BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716353.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 = 1,060,329 number of mapped reads = 987,165 (93.1%) number of supplementary alignments = 20,158 (1.9%) number of secondary alignments = 0 number of mapped bases = 77,859,954 bp number of sequenced bases = 77,825,978 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,680 duplication rate = 1.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.268 >>>>>>> ACTG content number of A's = 20,453,134 bp (26.28%) number of C's = 15,643,879 bp (20.1%) number of T's = 23,495,999 bp (30.19%) number of G's = 18,227,601 bp (23.42%) number of N's = 5,365 bp (0.01%) GC percentage = 43.52% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 500,554 number of insertions = 6,084 mapped reads with insertion percentage = 0.61% number of deletions = 17,861 mapped reads with deletion percentage = 1.78% homopolymer indels = 43.83% >>>>>>> Coverage mean coverageData = 0.0252X std coverageData = 0.2543X There is a 2.27% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 7560641 0.03033348911896994 0.49531052704331074 chr2 243199373 6297562 0.025894647351742968 0.27125803696259176 chr3 198022430 4961032 0.025052879110714882 0.16919678435165353 chr4 191154276 5063167 0.02648733319468093 0.21014267900651112 chr5 180915260 4482678 0.02477777717589992 0.16876234960662986 chr6 171115067 4307004 0.025170220691319953 0.1811083124302583 chr7 159138663 4048576 0.02544055557385197 0.28008733124430457 chr8 146364022 3817799 0.02608427226740189 0.27604248994041053 chr9 141213431 3158086 0.02236392089361528 0.22244396553156923 chr10 135534747 3603368 0.02658630410104355 0.25793772997251124 chr11 135006516 4295061 0.03181373112391109 0.28664288760232876 chr12 133851895 3417440 0.025531502561095605 0.17205390465227252 chr13 115169878 2726168 0.02367084212766119 0.16516549258212443 chr14 107349540 2207339 0.02056216542707123 0.16241730058338258 chr15 102531392 2128500 0.02075949578447155 0.1540156634572509 chr16 90354753 1743689 0.019298254293274423 0.15786427465126188 chr17 81195210 2489059 0.030655244317983783 0.2171217312895289 chr18 78077248 2023420 0.025915616288115072 0.33811037782133196 chr19 59128983 1510143 0.025539810146912218 0.32557073417533583 chr20 63025520 1608046 0.025514204404818875 0.17821151405256186 chr21 48129895 1031791 0.021437632473538536 0.17399385947312843 chr22 51304566 879515 0.01714301608164856 0.14156422646713354 chrMT 16571 26784 1.6163176633878462 1.5631789745433107 chrX 155270560 4240101 0.02730782319584601 0.19975085273656348 chrY 59373566 232985 0.003924052666804618 0.137084385289706