BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238657.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,545,586 number of mapped reads = 1,706,273 (67.03%) number of supplementary alignments = 15,382 (0.6%) number of secondary alignments = 0 number of mapped bases = 99,992,671 bp number of sequenced bases = 99,949,415 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 868,976 duplication rate = 24.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.5968 >>>>>>> ACTG content number of A's = 24,583,176 bp (24.6%) number of C's = 16,531,833 bp (16.54%) number of T's = 34,708,847 bp (34.73%) number of G's = 24,123,311 bp (24.14%) number of N's = 2,248 bp (0%) GC percentage = 40.68% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 564,438 number of insertions = 6,578 mapped reads with insertion percentage = 0.38% number of deletions = 26,101 mapped reads with deletion percentage = 1.52% homopolymer indels = 42.11% >>>>>>> Coverage mean coverageData = 0.0323X std coverageData = 1.0344X There is a 0.72% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.32% of reference with a coverageData >= 3X There is a 0.27% of reference with a coverageData >= 4X There is a 0.22% of reference with a coverageData >= 5X There is a 0.19% of reference with a coverageData >= 6X There is a 0.16% of reference with a coverageData >= 7X There is a 0.13% of reference with a coverageData >= 8X There is a 0.11% of reference with a coverageData >= 9X There is a 0.1% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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 6194434 0.02485223095993811 0.7983901933808089 chr2 243199373 10099004 0.041525616926652194 1.0442592792761838 chr3 198022430 9468852 0.047817067995782093 2.981225939133703 chr4 191154276 2933459 0.015346028670580197 0.3896666597898772 chr5 180915260 11479673 0.0634533151045412 0.907666614581459 chr6 171115067 3088933 0.018051788507905033 0.5588097702240309 chr7 159138663 9580448 0.06020188821116337 0.9423834187994882 chr8 146364022 2343099 0.01600870875220961 0.495611437608627 chr9 141213431 3325871 0.023552086911619616 0.5086987045356017 chr10 135534747 6185030 0.04563427561494618 0.742336734304642 chr11 135006516 2166969 0.01605084750131616 0.4102035518799915 chr12 133851895 4498124 0.03360523211120769 0.630640926352723 chr13 115169878 3980337 0.03456057320821335 0.7074283824739263 chr14 107349540 1730300 0.016118373679104726 0.5203674714030331 chr15 102531392 1657122 0.01616209404432937 0.5042976770318819 chr16 90354753 5985437 0.0662437425953674 0.8668102129397633 chr17 81195210 1657799 0.020417448270655374 0.46298262432651904 chr18 78077248 4472941 0.057288661096251754 1.7191830142628448 chr19 59128983 827071 0.013987573572844978 0.4672766700320715 chr20 63025520 1027129 0.016297033328721445 0.4163804993997667 chr21 48129895 624855 0.012982679476030438 0.35873437127780217 chr22 51304566 909764 0.017732612726906218 0.4232297070220754 chrMT 16571 20851 1.258282541789874 3.539807989133313 chrX 155270560 5427922 0.03495783102733706 0.6191506933098125 chrY 59373566 307247 0.005174811295653018 0.24089364987539688