BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716232.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 = 558,577 number of mapped reads = 488,440 (87.44%) number of supplementary alignments = 1,736 (0.31%) number of secondary alignments = 0 number of mapped bases = 28,048,441 bp number of sequenced bases = 28,039,473 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,106 duplication rate = 1.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4875 >>>>>>> ACTG content number of A's = 7,254,929 bp (25.87%) number of C's = 4,948,915 bp (17.65%) number of T's = 8,872,142 bp (31.64%) number of G's = 6,962,897 bp (24.83%) number of N's = 590 bp (0%) GC percentage = 42.48% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 147,243 number of insertions = 2,056 mapped reads with insertion percentage = 0.42% number of deletions = 5,596 mapped reads with deletion percentage = 1.14% homopolymer indels = 40.8% >>>>>>> Coverage mean coverageData = 0.0091X std coverageData = 0.1197X There is a 0.85% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0% 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 2272698 0.009118123721745914 0.1578002290009725 chr2 243199373 2338902 0.009617220518080859 0.1658292786365392 chr3 198022430 1843567 0.009309889793797602 0.10058335005594822 chr4 191154276 1788879 0.00935829968041102 0.11075897055256836 chr5 180915260 1670237 0.009232151008157078 0.10057542534569637 chr6 171115067 1590117 0.009292676722617303 0.10568070777793105 chr7 159138663 1551549 0.00974966718175834 0.13255106756837362 chr8 146364022 1413133 0.009654920524116234 0.1347345152406865 chr9 141213431 1176735 0.008333024639844634 0.1043988655354821 chr10 135534747 1368164 0.010094562688046335 0.13085199238427161 chr11 135006516 1271101 0.009415108527058057 0.11040585340741901 chr12 133851895 1239761 0.009262184894730104 0.10230293485633349 chr13 115169878 884816 0.007682703284621001 0.09156131931865397 chr14 107349540 865712 0.008064422073909212 0.09439367031726797 chr15 102531392 808099 0.00788147887429442 0.09262507288860784 chr16 90354753 843125 0.00933127447097332 0.1045709509772733 chr17 81195210 786763 0.009689771108418834 0.10451704993874722 chr18 78077248 733166 0.009390264369973696 0.13301136686773377 chr19 59128983 609778 0.010312675257749655 0.13562846378990423 chr20 63025520 612958 0.009725552442883454 0.10410283362356879 chr21 48129895 363390 0.007550193076465261 0.09967291809344467 chr22 51304566 354358 0.0069069485940101314 0.08723078643339369 chrMT 16571 8593 0.5185565143926136 0.8014979158893861 chrX 155270560 1543074 0.009937968923406986 0.10790514941622094 chrY 59373566 109766 0.00184873517618935 0.09397091741781025