BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173865.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 = 1,171,734 number of mapped reads = 1,146,755 (97.87%) number of supplementary alignments = 103,870 (8.86%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 573,848 number of mapped paired reads (second in pair) = 572,907 number of mapped paired reads (both in pair) = 1,131,646 number of mapped paired reads (singletons) = 15,109 number of mapped bases = 135,664,509 bp number of sequenced bases = 135,589,559 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 797,817 duplication rate = 60.05% >>>>>>> Insert size mean insert size = 807,409.3791 std insert size = 8,444,334.8009 median insert size = 189 >>>>>>> Mapping quality mean mapping quality = 53.1881 >>>>>>> ACTG content number of A's = 41,193,807 bp (30.38%) number of C's = 26,250,014 bp (19.36%) number of T's = 41,019,263 bp (30.25%) number of G's = 27,124,787 bp (20.01%) number of N's = 1,688 bp (0%) GC percentage = 39.36% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 1,338,305 number of insertions = 14,703 mapped reads with insertion percentage = 1.24% number of deletions = 29,832 mapped reads with deletion percentage = 2.54% homopolymer indels = 42.6% >>>>>>> Coverage mean coverageData = 0.0438X std coverageData = 0.7728X There is a 1.19% of reference with a coverageData >= 1X There is a 0.86% of reference with a coverageData >= 2X There is a 0.58% of reference with a coverageData >= 3X There is a 0.45% of reference with a coverageData >= 4X There is a 0.31% of reference with a coverageData >= 5X There is a 0.24% of reference with a coverageData >= 6X There is a 0.16% of reference with a coverageData >= 7X There is a 0.13% of reference with a coverageData >= 8X There is a 0.09% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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% 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 10569926 0.04240681911881776 0.5956031103821167 chr2 243199373 11921376 0.04901894216643396 1.9135866703114228 chr3 198022430 9637121 0.04866681516836249 0.5786029971749485 chr4 191154276 9162361 0.04793176062668878 0.6168457960482453 chr5 180915260 8215698 0.045411857462991236 0.5557706125329273 chr6 171115067 8255484 0.04824521969184631 0.6149474074053879 chr7 159138663 7521149 0.047261607319146574 0.6227340039375101 chr8 146364022 7123850 0.048672138840240395 0.6725720831713583 chr9 141213431 5712608 0.04045371576588915 0.5854513063615293 chr10 135534747 6636519 0.04896544352571079 0.6812744099007577 chr11 135006516 6694891 0.04958939167054722 0.5811688818317876 chr12 133851895 6247794 0.04667691854493356 0.5598911048396457 chr13 115169878 4497521 0.0390511918402831 0.5167293509431443 chr14 107349540 4165585 0.0388039389828778 0.5041234392897032 chr15 102531392 3842906 0.037480287012976475 0.4954365994877706 chr16 90354753 4172736 0.046181698930658356 0.5865019447668096 chr17 81195210 3747088 0.0461491262846663 0.5517085975754173 chr18 78077248 3708538 0.04749831858827811 0.7184132918627669 chr19 59128983 2330642 0.03941623687320988 0.5233431155400278 chr20 63025520 2869218 0.04552470173986665 0.5529138879597807 chr21 48129895 2021267 0.0419960816453059 0.5691371073149748 chr22 51304566 1600366 0.031193441924837646 0.47253852166418503 chrMT 16571 291407 17.585359966206024 15.627815601566812 chrX 155270560 3703142 0.02384960806478704 0.40057206460692607 chrY 59373566 1015316 0.017100471950766777 0.35888704044071745