BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506332.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 5,355,571 number of mapped reads = 3,875,841 (72.37%) number of supplementary alignments = 64,756 (1.21%) number of secondary alignments = 0 number of mapped bases = 300,321,109 bp number of sequenced bases = 300,194,920 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 383,852 duplication rate = 7.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.4611 >>>>>>> ACTG content number of A's = 81,336,920 bp (27.09%) number of C's = 56,547,877 bp (18.84%) number of T's = 88,628,685 bp (29.52%) number of G's = 73,609,028 bp (24.52%) number of N's = 72,410 bp (0.02%) GC percentage = 43.36% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 2,223,973 number of insertions = 24,399 mapped reads with insertion percentage = 0.62% number of deletions = 63,489 mapped reads with deletion percentage = 1.61% homopolymer indels = 43.63% >>>>>>> Coverage mean coverageData = 0.097X std coverageData = 0.6894X There is a 6.77% of reference with a coverageData >= 1X There is a 1.81% of reference with a coverageData >= 2X There is a 0.57% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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% 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 22244762 0.08924656600955871 1.1754761100134223 chr2 243199373 24400899 0.10033290258523817 0.7873511482596892 chr3 198022430 18311003 0.09246933794318149 0.4078072338950047 chr4 191154276 19264019 0.10077733756790248 0.5728892115946047 chr5 180915260 22917727 0.12667658327992895 0.49219743258199283 chr6 171115067 10049229 0.05872790266914368 0.35696281407996766 chr7 159138663 16542703 0.1039515017164622 0.8449650214488915 chr8 146364022 20261115 0.13842961352893132 0.8612351353385539 chr9 141213431 7991728 0.05659325705357304 0.6320929027156639 chr10 135534747 17293796 0.127596770442933 0.8121441858513674 chr11 135006516 12399152 0.09184113750480014 0.6529375113793199 chr12 133851895 12233072 0.09139259477798203 0.4215451696961601 chr13 115169878 6402630 0.055592921614452 0.3102755430258037 chr14 107349540 8927536 0.08316324410891747 0.4498892044685792 chr15 102531392 11156997 0.10881542503587584 0.46309674291887243 chr16 90354753 11503240 0.127311952255572 0.5860913864707148 chr17 81195210 7476868 0.09208508728532139 0.5061196429954498 chr18 78077248 5462339 0.06996070097142768 1.0740080321537109 chr19 59128983 7340942 0.12415133201259355 0.9607981705008014 chr20 63025520 7935028 0.12590182516542506 0.5201199748567377 chr21 48129895 4783632 0.09939003606801967 0.5548191271115325 chr22 51304566 3354118 0.06537659825443216 0.3555045717853383 chrMT 16571 31763 1.916782330577515 2.5923830913579913 chrX 155270560 21043083 0.13552525990760902 0.5855825813512944 chrY 59373566 993728 0.016736875800924606 0.5827134509969883