BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971282.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 14,131,660 number of mapped reads = 10,202,431 (72.2%) number of secondary alignments = 0 number of mapped bases = 402,724,951 bp number of sequenced bases = 402,684,310 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,072,311 duplication rate = 9.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2091 >>>>>>> ACTG content number of A's = 114,665,604 bp (28.48%) number of C's = 84,337,639 bp (20.94%) number of T's = 116,820,710 bp (29.01%) number of G's = 86,856,882 bp (21.57%) number of N's = 3,475 bp (0%) GC percentage = 42.51% >>>>>>> Mismatches and indels general error rate = 0.0027 number of mismatches = 1,087,611 number of insertions = 13,168 mapped reads with insertion percentage = 0.13% number of deletions = 31,727 mapped reads with deletion percentage = 0.31% homopolymer indels = 39.87% >>>>>>> Coverage mean coverageData = 0.1301X std coverageData = 1.6096X There is a 7.69% of reference with a coverageData >= 1X There is a 2.91% of reference with a coverageData >= 2X There is a 1.2% of reference with a coverageData >= 3X There is a 0.52% of reference with a coverageData >= 4X There is a 0.23% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 33081031 0.13272196019924862 2.1660107539347115 chr2 243199373 34431604 0.14157768408391413 0.7319311646159066 chr3 198022430 27656923 0.13966560757788904 0.5703809293600925 chr4 191154276 26085037 0.13646065129089763 0.6551490108601653 chr5 180915260 25189550 0.13923397064459903 0.5870399912518462 chr6 171115067 23423016 0.13688459123240151 0.611927268536222 chr7 159138663 22404591 0.14078659816313777 1.3924351865340003 chr8 146364022 21710014 0.14832889738435856 6.011019373805785 chr9 141213431 16941840 0.11997329064258767 0.662606980806655 chr10 135534747 19728229 0.14555845963249556 0.9571930624349044 chr11 135006516 18963739 0.14046536094598575 0.6991058668156641 chr12 133851895 18456934 0.13789071869322433 0.5872514595114532 chr13 115169878 12600818 0.10941070893554303 0.5035562790073731 chr14 107349540 12540791 0.11682202830119254 0.5629114431482942 chr15 102531392 11695067 0.11406328122415425 0.5130876615132896 chr16 90354753 11822542 0.13084582279805468 0.589455033255165 chr17 81195210 10586860 0.1303877408531858 0.573762692676343 chr18 78077248 10708503 0.13715266962278178 1.1242830354756705 chr19 59128983 7997929 0.13526241437299877 1.709524740561088 chr20 63025520 8935864 0.141781678278894 0.6137702254309856 chr21 48129895 5339344 0.11093612400359486 0.6173735223551017 chr22 51304566 4804598 0.09364854582338734 0.5252703316040614 chrMT 16571 36968 2.2308852815159015 3.0813858771987834 chrX 155270560 13535921 0.08717635203994885 0.49457572298262703 chrY 59373566 4047238 0.06816565472924432 0.7959230596021455