BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717023.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 = 1,452,398 number of mapped reads = 1,317,368 (90.7%) number of supplementary alignments = 5,769 (0.4%) number of secondary alignments = 0 number of mapped bases = 75,314,296 bp number of sequenced bases = 75,295,521 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,436 duplication rate = 1.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5215 >>>>>>> ACTG content number of A's = 17,862,534 bp (23.72%) number of C's = 15,204,583 bp (20.19%) number of T's = 22,899,320 bp (30.41%) number of G's = 19,327,384 bp (25.67%) number of N's = 1,700 bp (0%) GC percentage = 45.86% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 375,539 number of insertions = 3,646 mapped reads with insertion percentage = 0.28% number of deletions = 10,963 mapped reads with deletion percentage = 0.83% homopolymer indels = 41.77% >>>>>>> Coverage mean coverageData = 0.0243X std coverageData = 0.2049X There is a 2.22% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.02% 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 6487790 0.026029182892186253 0.2898643400126446 chr2 243199373 5883370 0.024191550855684155 0.23436412913066101 chr3 198022430 5125866 0.025885279763509617 0.17335257376157512 chr4 191154276 4465327 0.023359807028329307 0.1771072285893902 chr5 180915260 4675348 0.02584275091001168 0.1734320000504042 chr6 171115067 4418275 0.025820490722771944 0.18068566753749346 chr7 159138663 4272760 0.02684928928930363 0.2302604237469566 chr8 146364022 3797225 0.025943704935902895 0.19569371986360237 chr9 141213431 3311560 0.023450743860192733 0.21453367891121888 chr10 135534747 3684777 0.027186954501047616 0.21716707819963532 chr11 135006516 3376991 0.025013540827910855 0.1996105986304086 chr12 133851895 3641450 0.027205068706722457 0.17896837936848933 chr13 115169878 2125894 0.01845876749127059 0.14572475002404287 chr14 107349540 2313583 0.021551866919970034 0.1683942162240359 chr15 102531392 1964895 0.01916383813456858 0.14884889221840655 chr16 90354753 2152649 0.02382441353140548 0.17695664864318256 chr17 81195210 2201741 0.02711663656021088 0.18304831835736188 chr18 78077248 1920042 0.024591568596270198 0.3317331902403122 chr19 59128983 1650990 0.027921839954527884 0.2384789517683842 chr20 63025520 1644069 0.026085766527590728 0.17933042378017286 chr21 48129895 1020485 0.02120272649670231 0.17420720143160567 chr22 51304566 841420 0.01640048957825703 0.13835377890046535 chrMT 16571 8776 0.5295999034457788 0.7887894462322641 chrX 155270560 4108938 0.02646308482432214 0.1922654356628952 chrY 59373566 220075 0.0037066158364144745 0.09151661768121484