BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818747.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 = 270,672 number of mapped reads = 251,312 (92.85%) number of supplementary alignments = 1,819 (0.67%) number of secondary alignments = 0 number of mapped bases = 17,087,485 bp number of sequenced bases = 17,080,444 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,172 duplication rate = 11.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2928 >>>>>>> ACTG content number of A's = 4,875,259 bp (28.54%) number of C's = 3,830,510 bp (22.43%) number of T's = 4,858,990 bp (28.45%) number of G's = 3,514,406 bp (20.58%) number of N's = 1,279 bp (0.01%) GC percentage = 43% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 86,571 number of insertions = 1,857 mapped reads with insertion percentage = 0.73% number of deletions = 4,256 mapped reads with deletion percentage = 1.68% homopolymer indels = 40.73% >>>>>>> Coverage mean coverageData = 0.0055X std coverageData = 0.1003X There is a 0.46% of reference with a coverageData >= 1X There is a 0.07% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 1435981 0.005761193269002929 0.125760964684618 chr2 243199373 1479031 0.006081557619805212 0.14377955335189382 chr3 198022430 1157190 0.005843731944911493 0.08870618879234542 chr4 191154276 1101759 0.00576371621422688 0.09155468685936344 chr5 180915260 1091323 0.006032232991291061 0.09175998404357008 chr6 171115067 969293 0.005664568392449041 0.09067723924679602 chr7 159138663 910300 0.005720168705954253 0.09567632716831109 chr8 146364022 901537 0.006159553336133384 0.09499846257034462 chr9 141213431 749276 0.005305982544960614 0.09281439977346072 chr10 135534747 816808 0.006026557898101215 0.10390211862924266 chr11 135006516 816069 0.006044663799782819 0.09471072902887989 chr12 133851895 715922 0.005348613107046411 0.08659064068433936 chr13 115169878 537627 0.004668121642014763 0.079747886808438 chr14 107349540 531547 0.004951553588399168 0.08698898413572681 chr15 102531392 502925 0.0049050831183487685 0.08383755189663278 chr16 90354753 534925 0.005920275162503073 0.1139697554645594 chr17 81195210 479600 0.005906752381082579 0.09102043237366694 chr18 78077248 482661 0.006181839298434289 0.1038577853190746 chr19 59128983 356785 0.006034012118896075 0.11218928177750963 chr20 63025520 377130 0.005983766575825158 0.09258511212936507 chr21 48129895 225558 0.0046864428023373 0.08066206508951232 chr22 51304566 213424 0.004159941631705841 0.07802510736702925 chrMT 16571 1943 0.1172530324060105 0.41226239687296373 chrX 155270560 537645 0.003462633225512937 0.07122259500546871 chrY 59373566 161226 0.0027154508455833697 0.11201933936517584