BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716403.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 = 1,340,402 number of mapped reads = 1,216,735 (90.77%) number of supplementary alignments = 4,850 (0.36%) number of secondary alignments = 0 number of mapped bases = 69,875,521 bp number of sequenced bases = 69,857,104 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,863 duplication rate = 1.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7085 >>>>>>> ACTG content number of A's = 17,083,856 bp (24.46%) number of C's = 13,512,914 bp (19.34%) number of T's = 21,885,206 bp (31.33%) number of G's = 17,373,605 bp (24.87%) number of N's = 1,523 bp (0%) GC percentage = 44.21% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 340,747 number of insertions = 4,137 mapped reads with insertion percentage = 0.34% number of deletions = 10,593 mapped reads with deletion percentage = 0.86% homopolymer indels = 42.04% >>>>>>> Coverage mean coverageData = 0.0226X std coverageData = 0.1982X There is a 2.07% of reference with a coverageData >= 1X There is a 0.14% 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 5723419 0.02296250648057563 0.27368418881503365 chr2 243199373 6012954 0.02472438117675575 0.22929423509440286 chr3 198022430 4543391 0.022943820051092193 0.1619970675529435 chr4 191154276 4539153 0.02374601863470739 0.1754937422916839 chr5 180915260 3646878 0.020157934714849373 0.15353500475958873 chr6 171115067 4095476 0.023934046672815783 0.17401907810621206 chr7 159138663 3898233 0.02449582600803929 0.22281727350473046 chr8 146364022 3544500 0.02421701693876655 0.1874801144105009 chr9 141213431 3014654 0.02134821014298562 0.2024254943024087 chr10 135534747 3404271 0.02511733024447229 0.20004965633100208 chr11 135006516 3205330 0.02374203923609139 0.21475285708228573 chr12 133851895 3271335 0.024439960300898244 0.16875776855569347 chr13 115169878 2153647 0.018699741958570104 0.14563016613148855 chr14 107349540 2136990 0.019906838911466225 0.15786450076117509 chr15 102531392 2055253 0.020045109696745365 0.15195645379137598 chr16 90354753 2146631 0.023757809398250472 0.17349873437974503 chr17 81195210 1967267 0.024228855372133404 0.1744787037834928 chr18 78077248 1877725 0.024049579718793367 0.3571006274776151 chr19 59128983 1474125 0.024930667249933928 0.22308300232973738 chr20 63025520 1551198 0.024612220573507367 0.17145134724224037 chr21 48129895 929183 0.019305735032249707 0.15963923909040714 chr22 51304566 867559 0.016909976394693604 0.13902106259800356 chrMT 16571 5316 0.32080140003620783 0.6119848509071792 chrX 155270560 3614111 0.023276215401039323 0.18283829039807672 chrY 59373566 196922 0.0033166611552353114 0.08427014290584112