BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716485.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 = 656,491 number of mapped reads = 390,566 (59.49%) number of supplementary alignments = 1,715 (0.26%) number of secondary alignments = 0 number of mapped bases = 22,270,130 bp number of sequenced bases = 22,263,992 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,198 duplication rate = 1.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3977 >>>>>>> ACTG content number of A's = 5,678,874 bp (25.51%) number of C's = 4,240,105 bp (19.04%) number of T's = 7,065,128 bp (31.73%) number of G's = 5,279,571 bp (23.71%) number of N's = 314 bp (0%) GC percentage = 42.76% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 112,693 number of insertions = 1,498 mapped reads with insertion percentage = 0.38% number of deletions = 3,981 mapped reads with deletion percentage = 1.01% homopolymer indels = 40.23% >>>>>>> Coverage mean coverageData = 0.0072X std coverageData = 0.1007X There is a 0.69% of reference with a coverageData >= 1X There is a 0.02% 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 1834827 0.0073613738358549565 0.14275008816346207 chr2 243199373 1876941 0.00771770493010276 0.12740262645970424 chr3 198022430 1462826 0.007387173261130065 0.08885349072167256 chr4 191154276 1442739 0.0075475109957780905 0.09187250035253243 chr5 180915260 1350625 0.007465511753955968 0.0891907618897594 chr6 171115067 1268490 0.00741308186496517 0.09315543598767691 chr7 159138663 1227730 0.007714844255038136 0.11026180797161853 chr8 146364022 1108381 0.007572769488392441 0.09601486273427155 chr9 141213431 917696 0.006498645302372124 0.08918774426273343 chr10 135534747 1091786 0.00805539556583228 0.10253900172692933 chr11 135006516 991138 0.007341408617640352 0.09531845783354428 chr12 133851895 1013072 0.0075686040903642044 0.09004782139667 chr13 115169878 706878 0.00613769860900608 0.08082776231907132 chr14 107349540 653848 0.006090831875013158 0.0817785444810415 chr15 102531392 656847 0.006406301398892546 0.08259867523248894 chr16 90354753 651948 0.00721542562348657 0.08837690742972502 chr17 81195210 610314 0.007516625672869126 0.09071117305086301 chr18 78077248 577795 0.007400299252350698 0.11643629879693077 chr19 59128983 486022 0.008219691517440779 0.11894647798955855 chr20 63025520 470838 0.007470592864604687 0.08946180277998578 chr21 48129895 290519 0.006036144479434248 0.08225581917156088 chr22 51304566 270053 0.005263722531051135 0.07486100811009577 chrMT 16571 8583 0.517953050509927 0.8202626994593095 chrX 155270560 1231410 0.007930737159703681 0.0953609081010317 chrY 59373566 68824 0.0011591690483943645 0.042244573901434664