BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173863.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 = 2,207,840 number of mapped reads = 2,145,352 (97.17%) number of supplementary alignments = 203,817 (9.23%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,076,351 number of mapped paired reads (second in pair) = 1,069,001 number of mapped paired reads (both in pair) = 2,104,652 number of mapped paired reads (singletons) = 40,700 number of mapped bases = 253,217,321 bp number of sequenced bases = 253,067,366 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,655,123 duplication rate = 63.88% >>>>>>> Insert size mean insert size = 1,096,641.242 std insert size = 9,723,519.8438 median insert size = 205 >>>>>>> Mapping quality mean mapping quality = 53.0097 >>>>>>> ACTG content number of A's = 76,242,373 bp (30.13%) number of C's = 49,479,256 bp (19.55%) number of T's = 76,038,993 bp (30.05%) number of G's = 51,303,755 bp (20.27%) number of N's = 2,989 bp (0%) GC percentage = 39.82% >>>>>>> Mismatches and indels general error rate = 0.0113 number of mismatches = 2,782,724 number of insertions = 28,417 mapped reads with insertion percentage = 1.28% number of deletions = 59,939 mapped reads with deletion percentage = 2.72% homopolymer indels = 42.65% >>>>>>> Coverage mean coverageData = 0.0818X std coverageData = 1.3452X There is a 1.74% of reference with a coverageData >= 1X There is a 1.36% of reference with a coverageData >= 2X There is a 1.05% of reference with a coverageData >= 3X There is a 0.86% of reference with a coverageData >= 4X There is a 0.66% of reference with a coverageData >= 5X There is a 0.53% of reference with a coverageData >= 6X There is a 0.39% of reference with a coverageData >= 7X There is a 0.32% of reference with a coverageData >= 8X There is a 0.23% of reference with a coverageData >= 9X There is a 0.19% of reference with a coverageData >= 10X There is a 0.14% of reference with a coverageData >= 11X There is a 0.12% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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 20294155 0.08142067979040261 1.1624411835339867 chr2 243199373 22589621 0.09288519423937824 3.5056556502602936 chr3 198022430 16884502 0.08526560349754318 0.8418335935983676 chr4 191154276 17827629 0.09326304058194335 1.0845686882222203 chr5 180915260 16467953 0.0910257819047437 0.8765635750681087 chr6 171115067 15460490 0.09035142416769179 0.9268534631881793 chr7 159138663 13035308 0.08191163450958489 0.9474927130504599 chr8 146364022 13611152 0.09299520342506029 1.242448599555486 chr9 141213431 10947609 0.077525267408877 0.9855998182279779 chr10 135534747 12424798 0.0916724181438137 1.2045278922061953 chr11 135006516 11847438 0.0877545643796926 0.8735179707837631 chr12 133851895 11334246 0.08467751614573704 0.8400327884625822 chr13 115169878 8455881 0.07342094258361548 0.7889033022654414 chr14 107349540 7740806 0.07210842263506671 0.7696734384701693 chr15 102531392 7180650 0.07003367319932612 0.7434158462696956 chr16 90354753 7490065 0.08289619252237898 0.9517481521341519 chr17 81195210 6718518 0.08274525061269009 0.8250834041093195 chr18 78077248 7278509 0.09322189480858752 1.2640179798544104 chr19 59128983 4479418 0.07575672322995983 0.930956813447108 chr20 63025520 5406158 0.08577728513782988 0.8568909172000377 chr21 48129895 3756028 0.07803939734337671 0.9457801065444784 chr22 51304566 2952659 0.057551583225555404 0.7041490227067254 chrMT 16571 445072 26.858487719509988 23.88664495472104 chrX 155270560 6472246 0.0416836649523258 0.5929899100137405 chrY 59373566 2116410 0.035645660898993334 0.6915896321355632