BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174056.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 5,085,728 number of mapped reads = 4,944,755 (97.23%) number of supplementary alignments = 547,816 (10.77%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,471,801 number of mapped paired reads (second in pair) = 2,472,954 number of mapped paired reads (both in pair) = 4,845,762 number of mapped paired reads (singletons) = 98,993 number of mapped bases = 585,089,734 bp number of sequenced bases = 584,772,050 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,995,137 duplication rate = 65.8% >>>>>>> Insert size mean insert size = 968,605.9607 std insert size = 9,119,905.0474 median insert size = 207 >>>>>>> Mapping quality mean mapping quality = 52.5604 >>>>>>> ACTG content number of A's = 175,386,325 bp (29.99%) number of C's = 114,616,726 bp (19.6%) number of T's = 175,493,771 bp (30.01%) number of G's = 119,267,993 bp (20.4%) number of N's = 7,235 bp (0%) GC percentage = 40% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 5,999,039 number of insertions = 60,774 mapped reads with insertion percentage = 1.19% number of deletions = 130,596 mapped reads with deletion percentage = 2.58% homopolymer indels = 43.06% >>>>>>> Coverage mean coverageData = 0.189X std coverageData = 2.884X There is a 3.63% of reference with a coverageData >= 1X There is a 2.91% of reference with a coverageData >= 2X There is a 2.32% of reference with a coverageData >= 3X There is a 1.95% of reference with a coverageData >= 4X There is a 1.53% of reference with a coverageData >= 5X There is a 1.26% of reference with a coverageData >= 6X There is a 0.96% of reference with a coverageData >= 7X There is a 0.79% of reference with a coverageData >= 8X There is a 0.59% of reference with a coverageData >= 9X There is a 0.49% of reference with a coverageData >= 10X There is a 0.37% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.24% of reference with a coverageData >= 13X There is a 0.21% of reference with a coverageData >= 14X There is a 0.16% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% 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 44515157 0.17859597228445823 1.9580565966845433 chr2 243199373 49617345 0.2040192143094053 8.509887138247782 chr3 198022430 51031259 0.2577044378255534 1.558054383879945 chr4 191154276 28702792 0.1501551134540145 1.3733677280056074 chr5 180915260 37167210 0.20543988384396097 1.3570242878327594 chr6 171115067 33374683 0.19504233955037986 1.5583819122870213 chr7 159138663 32882313 0.2066268019356176 1.8363058260911458 chr8 146364022 32101858 0.219328886712337 1.709282969513137 chr9 141213431 24228142 0.1715710880220735 1.551453377088734 chr10 135534747 26106641 0.1926195427951771 2.6853462583213776 chr11 135006516 19794930 0.1466220341542626 1.1831774346736834 chr12 133851895 26215037 0.19585107106627067 1.3291152561911994 chr13 115169878 13662749 0.11863127093006037 1.0248257241549656 chr14 107349540 17616390 0.16410307859726272 1.216866211125013 chr15 102531392 22007997 0.21464642750583157 1.3816958914455852 chr16 90354753 20721700 0.22933713293422428 1.7629781321388243 chr17 81195210 24596634 0.3029320818309356 1.82585362967193 chr18 78077248 10843789 0.13888538950553175 2.28307074344533 chr19 59128983 9466737 0.16010315956220658 1.6402165117317054 chr20 63025520 25850095 0.41015282380851437 2.102152715238035 chr21 48129895 7179519 0.14916963770646083 1.1952329139266311 chr22 51304566 4640780 0.09045549669009967 0.8654238738605096 chrMT 16571 2612783 157.6720173797598 131.94307019437724 chrX 155270560 19261667 0.12405228009739902 1.0505782865409579 chrY 59373566 891527 0.015015554228290751 0.640993109093026