BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524770.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 = 1,056,132 number of mapped reads = 971,094 (91.95%) number of supplementary alignments = 3,799 (0.36%) number of secondary alignments = 0 number of mapped bases = 56,034,908 bp number of sequenced bases = 56,016,675 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,028 duplication rate = 2.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6859 >>>>>>> ACTG content number of A's = 13,149,591 bp (23.47%) number of C's = 10,901,115 bp (19.46%) number of T's = 17,595,594 bp (31.41%) number of G's = 14,363,575 bp (25.64%) number of N's = 6,800 bp (0.01%) GC percentage = 45.1% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 279,733 number of insertions = 3,251 mapped reads with insertion percentage = 0.33% number of deletions = 11,260 mapped reads with deletion percentage = 1.15% homopolymer indels = 43.46% >>>>>>> Coverage mean coverageData = 0.0181X std coverageData = 0.1773X There is a 1.67% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 4480404 0.017975497842390532 0.22990828121541657 chr2 243199373 4763204 0.019585593257265513 0.2534410227441456 chr3 198022430 3692772 0.018648251109735395 0.1457758738932167 chr4 191154276 3584019 0.018749353009503172 0.1609815406343841 chr5 180915260 3321009 0.01835671020786196 0.14416373686285006 chr6 171115067 3189162 0.018637528862376566 0.1546551129986442 chr7 159138663 3106428 0.019520259511040382 0.21418345244498974 chr8 146364022 2786291 0.01903672064983292 0.16556927420014453 chr9 141213431 2360518 0.016715959546369213 0.15826289599882154 chr10 135534747 2731954 0.020156853209015103 0.20587276780020883 chr11 135006516 2501271 0.01852703909491302 0.16219368276055532 chr12 133851895 2456441 0.01835193293303767 0.14563439933495045 chr13 115169878 1715998 0.014899711884734304 0.13093188840975967 chr14 107349540 1680660 0.015655959028795092 0.13697692265212355 chr15 102531392 1634381 0.015940298557538358 0.13552107433974125 chr16 90354753 1687979 0.018681684625932185 0.155734002244989 chr17 81195210 1614844 0.019888414599826765 0.15584167516832098 chr18 78077248 1497436 0.019178903436760476 0.23291042247121896 chr19 59128983 1257393 0.021265256667783377 0.2056657552830715 chr20 63025520 1234360 0.01958508236028834 0.15586097097915982 chr21 48129895 743571 0.015449254564133165 0.1431087300820857 chr22 51304566 713659 0.013910243388473454 0.12629559747258357 chrMT 16571 20907 1.261661939532919 1.3472005928265707 chrX 155270560 3068987 0.01976541464138469 0.15650974708981433 chrY 59373566 191260 0.0032212988520851182 0.09784019829414108