BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714249.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 361,044 number of mapped reads = 56,463 (15.64%) number of supplementary alignments = 933 (0.26%) number of secondary alignments = 0 number of mapped bases = 5,898,322 bp number of sequenced bases = 5,886,776 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 55,302 duplication rate = 32.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 11.2107 >>>>>>> ACTG content number of A's = 118,572 bp (2.01%) number of C's = 46,563 bp (0.79%) number of T's = 60,021 bp (1.02%) number of G's = 5,661,476 bp (96.17%) number of N's = 144 bp (0%) GC percentage = 96.96% >>>>>>> Mismatches and indels general error rate = 0.033 number of mismatches = 147,710 number of insertions = 6,825 mapped reads with insertion percentage = 8.24% number of deletions = 2,838 mapped reads with deletion percentage = 4.79% homopolymer indels = 63.05% >>>>>>> Coverage mean coverageData = 0.0019X std coverageData = 7.2576X There is a 0% of reference with a coverageData >= 1X There is a 0% 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 28979 1.1626450471310963E-4 0.17137735021635536 chr2 243199373 5691084 0.023400899146232584 25.892157676873445 chr3 198022430 7290 3.68140114228474E-5 0.013142164856756544 chr4 191154276 6593 3.449046570111777E-5 0.014647279530756839 chr5 180915260 5233 2.892514429131075E-5 0.007783671955712579 chr6 171115067 5631 3.2907680771325646E-5 0.01241722865712981 chr7 159138663 8752 5.499606340163861E-5 0.07237937687910143 chr8 146364022 4793 3.27471186874053E-5 0.01636429489835744 chr9 141213431 3222 2.281652656679661E-5 0.010891017533819972 chr10 135534747 19012 1.4027399187899764E-4 0.22259402744925527 chr11 135006516 5006 3.70796917683588E-5 0.020898337590030108 chr12 133851895 6665 4.979384117049669E-5 0.038046226084126236 chr13 115169878 2573 2.234091104967568E-5 0.009368788172528113 chr14 107349540 9062 8.441582516329366E-5 0.0857010115585883 chr15 102531392 3347 3.264366097750823E-5 0.012315419456905794 chr16 90354753 7872 8.71232529405509E-5 0.031992056319284624 chr17 81195210 6475 7.97460835435982E-5 0.06512783952548211 chr18 78077248 4005 5.129535303293477E-5 0.049584926902597554 chr19 59128983 2031 3.434863745246557E-5 0.007766889081679954 chr20 63025520 3453 5.4787330592433036E-5 0.014438424656444016 chr21 48129895 2166 4.500321473795029E-5 0.01357690965397984 chr22 51304566 878 1.7113486546207214E-5 0.004884386634172556 chrMT 16571 9066 0.5471003560436908 2.6305640369117307 chrX 155270560 50508 3.2529025463680947E-4 0.050442237629631875 chrY 59373566 4626 7.791346068046511E-5 0.021407445036708283