BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525057.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 = 1,152,567 number of mapped reads = 1,070,576 (92.89%) number of supplementary alignments = 5,207 (0.45%) number of secondary alignments = 0 number of mapped bases = 64,563,070 bp number of sequenced bases = 64,542,004 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 43,438 duplication rate = 3.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3408 >>>>>>> ACTG content number of A's = 17,047,975 bp (26.41%) number of C's = 12,665,233 bp (19.62%) number of T's = 19,667,799 bp (30.47%) number of G's = 15,153,450 bp (23.48%) number of N's = 7,547 bp (0.01%) GC percentage = 43.1% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 300,299 number of insertions = 3,948 mapped reads with insertion percentage = 0.37% number of deletions = 12,965 mapped reads with deletion percentage = 1.2% homopolymer indels = 43.59% >>>>>>> Coverage mean coverageData = 0.0209X std coverageData = 0.2061X There is a 1.89% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% 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 5235372 0.02100444917246565 0.34119880236173844 chr2 243199373 5632721 0.02316091908674452 0.24194994763197028 chr3 198022430 4476497 0.022606009834340482 0.16211734082641266 chr4 191154276 4335335 0.02267976992573266 0.175192444473624 chr5 180915260 4059634 0.022439422744106825 0.16135335161681358 chr6 171115067 3863810 0.022580185764705336 0.17264284353378256 chr7 159138663 3650128 0.022936776840961647 0.24257130902581484 chr8 146364022 3402868 0.02324934743867588 0.25066946613454727 chr9 141213431 2766724 0.019592498959960826 0.17487846502670853 chr10 135534747 3177550 0.0234445414945881 0.22842048757950936 chr11 135006516 3011645 0.022307404777410892 0.18066620236472686 chr12 133851895 2990178 0.022339452123557906 0.16337167455399768 chr13 115169878 2130452 0.01849834381173869 0.1463538616513809 chr14 107349540 2008033 0.018705557564568976 0.15172423208553662 chr15 102531392 1874982 0.018286906706582118 0.14573466855409456 chr16 90354753 1881980 0.020828788055012447 0.1637366766297268 chr17 81195210 1732298 0.021334977765313987 0.16319532792854693 chr18 78077248 1759164 0.022531070767248355 0.2786687320067264 chr19 59128983 1282811 0.021695130457427284 0.2740764235609915 chr20 63025520 1392934 0.022101110788137885 0.1629562704041772 chr21 48129895 884404 0.01837535693772031 0.15437439275806197 chr22 51304566 762320 0.014858716473695539 0.13020262877939245 chrMT 16571 13668 0.8248144348560739 1.1157994612043525 chrX 155270560 2052687 0.013220065671174239 0.1318526422000487 chrY 59373566 184875 0.0031137594127325957 0.11804905802162256