BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716963.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 = 640,611 number of mapped reads = 604,514 (94.37%) number of supplementary alignments = 15,151 (2.37%) number of secondary alignments = 0 number of mapped bases = 46,995,597 bp number of sequenced bases = 46,976,097 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,947 duplication rate = 1.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5726 >>>>>>> ACTG content number of A's = 11,980,936 bp (25.5%) number of C's = 9,799,302 bp (20.86%) number of T's = 13,399,911 bp (28.52%) number of G's = 11,793,890 bp (25.11%) number of N's = 2,058 bp (0%) GC percentage = 45.97% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 305,191 number of insertions = 4,712 mapped reads with insertion percentage = 0.77% number of deletions = 9,167 mapped reads with deletion percentage = 1.49% homopolymer indels = 37.63% >>>>>>> Coverage mean coverageData = 0.0152X std coverageData = 0.155X There is a 1.4% of reference with a coverageData >= 1X There is a 0.08% 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 3782798 0.0151766843541786 0.18997621774004375 chr2 243199373 3942431 0.01621069557609427 0.169465337780705 chr3 198022430 3078399 0.01554570863512785 0.13167948652578285 chr4 191154276 2933931 0.015348497880319455 0.16590934330594903 chr5 180915260 2656450 0.01468339376125596 0.1282547634725534 chr6 171115067 2606697 0.015233591323667599 0.13318421342954453 chr7 159138663 2561895 0.01609850775232415 0.1817437365200643 chr8 146364022 2411364 0.016475114355630375 0.15732851331749353 chr9 141213431 1933543 0.013692344887505778 0.14174934540457262 chr10 135534747 2321366 0.01712746031097103 0.20781308187585046 chr11 135006516 2139738 0.015849146125658114 0.15697618111057235 chr12 133851895 2108760 0.01575442768292522 0.13438888484157718 chr13 115169878 1408197 0.01222712938881467 0.11661959893617804 chr14 107349540 1421280 0.013239740011927391 0.12751811854036027 chr15 102531392 1368018 0.013342430774762134 0.12195245442159122 chr16 90354753 1476795 0.01634440857804127 0.142295165744132 chr17 81195210 1373177 0.01691204444203051 0.14620666572628832 chr18 78077248 1240766 0.015891518102687227 0.19711547905060905 chr19 59128983 1048268 0.017728497038415156 0.1672463108860396 chr20 63025520 1099618 0.01744718647303505 0.1444182978409868 chr21 48129895 645799 0.013417835214475328 0.14640077774860957 chr22 51304566 664011 0.01294253224946879 0.12304351837471142 chrMT 16571 6898 0.4162693862772313 0.6653763024143772 chrX 155270560 2592459 0.016696397565642836 0.1406748397068798 chrY 59373566 172939 0.002912727189065922 0.13477126797424538