BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716663.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 = 2,900,185 number of mapped reads = 2,669,669 (92.05%) number of supplementary alignments = 53,732 (1.85%) number of secondary alignments = 0 number of mapped bases = 208,472,344 bp number of sequenced bases = 208,379,053 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 143,783 duplication rate = 4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2738 >>>>>>> ACTG content number of A's = 53,553,004 bp (25.7%) number of C's = 43,152,806 bp (20.71%) number of T's = 63,634,041 bp (30.54%) number of G's = 48,024,010 bp (23.05%) number of N's = 15,192 bp (0.01%) GC percentage = 43.76% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 1,412,588 number of insertions = 16,963 mapped reads with insertion percentage = 0.63% number of deletions = 48,720 mapped reads with deletion percentage = 1.79% homopolymer indels = 42.98% >>>>>>> Coverage mean coverageData = 0.0673X std coverageData = 0.5393X There is a 5.44% of reference with a coverageData >= 1X There is a 0.89% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 16963983 0.06805994276740437 0.941718893966656 chr2 243199373 17696508 0.07276543430891165 0.673433677472094 chr3 198022430 13259017 0.06695714722822056 0.30431768330932385 chr4 191154276 13384236 0.07001797856721761 0.4332404654788499 chr5 180915260 12690359 0.07014532107462908 0.3185119360645092 chr6 171115067 11807443 0.06900294174562664 0.3540016443817803 chr7 159138663 11426042 0.07179928362223327 0.7622934605985943 chr8 146364022 10778201 0.07363968858412485 0.6968931256526326 chr9 141213431 8995335 0.06370027933107865 0.5047979446006724 chr10 135534747 10075593 0.07433955663044843 0.5759899028156203 chr11 135006516 9598331 0.07109531661419957 0.5071862440565742 chr12 133851895 9369787 0.07000115314019274 0.31771770307308717 chr13 115169878 6373878 0.055343273004074905 0.2768565768269587 chr14 107349540 6296461 0.058653823761145134 0.3213037097396092 chr15 102531392 6140831 0.059892203550694016 0.29239767911723513 chr16 90354753 6126964 0.06781009074309571 0.3443917137267128 chr17 81195210 5791570 0.07132896140055553 0.3775521801315788 chr18 78077248 5676284 0.07270087183400727 0.848893190380371 chr19 59128983 4195524 0.07095545681886664 0.655550407218542 chr20 63025520 4060928 0.06443307409443032 0.3280623401159703 chr21 48129895 2711036 0.0563274862743831 0.3550782958831408 chr22 51304566 2508924 0.048902547972046 0.2639552197396224 chrMT 16571 29862 1.8020638464787881 1.8302301575258741 chrX 155270560 11868494 0.07643750367101143 0.4002283056153851 chrY 59373566 646753 0.010892945187088813 0.36435248627789457