BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068077.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 = 2,446,800 number of mapped reads = 1,779,897 (72.74%) number of supplementary alignments = 17,770 (0.73%) number of secondary alignments = 0 number of mapped bases = 109,879,985 bp number of sequenced bases = 109,836,364 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 311,866 duplication rate = 13.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8988 >>>>>>> ACTG content number of A's = 28,100,595 bp (25.58%) number of C's = 20,145,192 bp (18.34%) number of T's = 34,940,639 bp (31.81%) number of G's = 26,647,938 bp (24.26%) number of N's = 2,000 bp (0%) GC percentage = 42.6% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 901,800 number of insertions = 7,719 mapped reads with insertion percentage = 0.43% number of deletions = 27,812 mapped reads with deletion percentage = 1.55% homopolymer indels = 45.16% >>>>>>> Coverage mean coverageData = 0.0355X std coverageData = 0.4062X There is a 1.94% of reference with a coverageData >= 1X There is a 0.79% of reference with a coverageData >= 2X There is a 0.37% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 11807716 0.047372864920565236 0.5250704931807142 chr2 243199373 7894321 0.03246028516693585 0.7515920568680675 chr3 198022430 4819588 0.024338596390318008 0.2619536331919879 chr4 191154276 4396438 0.02299942272805867 0.2843776394433159 chr5 180915260 6179722 0.03415810252822233 0.3144964810178158 chr6 171115067 4539069 0.026526413363704555 0.3173898206035295 chr7 159138663 5023579 0.03156730680840268 0.3692663063918037 chr8 146364022 3519202 0.024044173915909472 0.3234160320814296 chr9 141213431 3093611 0.021907342510501002 0.3011779591293161 chr10 135534747 10795803 0.07965339692558691 0.49483330519384533 chr11 135006516 3106640 0.023011037482072345 0.26625043273404614 chr12 133851895 4180133 0.031229539185829235 0.30139029867502687 chr13 115169878 3907943 0.03393198870975621 0.3232638187536412 chr14 107349540 2095813 0.019523260183508938 0.27490195992806815 chr15 102531392 4576911 0.0446391189149173 0.3997210091489935 chr16 90354753 2160223 0.023908238673398842 0.2659454854968378 chr17 81195210 5583185 0.0687624922701721 0.4472530983160038 chr18 78077248 2182454 0.027952496481433362 0.35893550631650895 chr19 59128983 1701018 0.02876792249242643 0.39905138510892335 chr20 63025520 2280374 0.03618175621557743 0.32735415647167687 chr21 48129895 2703363 0.056168063528914826 0.417168178064592 chr22 51304566 2580715 0.0503018581231152 0.3827704202213044 chrMT 16571 51166 3.087683302154366 3.055729953176123 chrX 155270560 10341042 0.06660014622218147 0.4555000456873517 chrY 59373566 359956 0.006062563262580522 0.1331668347891961