BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716200.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 = 1,459,559 number of mapped reads = 1,137,048 (77.9%) number of supplementary alignments = 24,136 (1.65%) number of secondary alignments = 0 number of mapped bases = 85,749,866 bp number of sequenced bases = 85,720,445 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,505 duplication rate = 1.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.021 >>>>>>> ACTG content number of A's = 22,437,495 bp (26.18%) number of C's = 17,779,607 bp (20.74%) number of T's = 25,465,667 bp (29.71%) number of G's = 20,027,059 bp (23.36%) number of N's = 10,617 bp (0.01%) GC percentage = 44.1% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 639,658 number of insertions = 7,404 mapped reads with insertion percentage = 0.64% number of deletions = 17,253 mapped reads with deletion percentage = 1.5% homopolymer indels = 40.37% >>>>>>> Coverage mean coverageData = 0.0277X std coverageData = 0.2388X There is a 2.49% of reference with a coverageData >= 1X There is a 0.21% 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 6769975 0.02716131648073206 0.2593782464348489 chr2 243199373 7388189 0.030379144933075135 0.3438264696365075 chr3 198022430 5745603 0.029014910078620892 0.18496703289520305 chr4 191154276 5485900 0.028698808704650688 0.19615683448938048 chr5 180915260 5146041 0.028444482792662155 0.18360537771858376 chr6 171115067 4977802 0.0290903781138104 0.19866701975024412 chr7 159138663 4656565 0.029261053927542423 0.28112514352431217 chr8 146364022 4403144 0.030083513283066243 0.28953483591488716 chr9 141213431 3606420 0.025538788870585548 0.2568039411754442 chr10 135534747 4037398 0.029788656336223508 0.24045829520627549 chr11 135006516 3923220 0.029059486284350896 0.24877477337409934 chr12 133851895 3910219 0.02921302683088648 0.18840013566949296 chr13 115169878 2714372 0.023568419513303643 0.1665470216692025 chr14 107349540 2610831 0.024320840126562257 0.19601122853150027 chr15 102531392 2492193 0.024306633816109705 0.1695419057073357 chr16 90354753 2481690 0.02746607032393747 0.19634270950798186 chr17 81195210 2360204 0.02906826646547253 0.1960223398618634 chr18 78077248 2327140 0.02980560995182617 0.4385470290147946 chr19 59128983 1683890 0.028478250674461966 0.24273240685554007 chr20 63025520 1840662 0.02920502678914827 0.1920489263563681 chr21 48129895 1120393 0.02327852574787458 0.18099846733024286 chr22 51304566 979487 0.019091614574811917 0.150297848526532 chrMT 16571 3536 0.21338482891798927 0.5228166317163706 chrX 155270560 4879629 0.031426620732223805 0.22642568361335944 chrY 59373566 205363 0.003458828799334707 0.09632755812824761