BamQC report ----------------------------------- >>>>>>> Input bam file = SRR21672009.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 = 480,982,134 number of mapped reads = 476,173,000 (99%) number of supplementary alignments = 2,059,318 (0.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 238,150,512 number of mapped paired reads (second in pair) = 238,022,488 number of mapped paired reads (both in pair) = 475,381,158 number of mapped paired reads (singletons) = 791,842 number of mapped bases = 70,657,728,169 bp number of sequenced bases = 70,629,076,859 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 106,866,634 duplication rate = 18.79% >>>>>>> Insert size mean insert size = 31,723.4388 std insert size = 1,667,969.0309 median insert size = 343 >>>>>>> Mapping quality mean mapping quality = 54.5176 >>>>>>> ACTG content number of A's = 20,944,827,201 bp (29.65%) number of C's = 14,449,532,689 bp (20.46%) number of T's = 20,744,989,801 bp (29.37%) number of G's = 14,489,483,874 bp (20.51%) number of N's = 243,294 bp (0%) GC percentage = 40.97% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 485,914,790 number of insertions = 9,977,326 mapped reads with insertion percentage = 1.99% number of deletions = 10,418,733 mapped reads with deletion percentage = 2.1% homopolymer indels = 45.72% >>>>>>> Coverage mean coverageData = 22.8245X std coverageData = 223.9669X There is a 91.66% of reference with a coverageData >= 1X There is a 91.6% of reference with a coverageData >= 2X There is a 91.56% of reference with a coverageData >= 3X There is a 91.5% of reference with a coverageData >= 4X There is a 91.44% of reference with a coverageData >= 5X There is a 91.37% of reference with a coverageData >= 6X There is a 91.28% of reference with a coverageData >= 7X There is a 91.15% of reference with a coverageData >= 8X There is a 90.97% of reference with a coverageData >= 9X There is a 90.71% of reference with a coverageData >= 10X There is a 90.33% of reference with a coverageData >= 11X There is a 89.75% of reference with a coverageData >= 12X There is a 88.91% of reference with a coverageData >= 13X There is a 87.71% of reference with a coverageData >= 14X There is a 86.04% of reference with a coverageData >= 15X There is a 83.82% of reference with a coverageData >= 16X There is a 80.98% of reference with a coverageData >= 17X There is a 77.46% of reference with a coverageData >= 18X There is a 73.27% of reference with a coverageData >= 19X There is a 68.45% of reference with a coverageData >= 20X There is a 63.1% of reference with a coverageData >= 21X There is a 57.36% of reference with a coverageData >= 22X There is a 51.37% of reference with a coverageData >= 23X There is a 45.33% of reference with a coverageData >= 24X There is a 39.39% of reference with a coverageData >= 25X There is a 33.71% of reference with a coverageData >= 26X There is a 28.42% of reference with a coverageData >= 27X There is a 23.62% of reference with a coverageData >= 28X There is a 19.35% of reference with a coverageData >= 29X There is a 15.64% of reference with a coverageData >= 30X There is a 12.49% of reference with a coverageData >= 31X There is a 9.86% of reference with a coverageData >= 32X There is a 7.71% of reference with a coverageData >= 33X There is a 5.99% of reference with a coverageData >= 34X There is a 4.63% of reference with a coverageData >= 35X There is a 3.57% of reference with a coverageData >= 36X There is a 2.76% of reference with a coverageData >= 37X There is a 2.15% of reference with a coverageData >= 38X There is a 1.69% of reference with a coverageData >= 39X There is a 1.35% of reference with a coverageData >= 40X There is a 1.1% of reference with a coverageData >= 41X There is a 0.92% of reference with a coverageData >= 42X There is a 0.79% of reference with a coverageData >= 43X There is a 0.69% of reference with a coverageData >= 44X There is a 0.61% of reference with a coverageData >= 45X There is a 0.56% of reference with a coverageData >= 46X There is a 0.52% of reference with a coverageData >= 47X There is a 0.48% of reference with a coverageData >= 48X There is a 0.46% of reference with a coverageData >= 49X There is a 0.43% of reference with a coverageData >= 50X There is a 0.41% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 5734306243 23.006186383784375 531.6166310437468 chr2 243199373 5982419591 24.59882818447891 120.8867307019772 chr3 198022430 4642104196 23.44231507511548 15.708998552625214 chr4 191154276 4659529467 24.375753263296083 172.63497685698528 chr5 180915260 4246304040 23.471232001103722 18.120189306662944 chr6 171115067 4074434393 23.8110790851632 119.50342263766186 chr7 159138663 3782942559 23.771360696928816 137.38358930909837 chr8 146364022 3519656036 24.04727601705288 224.1876721993861 chr9 141213431 3049402069 21.594277877151786 299.0000365390083 chr10 135534747 3633784919 26.810725658417322 480.2557756211953 chr11 135006516 3207370854 23.75715594349535 103.45040580040528 chr12 133851895 3100153764 23.16107488803203 17.11326311591968 chr13 115169878 2251732477 19.551401079021723 12.362187614878279 chr14 107349540 2117618549 19.726386801471158 15.217746837136247 chr15 102531392 1974195299 19.25454497877099 12.571261726351278 chr16 90354753 2209967075 24.458780546940346 181.95185282908483 chr17 81195210 1967738870 24.234666921854135 135.12069267809656 chr18 78077248 1966530377 25.186983754857753 296.77395211415563 chr19 59128983 1406437193 23.78591887839505 227.82797411938031 chr20 63025520 1468573192 23.301246733069398 63.12826701332883 chr21 48129895 980670831 20.37550322933387 81.46665884693867 chr22 51304566 851166237 16.59045779668032 15.876903633464066 chrMT 16571 25912302 1563.71383742683 176.07896318232685 chrX 155270560 3608431175 23.239635221255078 49.76881782758507 chrY 59373566 196346461 3.306967632700384 173.60272895069374