BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472437.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 = 16,242,822 number of mapped reads = 16,102,853 (99.14%) number of supplementary alignments = 53,941 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,070,654 number of mapped paired reads (second in pair) = 8,032,199 number of mapped paired reads (both in pair) = 16,030,734 number of mapped paired reads (singletons) = 72,119 number of mapped bases = 1,574,997,739 bp number of sequenced bases = 1,574,824,485 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,305,436 duplication rate = 47.92% >>>>>>> Insert size mean insert size = 14,734.6698 std insert size = 1,183,101.7224 median insert size = 198 >>>>>>> Mapping quality mean mapping quality = 54.7333 >>>>>>> ACTG content number of A's = 418,920,574 bp (26.6%) number of C's = 369,655,957 bp (23.47%) number of T's = 420,152,751 bp (26.68%) number of G's = 365,897,518 bp (23.23%) number of N's = 197,685 bp (0.01%) GC percentage = 46.71% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 8,039,875 number of insertions = 84,711 mapped reads with insertion percentage = 0.52% number of deletions = 75,289 mapped reads with deletion percentage = 0.46% homopolymer indels = 45.83% >>>>>>> Coverage mean coverageData = 0.5088X std coverageData = 17.4684X There is a 4.31% of reference with a coverageData >= 1X There is a 2% of reference with a coverageData >= 2X There is a 0.83% of reference with a coverageData >= 3X There is a 0.62% of reference with a coverageData >= 4X There is a 0.46% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.37% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.33% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.25% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.24% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 142768984 0.5727928918580307 17.435108807697706 chr2 243199373 103569189 0.42586125006169323 13.636701294191573 chr3 198022430 120084442 0.6064183840184165 18.606009302267424 chr4 191154276 40521775 0.2119846641568196 9.42760703363158 chr5 180915260 66990396 0.3702860444165959 12.872755646344903 chr6 171115067 136773169 0.7993052359322631 21.75562405663085 chr7 159138663 103730672 0.6518257100098924 18.384258659522924 chr8 146364022 137092206 0.9366523557271472 27.634610664631815 chr9 141213431 47253241 0.33462285184473706 11.856690713953029 chr10 135534747 33254080 0.24535464695263717 10.195851587151127 chr11 135006516 38847240 0.28774344491639203 8.222880944760364 chr12 133851895 75152145 0.5614574601278525 13.700867986546042 chr13 115169878 57912632 0.5028453012687918 19.28550467088604 chr14 107349540 13981753 0.13024511329997315 4.356787499348907 chr15 102531392 21941045 0.21399343724895495 7.31858776253279 chr16 90354753 103271155 1.142952103471524 36.7936987922869 chr17 81195210 58971535 0.7262932751821197 19.545562561187914 chr18 78077248 9700749 0.12424552924816203 5.527097850308186 chr19 59128983 37012126 0.6259557347705439 14.788140640555648 chr20 63025520 93870888 1.489410765670795 38.707447118339715 chr21 48129895 15681644 0.3258192023896998 17.138872800566745 chr22 51304566 12559726 0.2448071775911719 7.218956527618854 chrMT 16571 1651 0.09963188703156116 0.3775828521549137 chrX 155270560 103812229 0.6685892612224752 20.12101687633116 chrY 59373566 243067 0.004093858873155775 0.20879871860783036