BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068087.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 = 4,475,890 number of mapped reads = 4,199,435 (93.82%) number of supplementary alignments = 28,911 (0.65%) number of secondary alignments = 0 number of mapped bases = 269,474,545 bp number of sequenced bases = 269,374,091 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 775,886 duplication rate = 14.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.99 >>>>>>> ACTG content number of A's = 70,339,702 bp (26.11%) number of C's = 47,675,830 bp (17.7%) number of T's = 88,982,980 bp (33.03%) number of G's = 62,344,771 bp (23.14%) number of N's = 30,808 bp (0.01%) GC percentage = 40.84% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 1,456,988 number of insertions = 18,152 mapped reads with insertion percentage = 0.43% number of deletions = 58,104 mapped reads with deletion percentage = 1.37% homopolymer indels = 44.85% >>>>>>> Coverage mean coverageData = 0.087X std coverageData = 1.0522X There is a 5.41% of reference with a coverageData >= 1X There is a 1.88% of reference with a coverageData >= 2X There is a 0.71% of reference with a coverageData >= 3X There is a 0.28% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 32846686 0.1317817619399231 2.348138841118948 chr2 243199373 13540152 0.05567511064265778 1.6806569562273834 chr3 198022430 6443501 0.032539248205367445 0.28271904520253593 chr4 191154276 23590663 0.12341164159989808 0.6009019276931077 chr5 180915260 8176053 0.04519272171954981 0.33579380047199614 chr6 171115067 25333835 0.14805145709348902 0.735010884754987 chr7 159138663 14505620 0.09115082234918613 1.1554752688051428 chr8 146364022 9148143 0.06250267569170789 0.890603215080843 chr9 141213431 15416480 0.10917148525341049 0.8191988242224129 chr10 135534747 17317959 0.1277750494491276 0.7477931891426864 chr11 135006516 24485667 0.18136655715195257 1.063872838200456 chr12 133851895 7179709 0.053639203240267906 0.43388949474095345 chr13 115169878 7060818 0.06130785343021723 0.4230142712539286 chr14 107349540 5122221 0.04771535117896174 0.4328535651992332 chr15 102531392 3719357 0.03627529995886528 0.33720226609833565 chr16 90354753 6040704 0.06685540936623445 0.46599205454888537 chr17 81195210 3291963 0.040543807941379795 0.45734746018508277 chr18 78077248 4056201 0.05195112665856256 1.3437372610194498 chr19 59128983 5154014 0.0871656121668793 1.3610774120345395 chr20 63025520 5940379 0.09425354999054351 0.5031208571475925 chr21 48129895 6433217 0.13366364086188012 0.5961054260144663 chr22 51304566 615679 0.0120004718488409 0.15162710709867236 chrMT 16571 503721 30.39774304507875 19.218895832602737 chrX 155270560 22883652 0.14737920697909507 0.702988610251638 chrY 59373566 668151 0.011253341259644065 0.4656629679503136