BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716476.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 = 1,802,256 number of mapped reads = 1,666,769 (92.48%) number of supplementary alignments = 9,694 (0.54%) number of secondary alignments = 0 number of mapped bases = 97,539,824 bp number of sequenced bases = 97,513,601 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 78,152 duplication rate = 3.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.641 >>>>>>> ACTG content number of A's = 24,876,007 bp (25.51%) number of C's = 20,339,877 bp (20.86%) number of T's = 29,145,970 bp (29.89%) number of G's = 23,151,057 bp (23.74%) number of N's = 690 bp (0%) GC percentage = 44.6% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 463,887 number of insertions = 5,368 mapped reads with insertion percentage = 0.32% number of deletions = 16,787 mapped reads with deletion percentage = 1% homopolymer indels = 44.5% >>>>>>> Coverage mean coverageData = 0.0315X std coverageData = 0.2703X There is a 2.74% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 11124558 0.04463201718562619 0.3875187391310754 chr2 243199373 10048434 0.04131768053530303 0.3859005367715855 chr3 198022430 5207002 0.026295011125759844 0.1815086588107225 chr4 191154276 4244945 0.02220690579791163 0.1839587899471133 chr5 180915260 7528024 0.04161077401652022 0.23020414320704635 chr6 171115067 2816827 0.016461595401181126 0.16542069558340178 chr7 159138663 6936673 0.043588860615223345 0.46290116846004226 chr8 146364022 3651590 0.024948685818431526 0.2261226008798155 chr9 141213431 2822258 0.019985761835926215 0.2071080668927769 chr10 135534747 4599337 0.033934744423878255 0.24152626951588513 chr11 135006516 4446560 0.03293589177577177 0.26544701764554296 chr12 133851895 3891514 0.029073282825020894 0.1925855853915128 chr13 115169878 3036219 0.02636296098186368 0.1821826117149557 chr14 107349540 2215817 0.02064114107987794 0.16890378651441523 chr15 102531392 3698140 0.03606836821253729 0.2131954236937855 chr16 90354753 3107589 0.034393198994191264 0.21941163630381574 chr17 81195210 3909902 0.04815434309486976 0.2681889992321474 chr18 78077248 3142980 0.04025474873294715 0.41438302012792094 chr19 59128983 1637046 0.02768601651748348 0.31070102099500135 chr20 63025520 2783448 0.04416382443175399 0.23884672522017697 chr21 48129895 1308806 0.027193202893960187 0.19433124918542655 chr22 51304566 1242608 0.024220222426206667 0.1744812109703948 chrMT 16571 96157 5.8027276567497434 4.319717402471207 chrX 155270560 3825791 0.024639513118262728 0.19419550574222194 chrY 59373566 217599 0.003664913776612306 0.08939514926639731