BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004003.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,856,389 number of mapped reads = 2,116,037 (74.08%) number of supplementary alignments = 13,728 (0.48%) number of secondary alignments = 0 number of mapped bases = 137,535,906 bp number of sequenced bases = 137,462,442 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 179,912 duplication rate = 6.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3561 >>>>>>> ACTG content number of A's = 37,531,324 bp (27.3%) number of C's = 24,213,743 bp (17.61%) number of T's = 45,653,553 bp (33.21%) number of G's = 30,046,078 bp (21.86%) number of N's = 17,744 bp (0.01%) GC percentage = 39.47% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 1,464,629 number of insertions = 12,427 mapped reads with insertion percentage = 0.58% number of deletions = 45,915 mapped reads with deletion percentage = 2.14% homopolymer indels = 49.57% >>>>>>> Coverage mean coverageData = 0.0444X std coverageData = 0.4244X There is a 3.12% of reference with a coverageData >= 1X There is a 0.85% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 12135548 0.04868813546506671 0.692330932945723 chr2 243199373 12106465 0.04978000087195948 0.49369235628607816 chr3 198022430 9359345 0.04726406498496155 0.29375186569061956 chr4 191154276 9458842 0.04948276438241957 0.3124260175916256 chr5 180915260 8127460 0.044924126356173606 0.28726587752037813 chr6 171115067 8485232 0.04958787176818275 0.3424032873028843 chr7 159138663 7908175 0.04969361216764778 0.5541839913923812 chr8 146364022 8255124 0.05640131971776507 0.680543738142997 chr9 141213431 5237674 0.037090480437374264 0.38775187772439335 chr10 135534747 6244257 0.04607126318684905 0.3699614387409244 chr11 135006516 5834362 0.04321541043248609 0.3860353434488763 chr12 133851895 5756099 0.04300349277834281 0.2862171494970665 chr13 115169878 4006881 0.03479105013899555 0.2540384687166763 chr14 107349540 3539578 0.03297245614652843 0.25997033906842204 chr15 102531392 3659656 0.035693029506514456 0.25694683374788785 chr16 90354753 3720170 0.04117293088057028 0.2882848702126969 chr17 81195210 3136870 0.038633682947553184 0.28515726074937775 chr18 78077248 4059943 0.05199905355270719 0.7382807621472679 chr19 59128983 2137855 0.03615578843965573 0.45839390598015284 chr20 63025520 2951961 0.04683755088414979 0.29539545015519897 chr21 48129895 2130491 0.04426544042948774 0.29906057459831004 chr22 51304566 1382457 0.026946081173359893 0.2134365360787095 chrMT 16571 90864 5.483314223643715 4.619800473311806 chrX 155270560 7455950 0.04801908359189276 0.3187235715046854 chrY 59373566 354647 0.0059731463661791846 0.12838237785928336