BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173907.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 = 1,740,742 number of mapped reads = 1,698,564 (97.58%) number of supplementary alignments = 157,918 (9.07%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 850,419 number of mapped paired reads (second in pair) = 848,145 number of mapped paired reads (both in pair) = 1,672,248 number of mapped paired reads (singletons) = 26,316 number of mapped bases = 202,231,381 bp number of sequenced bases = 202,116,555 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,310,432 duplication rate = 65% >>>>>>> Insert size mean insert size = 1,096,044.0935 std insert size = 9,739,021.0423 median insert size = 207 >>>>>>> Mapping quality mean mapping quality = 53.1471 >>>>>>> ACTG content number of A's = 60,741,577 bp (30.05%) number of C's = 39,711,856 bp (19.65%) number of T's = 60,529,877 bp (29.95%) number of G's = 41,130,907 bp (20.35%) number of N's = 2,338 bp (0%) GC percentage = 40% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 2,083,333 number of insertions = 22,777 mapped reads with insertion percentage = 1.29% number of deletions = 46,142 mapped reads with deletion percentage = 2.64% homopolymer indels = 42.32% >>>>>>> Coverage mean coverageData = 0.0653X std coverageData = 1.0738X There is a 1.41% of reference with a coverageData >= 1X There is a 1.11% of reference with a coverageData >= 2X There is a 0.86% of reference with a coverageData >= 3X There is a 0.7% of reference with a coverageData >= 4X There is a 0.53% of reference with a coverageData >= 5X There is a 0.42% 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 0.18% of reference with a coverageData >= 9X There is a 0.15% of reference with a coverageData >= 10X There is a 0.11% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% 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 0.01% 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 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 16260518 0.06523762281819952 0.8706758710427116 chr2 243199373 18902401 0.07772388870426898 2.7142942802816625 chr3 198022430 14060488 0.07100452206348544 0.7610771911296728 chr4 191154276 13008438 0.0680520377163836 0.8451912977887166 chr5 180915260 12242807 0.06767149990553588 0.7427085116921004 chr6 171115067 11725366 0.06852328205557726 0.7907908822358112 chr7 159138663 11029967 0.06931041641338911 0.8410585611312704 chr8 146364022 10474065 0.07156174623296427 0.9467291751840676 chr9 141213431 8345865 0.05910107091725574 0.7907784172385132 chr10 135534747 10220263 0.07540695818762992 0.9822586493232764 chr11 135006516 9570827 0.07089159311392051 0.7594531451935772 chr12 133851895 9173195 0.06853242533473285 0.7444806825862731 chr13 115169878 6699279 0.05816867323589593 0.6941948994121099 chr14 107349540 6317872 0.05885327501170475 0.6910035591890009 chr15 102531392 5844870 0.057005663202153736 0.6679396847739162 chr16 90354753 5875314 0.06502495779054368 0.7562314908506441 chr17 81195210 5555580 0.068422509160331 0.7530118112425878 chr18 78077248 6026278 0.07718353495246144 0.9825993000077392 chr19 59128983 3476540 0.058795870038894464 0.7462111943501721 chr20 63025520 4338806 0.06884205001402606 0.7596908776804 chr21 48129895 2935576 0.06099277798133572 0.7436266174673224 chr22 51304566 2329793 0.04541102637921155 0.6038330417866709 chrMT 16571 272454 16.44161486935007 17.491049446815794 chrX 155270560 5968447 0.03843901252111154 0.5572673043088242 chrY 59373566 1576372 0.026550064383870763 0.5480871759514845