BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231837.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 = 4,456,816 number of mapped reads = 3,865,052 (86.72%) number of supplementary alignments = 22,899 (0.51%) number of secondary alignments = 0 number of mapped bases = 244,185,724 bp number of sequenced bases = 244,089,588 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 713,795 duplication rate = 14.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6577 >>>>>>> ACTG content number of A's = 61,637,055 bp (25.25%) number of C's = 43,519,515 bp (17.83%) number of T's = 80,592,824 bp (33.02%) number of G's = 58,249,240 bp (23.86%) number of N's = 90,954 bp (0.04%) GC percentage = 41.69% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 1,502,545 number of insertions = 15,188 mapped reads with insertion percentage = 0.39% number of deletions = 53,176 mapped reads with deletion percentage = 1.36% homopolymer indels = 44.45% >>>>>>> Coverage mean coverageData = 0.0789X std coverageData = 0.8773X There is a 4.84% of reference with a coverageData >= 1X There is a 1.68% of reference with a coverageData >= 2X There is a 0.67% of reference with a coverageData >= 3X There is a 0.28% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.06% 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 0.01% 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 20542052 0.08241524902760423 1.8598684621297878 chr2 243199373 22252354 0.09149840201273875 1.4301183040800645 chr3 198022430 13101819 0.06616330786365969 0.38821941533709986 chr4 191154276 19315335 0.10104579088777485 0.5044145179640924 chr5 180915260 17240668 0.09529692520133459 0.46817704907910374 chr6 171115067 11458048 0.06696107012014318 0.6433467902119282 chr7 159138663 14565738 0.09152859352601196 0.928448705663007 chr8 146364022 12912665 0.0882229445703535 0.824375845018232 chr9 141213431 8052647 0.05702465369600714 0.6607850793828934 chr10 135534747 10694506 0.0789060092464702 0.6112941551548823 chr11 135006516 9920810 0.07348393465690205 0.5625943530234571 chr12 133851895 11827502 0.08836260405577373 0.46500906911869844 chr13 115169878 10649738 0.09246982097176486 0.497017007472632 chr14 107349540 7525866 0.07010617837766235 0.42326325671733167 chr15 102531392 5960115 0.05812966042634045 0.4059198474629366 chr16 90354753 5451303 0.0603322218146067 0.42336456956604407 chr17 81195210 6056569 0.07459268841105282 0.4847143841119567 chr18 78077248 8007341 0.10255665004996077 1.4289079319157767 chr19 59128983 5245573 0.08871407444974996 1.1140199933390973 chr20 63025520 5878398 0.09327012295971536 0.5053234555895144 chr21 48129895 2446878 0.05083904712445352 0.37707248506734753 chr22 51304566 2961902 0.05773174262891143 0.36073707350597517 chrMT 16571 390034 23.53714320197936 13.519956267286013 chrX 155270560 11100651 0.07149230993950173 0.4663309555741482 chrY 59373566 627212 0.010563825659385188 0.2747704204187811