BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9867867.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 = 1,531,818 number of mapped reads = 1,416,433 (92.47%) number of supplementary alignments = 5,956 (0.39%) number of secondary alignments = 0 number of mapped bases = 83,713,841 bp number of sequenced bases = 83,689,314 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,578 duplication rate = 2.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7497 >>>>>>> ACTG content number of A's = 21,676,245 bp (25.9%) number of C's = 16,403,282 bp (19.6%) number of T's = 26,055,542 bp (31.13%) number of G's = 19,543,066 bp (23.35%) number of N's = 11,179 bp (0.01%) GC percentage = 42.95% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 415,462 number of insertions = 7,235 mapped reads with insertion percentage = 0.51% number of deletions = 15,595 mapped reads with deletion percentage = 1.09% homopolymer indels = 41.88% >>>>>>> Coverage mean coverageData = 0.027X std coverageData = 0.2615X There is a 2.45% of reference with a coverageData >= 1X There is a 0.18% 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 6653813 0.026695271503455954 0.44703526632366786 chr2 243199373 7113531 0.029249791692513943 0.35540834328996884 chr3 198022430 5535545 0.027954131256747027 0.18071151284964085 chr4 191154276 5501043 0.028778027439993026 0.20115467780079063 chr5 180915260 4978893 0.02752058062984847 0.17950922833364638 chr6 171115067 4805389 0.02808279296644287 0.20367180377192176 chr7 159138663 4571462 0.028726281306007954 0.318203483149421 chr8 146364022 4270071 0.029174321268651663 0.2772596012999204 chr9 141213431 3547301 0.02512013889103792 0.22705623175103962 chr10 135534747 4132155 0.030487790706541104 0.26652153052341915 chr11 135006516 3877922 0.028723961738261583 0.23386226235675814 chr12 133851895 3725246 0.027831103922734902 0.18237058983942137 chr13 115169878 2576620 0.022372342879446307 0.16176651978193174 chr14 107349540 2487651 0.023173373635322517 0.17103064619307765 chr15 102531392 2394900 0.023357724432337756 0.1656075933393253 chr16 90354753 2442667 0.027034183802151505 0.1892680565824859 chr17 81195210 2312499 0.028480731806716186 0.1909285091073725 chr18 78077248 2199786 0.028174481764521208 0.3948194175581304 chr19 59128983 1761838 0.029796521276207303 0.3542436508601506 chr20 63025520 1839847 0.0291920955194023 0.18843489075769781 chr21 48129895 1133267 0.023546010229193313 0.18799342048715664 chr22 51304566 1014455 0.019773191337394806 0.15268637238725027 chrMT 16571 10229 0.6172832056001448 0.8372937612336784 chrX 155270560 4556703 0.029346857511172754 0.20071213033798854 chrY 59373566 271008 0.004564455501965302 0.1692144144025409