BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525058.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,710,185 number of mapped reads = 1,349,689 (78.92%) number of supplementary alignments = 4,123 (0.24%) number of secondary alignments = 0 number of mapped bases = 78,006,979 bp number of sequenced bases = 77,982,262 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 74,873 duplication rate = 4.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0402 >>>>>>> ACTG content number of A's = 18,705,898 bp (23.99%) number of C's = 13,506,064 bp (17.32%) number of T's = 26,174,820 bp (33.57%) number of G's = 19,588,254 bp (25.12%) number of N's = 7,226 bp (0.01%) GC percentage = 42.44% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 378,639 number of insertions = 5,480 mapped reads with insertion percentage = 0.4% number of deletions = 15,273 mapped reads with deletion percentage = 1.12% homopolymer indels = 44.62% >>>>>>> Coverage mean coverageData = 0.0252X std coverageData = 0.2455X There is a 2.22% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 6717631 0.026951310985901214 0.4373812524824852 chr2 243199373 6517591 0.026799374190820797 0.3079475358269737 chr3 198022430 5050854 0.025506474190827775 0.17679672151804654 chr4 191154276 5047799 0.026406937399611193 0.20488567921018358 chr5 180915260 4743470 0.026219291838621022 0.1800413404257089 chr6 171115067 4395260 0.025685990585504664 0.19130567299033482 chr7 159138663 4141577 0.026024957869603314 0.2715072446240091 chr8 146364022 4189940 0.02862684382914812 0.25184755487070964 chr9 141213431 3127146 0.022144819921555477 0.19839060151827476 chr10 135534747 3797605 0.02801941999419529 0.27693623935024675 chr11 135006516 3624740 0.026848630032049712 0.20722859096731905 chr12 133851895 3462126 0.025865349160727236 0.18207949869000087 chr13 115169878 2487628 0.021599640836643067 0.163061034134448 chr14 107349540 2328203 0.02168805753615712 0.1660618345684047 chr15 102531392 2245225 0.021897927612257524 0.1657789917364864 chr16 90354753 2251665 0.024920271764784747 0.1896239141704434 chr17 81195210 1990761 0.024518207416422716 0.17991473417900064 chr18 78077248 2156734 0.027623079133116988 0.3253012634665751 chr19 59128983 1557121 0.026334310536002284 0.32900770553114417 chr20 63025520 1647191 0.026135302017341547 0.18502377494190747 chr21 48129895 1045438 0.021721177658916565 0.18834183678830174 chr22 51304566 923040 0.017991381118008094 0.14869715708657105 chrMT 16571 25087 1.5139098424959265 1.5778937836529032 chrX 155270560 4272392 0.02751578921335764 0.20203703473533471 chrY 59373566 260755 0.004391769226055918 0.15485356732639144