BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716764.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 = 851,141 number of mapped reads = 786,260 (92.38%) number of supplementary alignments = 3,159 (0.37%) number of secondary alignments = 0 number of mapped bases = 45,820,297 bp number of sequenced bases = 45,806,556 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,190 duplication rate = 2.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9271 >>>>>>> ACTG content number of A's = 11,316,944 bp (24.71%) number of C's = 8,217,275 bp (17.94%) number of T's = 14,310,698 bp (31.24%) number of G's = 11,960,756 bp (26.11%) number of N's = 883 bp (0%) GC percentage = 44.05% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 230,149 number of insertions = 3,309 mapped reads with insertion percentage = 0.42% number of deletions = 8,498 mapped reads with deletion percentage = 1.07% homopolymer indels = 43% >>>>>>> Coverage mean coverageData = 0.0148X std coverageData = 0.1652X There is a 1.37% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% 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 3709823 0.0148839067486215 0.2343557155388677 chr2 243199373 3879568 0.015952212179428604 0.22190298684946647 chr3 198022430 3045876 0.015381469664825344 0.13241185406631836 chr4 191154276 2950576 0.01543557414326426 0.15246035746364967 chr5 180915260 2647071 0.014631551810499568 0.1285946639502518 chr6 171115067 2604282 0.015219478013587195 0.1398895259958321 chr7 159138663 2576442 0.0161899185994795 0.17794871161676787 chr8 146364022 2305129 0.015749287075480886 0.187106575522835 chr9 141213431 1950962 0.013815697176849984 0.14085526840467705 chr10 135534747 2238547 0.01651640667466624 0.20295586122012754 chr11 135006516 2059735 0.015256559913004496 0.14373438926832013 chr12 133851895 2091248 0.015623596513146116 0.13314033652587565 chr13 115169878 1393005 0.012095219897688874 0.11656928275082405 chr14 107349540 1382346 0.012877055644579381 0.12205236155535841 chr15 102531392 1308947 0.01276630478205153 0.12031085245621803 chr16 90354753 1360305 0.015055157087308955 0.1366699959351805 chr17 81195210 1268500 0.015622842776070164 0.13791518567465802 chr18 78077248 1199444 0.015362273014540677 0.21088712478748248 chr19 59128983 960785 0.016248968800968554 0.1940659627181697 chr20 63025520 973331 0.01544344259277829 0.1343977451232823 chr21 48129895 610980 0.01269439711015368 0.13987171052463784 chr22 51304566 564142 0.010995941374886594 0.11212129414098963 chrMT 16571 23237 1.4022690241989018 1.3902485294192914 chrX 155270560 2536063 0.016333186407004652 0.14164378077821618 chrY 59373566 179953 0.003030860568489351 0.14913030176019493