BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716902.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 = 957,218 number of mapped reads = 827,769 (86.48%) number of supplementary alignments = 2,888 (0.3%) number of secondary alignments = 0 number of mapped bases = 46,705,323 bp number of sequenced bases = 46,691,684 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,654 duplication rate = 1.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.908 >>>>>>> ACTG content number of A's = 10,806,160 bp (23.14%) number of C's = 10,171,649 bp (21.78%) number of T's = 13,591,833 bp (29.11%) number of G's = 12,120,638 bp (25.96%) number of N's = 1,404 bp (0%) GC percentage = 47.74% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 245,573 number of insertions = 3,728 mapped reads with insertion percentage = 0.45% number of deletions = 8,076 mapped reads with deletion percentage = 0.96% homopolymer indels = 34.37% >>>>>>> Coverage mean coverageData = 0.0151X std coverageData = 0.1513X There is a 1.39% of reference with a coverageData >= 1X There is a 0.09% of reference with a coverageData >= 2X There is a 0.01% 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 4617823 0.018526826458739293 0.182105654401967 chr2 243199373 4058943 0.016689775758591284 0.18087870041262527 chr3 198022430 3211357 0.01621713762425802 0.14011853820351491 chr4 191154276 2792062 0.014606327718245759 0.14968015945630536 chr5 180915260 2671542 0.014766814032160692 0.13008075999324134 chr6 171115067 2055679 0.012013430705082212 0.12011988250496455 chr7 159138663 2720651 0.017096103163817582 0.16798735470428083 chr8 146364022 2701460 0.018457131493694535 0.1516902351673394 chr9 141213431 2034021 0.014403877772787774 0.1357254613471348 chr10 135534747 2489442 0.018367555590744565 0.2270439791475734 chr11 135006516 2023210 0.01498601741563348 0.14957330064615101 chr12 133851895 2268557 0.016948262107159558 0.1403209887639105 chr13 115169878 831460 0.007219422425714474 0.09144501755655747 chr14 107349540 1491224 0.013891293805264559 0.12884247129738544 chr15 102531392 945974 0.009226188990002203 0.10316846585814983 chr16 90354753 1277034 0.01413355642729719 0.13581765717854938 chr17 81195210 1941968 0.023917272952431554 0.1745170137201265 chr18 78077248 1242214 0.015910063838315613 0.16809932795597113 chr19 59128983 1277223 0.021600625195938174 0.18293879006836122 chr20 63025520 1222018 0.01938925692322729 0.1556234774133627 chr21 48129895 649276 0.013490077217080985 0.14393295225773828 chr22 51304566 541416 0.010552978851823831 0.11292134159398559 chrMT 16571 32105 1.9374207953653975 1.9928812449948599 chrX 155270560 1452929 0.009357401686449768 0.10774695141392786 chrY 59373566 155735 0.0026229686119914036 0.09400871242609966