BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174046.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 = 1,913,870 number of mapped reads = 1,865,652 (97.48%) number of supplementary alignments = 175,121 (9.15%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 933,647 number of mapped paired reads (second in pair) = 932,005 number of mapped paired reads (both in pair) = 1,835,258 number of mapped paired reads (singletons) = 30,394 number of mapped bases = 221,436,346 bp number of sequenced bases = 221,318,182 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,392,573 duplication rate = 64.02% >>>>>>> Insert size mean insert size = 1,238,424.5003 std insert size = 10,479,512.6222 median insert size = 201 >>>>>>> Mapping quality mean mapping quality = 53.078 >>>>>>> ACTG content number of A's = 66,763,196 bp (30.17%) number of C's = 43,347,438 bp (19.59%) number of T's = 66,447,253 bp (30.02%) number of G's = 44,757,496 bp (20.22%) number of N's = 2,799 bp (0%) GC percentage = 39.81% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 2,254,606 number of insertions = 24,651 mapped reads with insertion percentage = 1.27% number of deletions = 45,805 mapped reads with deletion percentage = 2.4% homopolymer indels = 43.63% >>>>>>> Coverage mean coverageData = 0.0715X std coverageData = 1.1511X There is a 1.67% of reference with a coverageData >= 1X There is a 1.3% of reference with a coverageData >= 2X There is a 0.97% of reference with a coverageData >= 3X There is a 0.77% of reference with a coverageData >= 4X There is a 0.56% of reference with a coverageData >= 5X There is a 0.44% of reference with a coverageData >= 6X There is a 0.31% of reference with a coverageData >= 7X There is a 0.25% of reference with a coverageData >= 8X There is a 0.17% of reference with a coverageData >= 9X There is a 0.14% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% 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% 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 16826597 0.06750874654791733 0.9071658270464442 chr2 243199373 20202441 0.08306946169635067 3.007277025680818 chr3 198022430 16832120 0.08500107790819454 0.7960832184741077 chr4 191154276 14876498 0.07782456302468484 0.9019159839964566 chr5 180915260 13535959 0.07481933254276063 0.7418274014540261 chr6 171115067 13858427 0.08098893477334758 0.829138795680299 chr7 159138663 13062178 0.08208048097023411 0.9539103690980472 chr8 146364022 10672776 0.07291939545088479 0.9847546155497141 chr9 141213431 9818047 0.06952629739589006 0.8273452376496805 chr10 135534747 11115613 0.0820130132385904 1.0358269243101001 chr11 135006516 9643740 0.07143166334282709 0.7304966273131719 chr12 133851895 10300054 0.07695112571996085 0.7521481041441596 chr13 115169878 7009933 0.06086602783411822 0.6769640281940067 chr14 107349540 7098492 0.0661250341640961 0.7022910958845696 chr15 102531392 6231634 0.060777815247061114 0.6605261230518173 chr16 90354753 6499122 0.07192894434673514 0.7938295949162288 chr17 81195210 5940755 0.07316632348139748 0.7434012914270872 chr18 78077248 6419494 0.08221977803316019 1.0368827285591768 chr19 59128983 3724631 0.06299162967169586 0.7125012131630303 chr20 63025520 4397176 0.0697681827932558 0.7191413994292072 chr21 48129895 3211069 0.06671672564421759 0.831613087437598 chr22 51304566 2540236 0.04951286402071894 0.6387366174313701 chrMT 16571 313132 18.896385251342707 17.548865474301707 chrX 155270560 5528029 0.03560255723944063 0.5066375123284801 chrY 59373566 1778193 0.02994923700557248 0.553052906837211