BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472381.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 = 20,366,332 number of mapped reads = 20,173,789 (99.05%) number of supplementary alignments = 75,758 (0.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,127,359 number of mapped paired reads (second in pair) = 10,046,430 number of mapped paired reads (both in pair) = 20,044,088 number of mapped paired reads (singletons) = 129,701 number of mapped bases = 1,981,621,356 bp number of sequenced bases = 1,981,392,571 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,679,255 duplication rate = 48.25% >>>>>>> Insert size mean insert size = 19,625.9452 std insert size = 1,392,295.0128 median insert size = 220 >>>>>>> Mapping quality mean mapping quality = 54.9669 >>>>>>> ACTG content number of A's = 534,695,088 bp (26.99%) number of C's = 457,451,125 bp (23.09%) number of T's = 535,582,698 bp (27.03%) number of G's = 453,414,799 bp (22.88%) number of N's = 248,861 bp (0.01%) GC percentage = 45.97% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 11,134,111 number of insertions = 117,972 mapped reads with insertion percentage = 0.58% number of deletions = 94,606 mapped reads with deletion percentage = 0.46% homopolymer indels = 45.62% >>>>>>> Coverage mean coverageData = 0.6401X std coverageData = 17.9791X There is a 5.39% of reference with a coverageData >= 1X There is a 2.27% of reference with a coverageData >= 2X There is a 0.96% of reference with a coverageData >= 3X There is a 0.71% of reference with a coverageData >= 4X There is a 0.55% of reference with a coverageData >= 5X There is a 0.5% of reference with a coverageData >= 6X There is a 0.46% of reference with a coverageData >= 7X There is a 0.44% of reference with a coverageData >= 8X There is a 0.42% of reference with a coverageData >= 9X There is a 0.41% of reference with a coverageData >= 10X There is a 0.39% of reference with a coverageData >= 11X There is a 0.38% of reference with a coverageData >= 12X There is a 0.37% of reference with a coverageData >= 13X There is a 0.36% of reference with a coverageData >= 14X There is a 0.36% of reference with a coverageData >= 15X There is a 0.35% of reference with a coverageData >= 16X There is a 0.34% of reference with a coverageData >= 17X There is a 0.33% of reference with a coverageData >= 18X There is a 0.33% of reference with a coverageData >= 19X There is a 0.32% of reference with a coverageData >= 20X There is a 0.31% of reference with a coverageData >= 21X There is a 0.31% of reference with a coverageData >= 22X There is a 0.3% of reference with a coverageData >= 23X There is a 0.3% of reference with a coverageData >= 24X There is a 0.29% of reference with a coverageData >= 25X There is a 0.29% of reference with a coverageData >= 26X There is a 0.28% of reference with a coverageData >= 27X There is a 0.28% of reference with a coverageData >= 28X There is a 0.27% of reference with a coverageData >= 29X There is a 0.27% of reference with a coverageData >= 30X There is a 0.27% of reference with a coverageData >= 31X There is a 0.26% of reference with a coverageData >= 32X There is a 0.26% of reference with a coverageData >= 33X There is a 0.26% of reference with a coverageData >= 34X There is a 0.25% of reference with a coverageData >= 35X There is a 0.25% of reference with a coverageData >= 36X There is a 0.25% of reference with a coverageData >= 37X There is a 0.24% of reference with a coverageData >= 38X There is a 0.24% of reference with a coverageData >= 39X There is a 0.24% of reference with a coverageData >= 40X There is a 0.23% of reference with a coverageData >= 41X There is a 0.23% of reference with a coverageData >= 42X There is a 0.23% of reference with a coverageData >= 43X There is a 0.23% of reference with a coverageData >= 44X There is a 0.22% of reference with a coverageData >= 45X There is a 0.22% of reference with a coverageData >= 46X There is a 0.22% of reference with a coverageData >= 47X There is a 0.22% of reference with a coverageData >= 48X There is a 0.21% of reference with a coverageData >= 49X There is a 0.21% of reference with a coverageData >= 50X There is a 0.21% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 204846622 0.8218499965141511 24.774383777173057 chr2 243199373 168605196 0.6932797314407549 19.37000863841567 chr3 198022430 125279377 0.6326524576029089 13.156861760322126 chr4 191154276 56349458 0.2947852341006486 11.328381849213134 chr5 180915260 70589171 0.39017809221842314 11.871909806582492 chr6 171115067 168755117 0.986208403261181 22.837603042389514 chr7 159138663 150737278 0.9472071409824525 24.547681981857956 chr8 146364022 88377613 0.6038206096850769 14.4770222344564 chr9 141213431 65565781 0.46430272627537816 9.975052312718205 chr10 135534747 67388344 0.49720345145145695 15.721624988662246 chr11 135006516 73651847 0.5455429054994649 16.580942928450696 chr12 133851895 102907617 0.7688170346785154 17.91384400151945 chr13 115169878 70322353 0.610596748222656 20.28303681419308 chr14 107349540 52509158 0.48914190037516697 19.741473497653395 chr15 102531392 36490326 0.3558941831200341 10.115336306429626 chr16 90354753 81878565 0.906189904586425 19.002189617967037 chr17 81195210 97689483 1.203143424347323 24.014792197872545 chr18 78077248 26081432 0.33404650737689934 10.194101582222125 chr19 59128983 54836939 0.9274121795735942 19.766490655802674 chr20 63025520 57870948 0.918214526433102 26.87418470035692 chr21 48129895 16724193 0.34748035498519164 17.85616119670298 chr22 51304566 28926860 0.5638262294237125 17.676492713360993 chrMT 16571 10548 0.6365337034578481 1.0601897580575539 chrX 155270560 114896793 0.7399779649149201 16.296464764908023 chrY 59373566 330337 0.005563704898573887 0.3780540509281354