BamQC report ----------------------------------- >>>>>>> Input bam file = SRR21671997.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP398595/SRP398595.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 = 303,531,990 number of mapped reads = 294,873,216 (97.15%) number of supplementary alignments = 1,226,045 (0.4%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 147,468,611 number of mapped paired reads (second in pair) = 147,404,605 number of mapped paired reads (both in pair) = 294,358,612 number of mapped paired reads (singletons) = 514,604 number of mapped bases = 43,767,097,941 bp number of sequenced bases = 43,749,334,937 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 109,450,257 duplication rate = 34.82% >>>>>>> Insert size mean insert size = 25,913.328 std insert size = 1,483,254.2894 median insert size = 307 >>>>>>> Mapping quality mean mapping quality = 54.5801 >>>>>>> ACTG content number of A's = 12,775,152,958 bp (29.2%) number of C's = 9,130,386,868 bp (20.87%) number of T's = 12,672,062,638 bp (28.97%) number of G's = 9,171,358,709 bp (20.96%) number of N's = 373,764 bp (0%) GC percentage = 41.83% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 286,344,297 number of insertions = 5,977,147 mapped reads with insertion percentage = 1.92% number of deletions = 6,535,511 mapped reads with deletion percentage = 2.13% homopolymer indels = 45.76% >>>>>>> Coverage mean coverageData = 14.1381X std coverageData = 140.7622X There is a 92.16% of reference with a coverageData >= 1X There is a 91.83% of reference with a coverageData >= 2X There is a 91.24% of reference with a coverageData >= 3X There is a 90.29% of reference with a coverageData >= 4X There is a 88.86% of reference with a coverageData >= 5X There is a 86.86% of reference with a coverageData >= 6X There is a 84.2% of reference with a coverageData >= 7X There is a 80.84% of reference with a coverageData >= 8X There is a 76.78% of reference with a coverageData >= 9X There is a 72.05% of reference with a coverageData >= 10X There is a 66.76% of reference with a coverageData >= 11X There is a 61.05% of reference with a coverageData >= 12X There is a 55.08% of reference with a coverageData >= 13X There is a 49.02% of reference with a coverageData >= 14X There is a 43.05% of reference with a coverageData >= 15X There is a 37.31% of reference with a coverageData >= 16X There is a 31.92% of reference with a coverageData >= 17X There is a 26.99% of reference with a coverageData >= 18X There is a 22.55% of reference with a coverageData >= 19X There is a 18.64% of reference with a coverageData >= 20X There is a 15.26% of reference with a coverageData >= 21X There is a 12.37% of reference with a coverageData >= 22X There is a 9.95% of reference with a coverageData >= 23X There is a 7.95% of reference with a coverageData >= 24X There is a 6.31% of reference with a coverageData >= 25X There is a 4.99% of reference with a coverageData >= 26X There is a 3.93% of reference with a coverageData >= 27X There is a 3.09% of reference with a coverageData >= 28X There is a 2.44% of reference with a coverageData >= 29X There is a 1.93% of reference with a coverageData >= 30X There is a 1.54% of reference with a coverageData >= 31X There is a 1.23% of reference with a coverageData >= 32X There is a 1% of reference with a coverageData >= 33X There is a 0.82% of reference with a coverageData >= 34X There is a 0.69% of reference with a coverageData >= 35X There is a 0.59% of reference with a coverageData >= 36X There is a 0.51% of reference with a coverageData >= 37X There is a 0.45% of reference with a coverageData >= 38X There is a 0.4% of reference with a coverageData >= 39X There is a 0.36% of reference with a coverageData >= 40X There is a 0.33% of reference with a coverageData >= 41X There is a 0.31% of reference with a coverageData >= 42X There is a 0.29% of reference with a coverageData >= 43X There is a 0.27% of reference with a coverageData >= 44X There is a 0.26% of reference with a coverageData >= 45X There is a 0.24% of reference with a coverageData >= 46X There is a 0.23% of reference with a coverageData >= 47X There is a 0.22% of reference with a coverageData >= 48X There is a 0.21% of reference with a coverageData >= 49X There is a 0.21% of reference with a coverageData >= 50X There is a 0.2% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3627108957 14.552055848237988 321.6198457245187 chr2 243199373 3803363677 15.638871227681989 103.96535521547253 chr3 198022430 2890574127 14.597205614535687 9.87700022377523 chr4 191154276 2855051866 14.935851427147776 85.29075859005276 chr5 180915260 2643480163 14.611703639593475 13.861795765266516 chr6 171115067 2512581663 14.683579342548486 49.25359908477289 chr7 159138663 2402550067 15.097211587105015 142.53089553004543 chr8 146364022 2178938205 14.887116213573306 36.701656160007204 chr9 141213431 1933158255 13.68962032372119 252.52777852057096 chr10 135534747 2271868015 16.762255180215888 266.89840732442684 chr11 135006516 2048505287 15.17338086852045 89.20878330131993 chr12 133851895 1951642545 14.580611989094365 11.920599970655353 chr13 115169878 1387803714 12.05005803687662 9.394052379228212 chr14 107349540 1346025907 12.53872077141644 11.94191926422078 chr15 102531392 1271094305 12.397123263478175 9.376644568156303 chr16 90354753 1393894081 15.42690378446389 90.95669839903297 chr17 81195210 1279811788 15.762158728328926 70.61467593273711 chr18 78077248 1239630801 15.87697866861291 212.00144209353482 chr19 59128983 940072179 15.898669845209414 148.08295780416145 chr20 63025520 948406997 15.047983689781535 36.81188032208177 chr21 48129895 623953537 12.963949682416718 66.69120586638175 chr22 51304566 590395305 11.507656160662192 64.78685200708875 chrMT 16571 16508077 996.202824210971 111.38179857302217 chrX 155270560 1158248076 7.459547231619439 25.50126883632623 chrY 59373566 452430347 7.620063564987826 144.82014607397437