BamQC report ----------------------------------- >>>>>>> Input bam file = SRR16328250.sorted.bam outfile = /mainsd2/zhouyj/SRP341378/SRP341378.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 = 726,500,714 number of mapped reads = 712,689,196 (98.1%) number of supplementary alignments = 31,298,934 (4.31%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 358,720,128 number of mapped paired reads (second in pair) = 353,969,068 number of mapped paired reads (both in pair) = 704,547,030 number of mapped paired reads (singletons) = 8,142,166 number of mapped bases = 98,470,206,963 bp number of sequenced bases = 98,388,671,944 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 279,823,787 duplication rate = 31.81% >>>>>>> Insert size mean insert size = 185,359.902 std insert size = 4,172,750.265 median insert size = 404 >>>>>>> Mapping quality mean mapping quality = 53.5767 >>>>>>> ACTG content number of A's = 28,338,120,307 bp (28.8%) number of C's = 20,196,685,694 bp (20.53%) number of T's = 28,076,083,564 bp (28.54%) number of G's = 21,776,004,838 bp (22.13%) number of N's = 1,777,541 bp (0%) GC percentage = 42.66% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 916,558,053 number of insertions = 18,122,933 mapped reads with insertion percentage = 2.42% number of deletions = 44,832,590 mapped reads with deletion percentage = 6.03% homopolymer indels = 44.32% >>>>>>> Coverage mean coverageData = 31.8088X std coverageData = 1,659.1312X There is a 91.68% of reference with a coverageData >= 1X There is a 91.56% of reference with a coverageData >= 2X There is a 91.45% of reference with a coverageData >= 3X There is a 91.31% of reference with a coverageData >= 4X There is a 91.12% of reference with a coverageData >= 5X There is a 90.86% of reference with a coverageData >= 6X There is a 90.53% of reference with a coverageData >= 7X There is a 90.1% of reference with a coverageData >= 8X There is a 89.56% of reference with a coverageData >= 9X There is a 88.89% of reference with a coverageData >= 10X There is a 88.08% of reference with a coverageData >= 11X There is a 87.09% of reference with a coverageData >= 12X There is a 85.91% of reference with a coverageData >= 13X There is a 84.52% of reference with a coverageData >= 14X There is a 82.93% of reference with a coverageData >= 15X There is a 81.13% of reference with a coverageData >= 16X There is a 79.13% of reference with a coverageData >= 17X There is a 76.94% of reference with a coverageData >= 18X There is a 74.6% of reference with a coverageData >= 19X There is a 72.13% of reference with a coverageData >= 20X There is a 69.55% of reference with a coverageData >= 21X There is a 66.88% of reference with a coverageData >= 22X There is a 64.15% of reference with a coverageData >= 23X There is a 61.38% of reference with a coverageData >= 24X There is a 58.58% of reference with a coverageData >= 25X There is a 55.79% of reference with a coverageData >= 26X There is a 53% of reference with a coverageData >= 27X There is a 50.24% of reference with a coverageData >= 28X There is a 47.51% of reference with a coverageData >= 29X There is a 44.84% of reference with a coverageData >= 30X There is a 42.22% of reference with a coverageData >= 31X There is a 39.67% of reference with a coverageData >= 32X There is a 37.21% of reference with a coverageData >= 33X There is a 34.83% of reference with a coverageData >= 34X There is a 32.53% of reference with a coverageData >= 35X There is a 30.34% of reference with a coverageData >= 36X There is a 28.25% of reference with a coverageData >= 37X There is a 26.27% of reference with a coverageData >= 38X There is a 24.39% of reference with a coverageData >= 39X There is a 22.61% of reference with a coverageData >= 40X There is a 20.94% of reference with a coverageData >= 41X There is a 19.37% of reference with a coverageData >= 42X There is a 17.91% of reference with a coverageData >= 43X There is a 16.54% of reference with a coverageData >= 44X There is a 15.27% of reference with a coverageData >= 45X There is a 14.09% of reference with a coverageData >= 46X There is a 13% of reference with a coverageData >= 47X There is a 12% of reference with a coverageData >= 48X There is a 11.07% of reference with a coverageData >= 49X There is a 10.21% of reference with a coverageData >= 50X There is a 9.43% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7723528636 30.986998567999557 785.4263901175956 chr2 243199373 9246739225 38.021229705226254 5791.9961098346175 chr3 198022430 7045408589 35.57884118985915 42.04347511000937 chr4 191154276 5480057543 28.668244612011712 173.74855482777764 chr5 180915260 6587148061 36.4101295877418 21.157317795874853 chr6 171115067 4664551206 27.259733977721552 124.14514265595282 chr7 159138663 6676809081 41.95592042268195 210.2691762027791 chr8 146364022 5543196036 37.87266816157867 582.9917630712843 chr9 141213431 3258056264 23.071858256882095 337.4779056471989 chr10 135534747 4888383172 36.06737962184708 706.9054720911481 chr11 135006516 3432401724 25.42397082523039 118.50558196144242 chr12 133851895 4796165900 35.8318864294002 68.2276355018779 chr13 115169878 2478372216 21.519274475570775 21.336466580688498 chr14 107349540 3637151131 33.88138534175368 45.74024513897409 chr15 102531392 3097734818 30.212550103679465 32.45795352550156 chr16 90354753 3306223292 36.59158131946861 263.34411320912585 chr17 81195210 3484788946 42.91865180224301 143.13547331002246 chr18 78077248 2427644228 31.092850864825564 334.760570788835 chr19 59128983 1830414151 30.95629348132032 439.9970659056589 chr20 63025520 3429935509 54.42137580142139 105.57727888623788 chr21 48129895 1124557601 23.36505411034036 81.97259658113862 chr22 51304566 947907283 18.47608033561769 24.18686396431327 chrMT 16571 632967534 38197.30456822159 6135.55338532927 chrX 155270560 2491844721 16.048404288617238 44.5703527402757 chrY 59373566 238220096 4.012224834196417 199.33914568820455