BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716177.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 = 433,173 number of mapped reads = 397,302 (91.72%) number of supplementary alignments = 8,110 (1.87%) number of secondary alignments = 0 number of mapped bases = 31,316,081 bp number of sequenced bases = 31,302,337 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,796 duplication rate = 1.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.4179 >>>>>>> ACTG content number of A's = 7,816,796 bp (24.97%) number of C's = 6,206,430 bp (19.83%) number of T's = 9,924,533 bp (31.71%) number of G's = 7,352,460 bp (23.49%) number of N's = 2,118 bp (0.01%) GC percentage = 43.32% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 203,289 number of insertions = 2,774 mapped reads with insertion percentage = 0.69% number of deletions = 6,974 mapped reads with deletion percentage = 1.73% homopolymer indels = 41.58% >>>>>>> Coverage mean coverageData = 0.0101X std coverageData = 0.1339X There is a 0.96% of reference with a coverageData >= 1X There is a 0.03% 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 3213118 0.012891113318429806 0.25615535094723885 chr2 243199373 2675177 0.010999933786835872 0.13635102325094142 chr3 198022430 2024899 0.010225604240893317 0.10397118389188621 chr4 191154276 2047892 0.010713294218958513 0.11287677091112708 chr5 180915260 1902600 0.010516525803295974 0.10573465753088968 chr6 171115067 1828740 0.010687194482996638 0.1083429355371476 chr7 159138663 1701116 0.010689520496976903 0.15064838820784865 chr8 146364022 1641199 0.011213131325401813 0.14537876991396173 chr9 141213431 747731 0.0052950416593163865 0.0896058087553281 chr10 135534747 1479327 0.010914743508541025 0.1280618728471849 chr11 135006516 1524725 0.011293714149322986 0.1225954685138744 chr12 133851895 1433527 0.010709799812695965 0.10650728532747478 chr13 115169878 1161125 0.01008184622718798 0.10334554429629172 chr14 107349540 513328 0.004781836978528273 0.07535642085473462 chr15 102531392 912910 0.008903712143106377 0.09705064128176735 chr16 90354753 742424 0.008216767523010107 0.09622477165864245 chr17 81195210 979943 0.012068975497446217 0.11795339398191933 chr18 78077248 841389 0.010776365990768528 0.15350818171726274 chr19 59128983 653214 0.01104727270550214 0.18063370494761022 chr20 63025520 671615 0.01065623893305442 0.1094262637953036 chr21 48129895 419013 0.008705878124188719 0.10002523965650527 chr22 51304566 359139 0.007000137180772565 0.08639398595533054 chrMT 16571 1395 0.08418321163478366 0.31512516465129303 chrX 155270560 1742704 0.011223660170994423 0.11389702498677858 chrY 59373566 97831 0.001647719795034713 0.06377487459796903