BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716669.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 = 1,714,545 number of mapped reads = 1,551,074 (90.47%) number of supplementary alignments = 7,711 (0.45%) number of secondary alignments = 0 number of mapped bases = 89,831,833 bp number of sequenced bases = 89,806,200 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 53,101 duplication rate = 2.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4928 >>>>>>> ACTG content number of A's = 22,139,619 bp (24.65%) number of C's = 16,972,720 bp (18.9%) number of T's = 28,656,028 bp (31.91%) number of G's = 22,037,202 bp (24.54%) number of N's = 631 bp (0%) GC percentage = 43.44% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 451,913 number of insertions = 5,003 mapped reads with insertion percentage = 0.32% number of deletions = 16,216 mapped reads with deletion percentage = 1.04% homopolymer indels = 42.6% >>>>>>> Coverage mean coverageData = 0.029X std coverageData = 0.2632X There is a 2.62% 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 10692982 0.0429005230041132 0.43668487300952935 chr2 243199373 9267764 0.03810768048320585 0.3952425945128709 chr3 198022430 5807480 0.02932738478161287 0.18627965595888377 chr4 191154276 3754202 0.019639644367672945 0.16525771760724034 chr5 180915260 6536515 0.036130257889798796 0.20691313137614217 chr6 171115067 3424990 0.020015712584795353 0.1740653225922989 chr7 159138663 4734710 0.029752103673260092 0.3361488589616824 chr8 146364022 4067886 0.027792936709541912 0.2296250039261619 chr9 141213431 2505515 0.017742752812230728 0.20277158683721155 chr10 135534747 4123823 0.03042631569600377 0.23346694824579783 chr11 135006516 3948439 0.02924628467562262 0.25317142929124725 chr12 133851895 3605024 0.02693293210380025 0.17961981905151472 chr13 115169878 2576775 0.02237368871746135 0.16200175738730577 chr14 107349540 1978911 0.018434275545102477 0.15567642357064052 chr15 102531392 3960594 0.0386281110862125 0.21659189768610312 chr16 90354753 2702292 0.02990757995874329 0.19928594371543212 chr17 81195210 3441647 0.04238731570495353 0.24340530772224767 chr18 78077248 2878584 0.036868410116094257 0.4389014680428216 chr19 59128983 1430303 0.024189541700725684 0.32250308245953124 chr20 63025520 2438117 0.03868459950826268 0.21362218522340307 chr21 48129895 1175928 0.024432382410142388 0.17777613129598735 chr22 51304566 1076544 0.020983395512984167 0.15789966467734193 chrMT 16571 46706 2.818538410476133 2.34557782532724 chrX 155270560 3441067 0.022161747854841252 0.18770678378361286 chrY 59373566 215035 0.003621729575750933 0.08661182486503388