 7.348166119838455 chr15 102531392 26678737 0.26020067102961014 13.738552494774574 chr16 90354753 87606705 0.9695860161335398 39.33145838319851 chr17 81195210 39136291 0.48200246048997225 14.31904628164047 chr18 78077248 14731985 0.18868473694154794 8.87242195506423 chr19 59128983 20339390 0.3439834234930102 11.170242497866836 chr20 63025520 50908564 0.8077452435140559 20.89277632701748 chr21 48129895 13043009 0.27099599947184594 13.138134889966414 chr22 51304566 13036104 0.25409247200336904 8.82844757210947 chrMT 16571 3262 0.19684991853237585 0.4919161593194649 chrX 155270560 76855458 0.4949776570651899 32.10773568117267 chrY 59373566 1080761 0.01820273015099009 1.0164269256314082