BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716760.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 = 1,010,192 number of mapped reads = 846,759 (83.82%) number of supplementary alignments = 2,116 (0.21%) number of secondary alignments = 0 number of mapped bases = 47,164,867 bp number of sequenced bases = 47,152,200 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,566 duplication rate = 1.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.216 >>>>>>> ACTG content number of A's = 11,292,500 bp (23.95%) number of C's = 9,346,681 bp (19.82%) number of T's = 14,044,885 bp (29.79%) number of G's = 12,466,823 bp (26.44%) number of N's = 1,311 bp (0%) GC percentage = 46.26% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 243,600 number of insertions = 3,381 mapped reads with insertion percentage = 0.4% number of deletions = 7,760 mapped reads with deletion percentage = 0.91% homopolymer indels = 35.66% >>>>>>> Coverage mean coverageData = 0.0152X std coverageData = 0.1488X There is a 1.41% 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 4615613 0.01851795988103075 0.17869032842348243 chr2 243199373 4076154 0.01676054485551655 0.18016245826158972 chr3 198022430 3196080 0.016139989798125393 0.13797465773127665 chr4 191154276 3069842 0.016059499500811585 0.146031579698446 chr5 180915260 2880830 0.015923642925422653 0.13446203218950453 chr6 171115067 2022474 0.011819379996502587 0.11970188513205861 chr7 159138663 2772219 0.01742014761051499 0.17810275573823298 chr8 146364022 2920609 0.019954418853015667 0.15775218888592374 chr9 141213431 2050971 0.014523908848302113 0.13666597996662128 chr10 135534747 2451127 0.018084860556090463 0.19595047191696455 chr11 135006516 1943598 0.014396327359488337 0.1470235459795844 chr12 133851895 2274683 0.01699402910956173 0.13857059464958948 chr13 115169878 839708 0.007291038373766446 0.09145706062289476 chr14 107349540 1507721 0.014044969358974431 0.12933466965595067 chr15 102531392 945631 0.00922284367308697 0.1038495091959246 chr16 90354753 1256196 0.013902932145694649 0.13154540547458884 chr17 81195210 1861656 0.022928150564546848 0.1688348077422186 chr18 78077248 1264317 0.01619315527104644 0.17009189045341763 chr19 59128983 1235613 0.02089690938875103 0.17813769770579763 chr20 63025520 1184674 0.018796735036854913 0.15038162293736462 chr21 48129895 623107 0.012946361092206829 0.12929775371202842 chr22 51304566 497889 0.009704574832579228 0.10583262643930597 chrMT 16571 3352 0.20228109347655543 0.45826045175535945 chrX 155270560 1529442 0.009850173786969018 0.11431005364762802 chrY 59373566 141361 0.0023808743439799455 0.07861374468744053