BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524700.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 = 1,691,402 number of mapped reads = 1,549,825 (91.63%) number of supplementary alignments = 6,611 (0.39%) number of secondary alignments = 0 number of mapped bases = 89,818,050 bp number of sequenced bases = 89,787,410 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 57,977 duplication rate = 2.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2667 >>>>>>> ACTG content number of A's = 22,426,767 bp (24.98%) number of C's = 17,747,012 bp (19.77%) number of T's = 29,514,643 bp (32.87%) number of G's = 20,097,099 bp (22.38%) number of N's = 1,889 bp (0%) GC percentage = 42.15% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 455,647 number of insertions = 7,006 mapped reads with insertion percentage = 0.45% number of deletions = 19,370 mapped reads with deletion percentage = 1.24% homopolymer indels = 43.64% >>>>>>> Coverage mean coverageData = 0.029X std coverageData = 0.2929X There is a 2.63% of reference with a coverageData >= 1X There is a 0.19% 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 9776528 0.03922368562524063 0.5764162081329517 chr2 243199373 7689053 0.03161625338565326 0.3832783869876096 chr3 198022430 7210704 0.03641357193728004 0.20765339929331694 chr4 191154276 5274335 0.02759203252141741 0.189858516150053 chr5 180915260 4163748 0.023014907642395672 0.1645282927410203 chr6 171115067 4633051 0.02707564612063063 0.2039476422796928 chr7 159138663 5377779 0.03379303871617924 0.41518530766589756 chr8 146364022 4273650 0.02919877399925509 0.2864251788862962 chr9 141213431 3010429 0.021318290892599304 0.2060368550003432 chr10 135534747 4939645 0.036445598706876255 0.2954168231932987 chr11 135006516 4250691 0.03148508032012322 0.24092971087211845 chr12 133851895 4134834 0.03089111289757982 0.1924661433157588 chr13 115169878 2931054 0.02544983159572332 0.17422097811743 chr14 107349540 3415797 0.0318193911217505 0.196240044928636 chr15 102531392 2504217 0.024423905217243125 0.1699358658536095 chr16 90354753 2397068 0.026529517489799346 0.19389851243819894 chr17 81195210 1761199 0.021690922407861253 0.16562157780663725 chr18 78077248 1965004 0.025167434180057166 0.39505205912027064 chr19 59128983 1570442 0.026559597684945806 0.3889554253127421 chr20 63025520 1639489 0.026013097551594973 0.17647482954273278 chr21 48129895 1173079 0.024373188431015692 0.17910989606165537 chr22 51304566 720505 0.014043681804071785 0.12680920976596072 chrMT 16571 5529 0.3336551807374329 0.6405060922217037 chrX 155270560 4730338 0.030465131316586996 0.20550872000586737 chrY 59373566 269882 0.004545490833412297 0.14197693541921702