BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716417.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 = 1,068,348 number of mapped reads = 963,101 (90.15%) number of supplementary alignments = 4,839 (0.45%) number of secondary alignments = 0 number of mapped bases = 56,060,951 bp number of sequenced bases = 56,044,946 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,025 duplication rate = 2.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4422 >>>>>>> ACTG content number of A's = 13,475,213 bp (24.04%) number of C's = 10,267,156 bp (18.32%) number of T's = 18,203,760 bp (32.48%) number of G's = 14,098,001 bp (25.15%) number of N's = 816 bp (0%) GC percentage = 43.47% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 283,493 number of insertions = 4,046 mapped reads with insertion percentage = 0.42% number of deletions = 10,040 mapped reads with deletion percentage = 1.03% homopolymer indels = 40.86% >>>>>>> Coverage mean coverageData = 0.0181X std coverageData = 0.2002X There is a 1.67% of reference with a coverageData >= 1X There is a 0.1% 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 5703421 0.022882273982378562 0.3378012676427407 chr2 243199373 5070992 0.020851172177980902 0.22839018966908656 chr3 198022430 4071208 0.02055932754688446 0.15289694543544027 chr4 191154276 2817030 0.014736944728351251 0.13721485271218833 chr5 180915260 2581661 0.014270001325482439 0.12694489359057987 chr6 171115067 4252282 0.024850424188537414 0.1891638742659404 chr7 159138663 3480233 0.021869185868427208 0.3680688304227111 chr8 146364022 3508591 0.02397167659139621 0.18995285367668185 chr9 141213431 2170805 0.015372510848490043 0.15796067527608804 chr10 135534747 2901739 0.021409557801439657 0.18879695866601975 chr11 135006516 1939198 0.014363736339955621 0.16239183408392416 chr12 133851895 2401260 0.017939678777054296 0.143797512636655 chr13 115169878 1225920 0.010644449931604513 0.10962522588404014 chr14 107349540 1310843 0.012210979199351948 0.1227260719786622 chr15 102531392 1785284 0.01741207219736176 0.13975177081576412 chr16 90354753 1270111 0.014056936218950208 0.13366665481887735 chr17 81195210 1706839 0.02102142478601878 0.15798025224808143 chr18 78077248 1149490 0.014722470751018273 0.25605595395281333 chr19 59128983 1148437 0.01942257319054515 0.22285076158024253 chr20 63025520 910289 0.014443181111397415 0.12803001847712628 chr21 48129895 580781 0.012066949242253697 0.12728265710307396 chr22 51304566 1010357 0.019693315405884145 0.14968256129511812 chrMT 16571 63792 3.849616800434494 2.839857399071956 chrX 155270560 2848186 0.01834337430096214 0.15567124676159827 chrY 59373566 152202 0.0025634640169667424 0.06908534902895518