BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818740.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 609,774 number of mapped reads = 593,593 (97.35%) number of supplementary alignments = 5,061 (0.83%) number of secondary alignments = 0 number of mapped bases = 40,292,281 bp number of sequenced bases = 40,276,065 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 156,592 duplication rate = 23.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5684 >>>>>>> ACTG content number of A's = 11,273,995 bp (27.99%) number of C's = 8,270,525 bp (20.53%) number of T's = 11,628,883 bp (28.87%) number of G's = 9,100,238 bp (22.59%) number of N's = 2,424 bp (0.01%) GC percentage = 43.13% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 192,616 number of insertions = 3,778 mapped reads with insertion percentage = 0.63% number of deletions = 10,086 mapped reads with deletion percentage = 1.68% homopolymer indels = 42.75% >>>>>>> Coverage mean coverageData = 0.013X std coverageData = 0.1901X There is a 0.88% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% 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 3314522 0.01329794881433816 0.24983737719036972 chr2 243199373 3531729 0.014521949445979863 0.2593354423450437 chr3 198022430 2775151 0.014014326558865075 0.16820517065476703 chr4 191154276 2697391 0.014111068067344724 0.17467087921219182 chr5 180915260 2494709 0.01378937851898176 0.16772074835621853 chr6 171115067 2400067 0.01402604131873437 0.1743945086995249 chr7 159138663 2207512 0.013871625904008004 0.17544282509381295 chr8 146364022 2080450 0.0142142172070128 0.18370543205549622 chr9 141213431 1771484 0.012544727420439208 0.17336847939068806 chr10 135534747 1911107 0.014100494834730462 0.20478521005161407 chr11 135006516 1885884 0.01396883688191761 0.17519627337596266 chr12 133851895 1808127 0.013508415401963491 0.16842019622766924 chr13 115169878 1335344 0.011594559473267829 0.15055635463942968 chr14 107349540 1257748 0.011716379967720403 0.16149343021155227 chr15 102531392 1151885 0.011234461734412032 0.14982624559607108 chr16 90354753 1162733 0.012868531664294407 0.2055783673057245 chr17 81195210 1044145 0.012859687166274957 0.16439404281906378 chr18 78077248 1093550 0.01400600082625863 0.223389421967273 chr19 59128983 769608 0.013015748977113306 0.21242197038977365 chr20 63025520 870126 0.013805931311633764 0.173320324726569 chr21 48129895 558426 0.011602477005196043 0.16342366578836495 chr22 51304566 480655 0.009368659311921672 0.14413093700289498 chrMT 16571 67441 4.069820771226842 4.071157072540443 chrX 155270560 1262819 0.00813302277006021 0.13329579043135548 chrY 59373566 359668 0.006057712619114035 0.21176518959810908