BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716880.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 = 566,950 number of mapped reads = 523,212 (92.29%) number of supplementary alignments = 1,474 (0.26%) number of secondary alignments = 0 number of mapped bases = 30,303,297 bp number of sequenced bases = 30,294,022 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,179 duplication rate = 1.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2008 >>>>>>> ACTG content number of A's = 7,608,473 bp (25.12%) number of C's = 6,152,589 bp (20.31%) number of T's = 9,251,733 bp (30.54%) number of G's = 7,280,851 bp (24.03%) number of N's = 376 bp (0%) GC percentage = 44.34% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 143,994 number of insertions = 1,604 mapped reads with insertion percentage = 0.31% number of deletions = 5,811 mapped reads with deletion percentage = 1.1% homopolymer indels = 44.5% >>>>>>> Coverage mean coverageData = 0.0098X std coverageData = 0.1172X There is a 0.93% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0% 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 3555465 0.014264618421953701 0.15843359496564718 chr2 243199373 3047381 0.012530381811469555 0.14864781763851817 chr3 198022430 1971642 0.009956659960187339 0.10404222875289337 chr4 191154276 1270770 0.006647876399061039 0.08559298786568888 chr5 180915260 2225058 0.012298896179349381 0.11447253279400285 chr6 171115067 1090031 0.006370163768220364 0.08651507563119305 chr7 159138663 2145466 0.01348173950663391 0.16565259913071997 chr8 146364022 1381352 0.009437783829143476 0.10606134165700763 chr9 141213431 872682 0.0061798795894988205 0.09165700012816817 chr10 135534747 1364675 0.01006882021183837 0.1290873518064534 chr11 135006516 1251941 0.009273189451092864 0.11270521700945847 chr12 133851895 1210356 0.009042501789010907 0.09859590028152772 chr13 115169878 927485 0.008053190783096948 0.0925309946539547 chr14 107349540 608001 0.005663750398930447 0.07989753535262487 chr15 102531392 1297788 0.012657469821535242 0.11679463665204873 chr16 90354753 912301 0.01009687891017753 0.10710448970107601 chr17 81195210 1160724 0.01429547383398602 0.12806337397561413 chr18 78077248 936590 0.011995684069192603 0.15688952901388348 chr19 59128983 483843 0.008182839877357606 0.12287924222116613 chr20 63025520 805448 0.012779712091229077 0.11658765222719679 chr21 48129895 368347 0.007653185198097772 0.09115407638857091 chr22 51304566 331239 0.006456325934030901 0.08290058041920488 chrMT 16571 366 0.022086778106330335 0.1469658203093905 chrX 155270560 1017397 0.00655241405711424 0.09007675463204644 chrY 59373566 66949 0.0011275893383260827 0.040719831127667055