BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524821.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 = 1,727,985 number of mapped reads = 1,555,297 (90.01%) number of supplementary alignments = 4,798 (0.28%) number of secondary alignments = 0 number of mapped bases = 88,127,960 bp number of sequenced bases = 88,101,276 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,756 duplication rate = 3.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6303 >>>>>>> ACTG content number of A's = 22,388,758 bp (25.41%) number of C's = 15,438,972 bp (17.52%) number of T's = 27,843,545 bp (31.6%) number of G's = 22,419,656 bp (25.45%) number of N's = 10,345 bp (0.01%) GC percentage = 42.97% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 448,761 number of insertions = 6,155 mapped reads with insertion percentage = 0.39% number of deletions = 16,692 mapped reads with deletion percentage = 1.06% homopolymer indels = 42.19% >>>>>>> Coverage mean coverageData = 0.0285X std coverageData = 0.2461X There is a 2.5% of reference with a coverageData >= 1X There is a 0.25% 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 7056691 0.02831162855959344 0.2740595776061833 chr2 243199373 7354935 0.030242409383185374 0.4180949945880459 chr3 198022430 5752995 0.02905223918320768 0.19372319456546966 chr4 191154276 5557377 0.029072731807474713 0.2220805983072458 chr5 180915260 5171174 0.028583404186026097 0.18835791341953032 chr6 171115067 4950813 0.028932653838133378 0.2105292424129439 chr7 159138663 4858739 0.030531480586838914 0.28797474378446036 chr8 146364022 4386402 0.029969127249044852 0.21634118916918008 chr9 141213431 3761794 0.02663906664798761 0.21374238746854946 chr10 135534747 4292757 0.03167274145573902 0.3064742290812299 chr11 135006516 4013548 0.02972855028715799 0.23176242775452557 chr12 133851895 3948055 0.029495697464723976 0.19366710620929461 chr13 115169878 2784071 0.024173603795950883 0.17322127855053082 chr14 107349540 2663444 0.024810949352926895 0.17853216480888467 chr15 102531392 2561509 0.024982680426303 0.1798655725791208 chr16 90354753 2731678 0.03023280911409276 0.2157194321851169 chr17 81195210 2576475 0.031731859551813464 0.2083560871345068 chr18 78077248 2310460 0.029591975372902486 0.31075811113666635 chr19 59128983 1976855 0.03343292746976555 0.2570522870315044 chr20 63025520 1953970 0.03100283821537688 0.2080418943297073 chr21 48129895 1167043 0.02424777781044401 0.19443511782524184 chr22 51304566 1160383 0.0226175385637216 0.17138856688376514 chrMT 16571 10826 0.6533099993965361 0.9821675342767695 chrX 155270560 4815510 0.03101367058893843 0.21466604887873406 chrY 59373566 310456 0.0052288589167778805 0.1485586109958211