BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231885.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 10,105,879 number of mapped reads = 4,126,717 (40.83%) number of supplementary alignments = 26,933 (0.27%) number of secondary alignments = 0 number of mapped bases = 262,975,997 bp number of sequenced bases = 262,875,476 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 300,319 duplication rate = 2.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.1979 >>>>>>> ACTG content number of A's = 74,579,711 bp (28.37%) number of C's = 53,320,838 bp (20.28%) number of T's = 69,826,615 bp (26.56%) number of G's = 65,128,191 bp (24.78%) number of N's = 20,121 bp (0.01%) GC percentage = 45.06% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 1,939,831 number of insertions = 24,090 mapped reads with insertion percentage = 0.57% number of deletions = 62,711 mapped reads with deletion percentage = 1.5% homopolymer indels = 42.38% >>>>>>> Coverage mean coverageData = 0.0849X std coverageData = 15.9864X There is a 6.76% of reference with a coverageData >= 1X There is a 0.97% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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% 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 27254513 0.109345817838504 2.301041412275541 chr2 243199373 21645801 0.0890043454182754 56.94524522876567 chr3 198022430 26312143 0.13287455870529413 0.44037137913043756 chr4 191154276 12252047 0.06409507156408052 0.3763927272035338 chr5 180915260 10686554 0.059069389724227796 0.2956222786386976 chr6 171115067 17488310 0.10220204629905559 0.6761225850696178 chr7 159138663 15749774 0.09896887219669553 1.160585264122298 chr8 146364022 7901059 0.05398224845174041 0.7019424499842758 chr9 141213431 11974992 0.0848006589401542 0.668984368002997 chr10 135534747 13889689 0.10248065022027156 1.0362527540645363 chr11 135006516 13302737 0.09853403668308869 0.7790943514176261 chr12 133851895 7275669 0.05435611501802048 0.28921531745631274 chr13 115169878 11234592 0.09754800643272367 0.358741205068011 chr14 107349540 11381330 0.10602122747801249 0.6429713800939272 chr15 102531392 6528623 0.06367438179323655 0.2949427705934302 chr16 90354753 6513220 0.07208497377000189 0.4605776011719063 chr17 81195210 7159561 0.0881771350797664 0.4432286819811279 chr18 78077248 5873490 0.07522665245578328 1.5874769578710266 chr19 59128983 8159815 0.13800025953431333 1.244954859359798 chr20 63025520 6665871 0.10576463312004407 0.41492961248256055 chr21 48129895 5089821 0.10575175782120447 0.4373105809184472 chr22 51304566 2422086 0.04720995008514447 0.2484726509025131 chrMT 16571 233653 14.100114658137711 9.42220745075393 chrX 155270560 5395825 0.03475111444178471 0.35408057438898827 chrY 59373566 584822 0.009849871574161471 0.24630151898835864