BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716985.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 = 2,246,307 number of mapped reads = 1,887,942 (84.05%) number of supplementary alignments = 7,524 (0.33%) number of secondary alignments = 0 number of mapped bases = 106,345,712 bp number of sequenced bases = 106,314,844 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 56,687 duplication rate = 2.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.333 >>>>>>> ACTG content number of A's = 27,048,880 bp (25.44%) number of C's = 21,240,036 bp (19.98%) number of T's = 32,828,223 bp (30.88%) number of G's = 25,195,949 bp (23.7%) number of N's = 1,756 bp (0%) GC percentage = 43.68% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 546,047 number of insertions = 6,183 mapped reads with insertion percentage = 0.33% number of deletions = 19,704 mapped reads with deletion percentage = 1.04% homopolymer indels = 42.36% >>>>>>> Coverage mean coverageData = 0.0344X std coverageData = 0.289X There is a 3.06% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 8888510 0.0356609342209021 0.3655328244201243 chr2 243199373 10478776 0.04308718345256589 0.4119481130747272 chr3 198022430 7479909 0.03777303914511099 0.22360145197998907 chr4 191154276 5987022 0.031320366592270214 0.20469435994475377 chr5 180915260 5762902 0.03185415094337537 0.19565371887790037 chr6 171115067 5974586 0.03491560448034655 0.2305146102686645 chr7 159138663 5213015 0.03275769006554994 0.5595829471024234 chr8 146364022 8641273 0.059039597859643404 0.31278766095534155 chr9 141213431 4732744 0.03351482905333558 0.2310417539122312 chr10 135534747 5257390 0.038789979074517325 0.35880723822282845 chr11 135006516 3589466 0.02658735375409584 0.21490193217112089 chr12 133851895 4835062 0.036122477010878326 0.2177980387471737 chr13 115169878 2820027 0.02448580348413671 0.17064194017471676 chr14 107349540 3392991 0.031606944938935 0.20304668004956822 chr15 102531392 2535965 0.02473354697066826 0.17697936816092633 chr16 90354753 3312542 0.03666151353432398 0.2263291139488795 chr17 81195210 3757273 0.046274564718780824 0.24432457461741777 chr18 78077248 2379625 0.030477828829212832 0.31137818754550345 chr19 59128983 2196048 0.03713995892674156 0.3431409387345351 chr20 63025520 2389937 0.037920147267329174 0.218942034766951 chr21 48129895 1037895 0.02156445593741686 0.1658026484484241 chr22 51304566 1608531 0.03135258955314036 0.19810897382496037 chrMT 16571 12187 0.7354414338301852 0.9777617595355041 chrX 155270560 3822111 0.024615812553261868 0.19999957482058292 chrY 59373566 239925 0.004040939700337352 0.09568770055854155