BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525189.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 = 2,098,522 number of mapped reads = 1,909,425 (90.99%) number of supplementary alignments = 5,039 (0.24%) number of secondary alignments = 0 number of mapped bases = 108,767,024 bp number of sequenced bases = 108,733,044 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 82,210 duplication rate = 3.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3504 >>>>>>> ACTG content number of A's = 26,313,008 bp (24.2%) number of C's = 18,490,530 bp (17.01%) number of T's = 36,803,067 bp (33.85%) number of G's = 27,123,898 bp (24.95%) number of N's = 2,541 bp (0%) GC percentage = 41.95% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 573,929 number of insertions = 7,572 mapped reads with insertion percentage = 0.39% number of deletions = 21,396 mapped reads with deletion percentage = 1.11% homopolymer indels = 42.99% >>>>>>> Coverage mean coverageData = 0.0351X std coverageData = 0.3455X There is a 3.12% of reference with a coverageData >= 1X There is a 0.28% of reference with a coverageData >= 2X There is a 0.04% 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 12216798 0.04901411258670445 0.6081004297197456 chr2 243199373 8566975 0.03522613933712732 0.4817594115178545 chr3 198022430 6744350 0.034058515492411644 0.20819517072710902 chr4 191154276 5651418 0.029564695691139026 0.20272391149933322 chr5 180915260 4751193 0.026261980332670666 0.18133274860155227 chr6 171115067 6557626 0.03832290233097942 0.24893030598903654 chr7 159138663 7974016 0.0501073456926052 0.6314595945078604 chr8 146364022 7047817 0.04815266008473038 0.32722384461006304 chr9 141213431 3456569 0.024477622103806825 0.23791582763841446 chr10 135534747 7242577 0.053437049615033407 0.38516186858599116 chr11 135006516 4926809 0.03649312008021894 0.28313129401268217 chr12 133851895 4636250 0.034637163709934776 0.2087094570793404 chr13 115169878 3325413 0.028873982136197105 0.19024298290660985 chr14 107349540 2485693 0.023155134153346163 0.17503169663947563 chr15 102531392 2935064 0.028626003634087013 0.1936320583282626 chr16 90354753 2670327 0.0295538077559683 0.21839058148181728 chr17 81195210 1870139 0.023032627170987058 0.17577784340844507 chr18 78077248 2303071 0.029497338328318128 0.47755373891334624 chr19 59128983 2071088 0.03502661292178829 0.4319736341362867 chr20 63025520 1957843 0.031064289513200366 0.1996657590163082 chr21 48129895 1798782 0.03737348689416422 0.22553673726706525 chr22 51304566 1186246 0.023121645742018363 0.16722493075472608 chrMT 16571 9459 0.570816486633275 0.8445650313993174 chrX 155270560 6043726 0.038923837203910384 0.24246716577685032 chrY 59373566 337775 0.005688979503100757 0.14212198337120077