BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716519.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 = 1,009,137 number of mapped reads = 908,924 (90.07%) number of supplementary alignments = 4,568 (0.45%) number of secondary alignments = 0 number of mapped bases = 51,951,053 bp number of sequenced bases = 51,936,927 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,973 duplication rate = 1.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.4603 >>>>>>> ACTG content number of A's = 12,755,154 bp (24.56%) number of C's = 10,283,730 bp (19.8%) number of T's = 16,040,284 bp (30.88%) number of G's = 12,856,586 bp (24.75%) number of N's = 1,173 bp (0%) GC percentage = 44.55% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 253,890 number of insertions = 3,317 mapped reads with insertion percentage = 0.36% number of deletions = 8,308 mapped reads with deletion percentage = 0.91% homopolymer indels = 41.09% >>>>>>> Coverage mean coverageData = 0.0168X std coverageData = 0.1527X There is a 1.57% 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 6254776 0.025094324639616444 0.20623290350460072 chr2 243199373 4258260 0.017509337904419678 0.17045342521998644 chr3 198022430 3459659 0.01747104608301191 0.13904710979865795 chr4 191154276 3146141 0.016458648301437943 0.14045249568849152 chr5 180915260 2627767 0.014524849921449413 0.12697880472000386 chr6 171115067 2735558 0.01598665767988742 0.1368627382514993 chr7 159138663 2609575 0.01639812067542631 0.1450109882818241 chr8 146364022 3288160 0.022465630248941916 0.16560427130323663 chr9 141213431 1895309 0.01342159160483821 0.15096289971111748 chr10 135534747 2522340 0.01861028301473127 0.17388477095124416 chr11 135006516 2118356 0.015690768584828898 0.15524357957382356 chr12 133851895 2358686 0.017621610810963865 0.14009855704882335 chr13 115169878 846520 0.007350185783821009 0.08943795570866817 chr14 107349540 1254004 0.01168150324631107 0.1193734608926019 chr15 102531392 1621370 0.01581340083630192 0.13257635325904166 chr16 90354753 1730703 0.019154531914884435 0.15218021648853688 chr17 81195210 1407216 0.017331268679519396 0.14026980723859958 chr18 78077248 1288591 0.016504052499391374 0.22796926003749346 chr19 59128983 1030362 0.017425667544459542 0.16672671634436206 chr20 63025520 1205428 0.01912603021760074 0.14582958988090117 chr21 48129895 655051 0.013610065012608068 0.12803338455312713 chr22 51304566 773264 0.015072030820804527 0.12956784977608451 chrMT 16571 1202 0.07253635869893187 0.29116196173872677 chrX 155270560 2720801 0.017522967650789693 0.14685987659978508 chrY 59373566 141954 0.002390861953617541 0.0632719956722222