BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084988.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,891,243 number of mapped reads = 2,622,223 (90.7%) number of supplementary alignments = 23,551 (0.81%) number of secondary alignments = 0 number of mapped bases = 175,512,785 bp number of sequenced bases = 175,444,452 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 102,478 duplication rate = 2.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1053 >>>>>>> ACTG content number of A's = 49,736,942 bp (28.35%) number of C's = 33,225,150 bp (18.94%) number of T's = 53,457,663 bp (30.47%) number of G's = 39,002,578 bp (22.23%) number of N's = 22,119 bp (0.01%) GC percentage = 41.17% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,474,499 number of insertions = 14,581 mapped reads with insertion percentage = 0.55% number of deletions = 42,022 mapped reads with deletion percentage = 1.59% homopolymer indels = 46.64% >>>>>>> Coverage mean coverageData = 0.0567X std coverageData = 0.4502X There is a 4.85% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.02% 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 14263673 0.05722622853565528 0.7631214976103023 chr2 243199373 14700110 0.060444687083958885 0.550897020299289 chr3 198022430 11980151 0.06049895963805716 0.287242174108148 chr4 191154276 11386456 0.05956683909074574 0.2905533067365781 chr5 180915260 10504745 0.058064449621331005 0.2726028070081933 chr6 171115067 10028485 0.058606674302970646 0.34674768777322856 chr7 159138663 8789571 0.05523215310662752 0.36511341890219523 chr8 146364022 8551988 0.058429577727783406 0.7427730070013729 chr9 141213431 7276430 0.05152788901503286 0.4107029134464751 chr10 135534747 8376666 0.061804564404432764 0.5783056458803154 chr11 135006516 8473369 0.06276266695157143 0.44400656323081994 chr12 133851895 8481896 0.06336776927962058 0.29015840557224604 chr13 115169878 5373159 0.04665420414876188 0.24266572966220754 chr14 107349540 5506996 0.05129967021749697 0.28045833627092803 chr15 102531392 4828966 0.04709743919208666 0.24908130294799127 chr16 90354753 5218238 0.057752778096798074 0.3165085321578891 chr17 81195210 4589677 0.056526450267201725 0.3103533438758851 chr18 78077248 4522882 0.05792829685800401 0.7505183764701481 chr19 59128983 3571973 0.06040985010684185 0.5771849248373055 chr20 63025520 3354204 0.05321977510062591 0.272412859000629 chr21 48129895 2347038 0.048764660716587895 0.2744889057269095 chr22 51304566 1891837 0.03687463217211505 0.21799830527740743 chrMT 16571 32484 1.9602920765192202 1.7896516091042398 chrX 155270560 10988773 0.07077177412125003 0.3435243715107043 chrY 59373566 473018 0.007966811358441904 0.1520450463178465