BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063524.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 = 3,756,295 number of mapped reads = 3,471,471 (92.42%) number of supplementary alignments = 21,995 (0.59%) number of secondary alignments = 0 number of mapped bases = 221,766,499 bp number of sequenced bases = 221,669,120 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 384,081 duplication rate = 9.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4656 >>>>>>> ACTG content number of A's = 57,084,828 bp (25.75%) number of C's = 39,735,126 bp (17.93%) number of T's = 72,297,910 bp (32.62%) number of G's = 52,526,357 bp (23.7%) number of N's = 24,899 bp (0.01%) GC percentage = 41.62% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 1,193,038 number of insertions = 13,244 mapped reads with insertion percentage = 0.38% number of deletions = 55,253 mapped reads with deletion percentage = 1.58% homopolymer indels = 44.27% >>>>>>> Coverage mean coverageData = 0.0716X std coverageData = 0.7034X There is a 5.51% of reference with a coverageData >= 1X There is a 1.14% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% 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% 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 20250806 0.08124676247045338 1.492285261191319 chr2 243199373 22753206 0.09355783166431107 1.1310883909475 chr3 198022430 13776083 0.06956829587436131 0.3295551554847764 chr4 191154276 10044150 0.052544730937643266 0.3047429241583022 chr5 180915260 11101582 0.06136343611920852 0.3110163938815516 chr6 171115067 16603603 0.09703180024468565 0.5201219640732093 chr7 159138663 21266282 0.13363366009930597 1.0175192735775984 chr8 146364022 9290828 0.0634775395827808 0.6752814716719121 chr9 141213431 7430604 0.05261966901717727 0.4697978812707199 chr10 135534747 11771156 0.08684972865297783 0.5036292390616106 chr11 135006516 10834202 0.08024947477349909 0.46205070888317107 chr12 133851895 8554032 0.06390669328962433 0.33386557890802737 chr13 115169878 4238198 0.03679953537851277 0.2782807975212849 chr14 107349540 3989717 0.0371656646130016 0.28432498029134085 chr15 102531392 4151732 0.04049230112861435 0.3043879555088829 chr16 90354753 4709008 0.052116881997342185 0.31384274709881477 chr17 81195210 6424329 0.07912201963638003 0.37894323502219757 chr18 78077248 5782140 0.07405665732480735 0.8682293100632843 chr19 59128983 4688978 0.07930083965760074 0.9804577502368329 chr20 63025520 3000027 0.047600194333977726 0.2912596816594261 chr21 48129895 3578375 0.07434828187345931 0.3554601284798447 chr22 51304566 2299816 0.04482673140632356 0.25900732365103585 chrMT 16571 290441 17.527065355138497 9.87117608505798 chrX 155270560 14337051 0.09233592639841062 0.4442958420807362 chrY 59373566 600153 0.01010808412619178 0.2692781424958438