BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038474.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 75,410,056 number of mapped reads = 74,930,260 (99.36%) number of supplementary alignments = 105,450 (0.14%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 37,663,701 number of mapped paired reads (second in pair) = 37,266,559 number of mapped paired reads (both in pair) = 74,508,080 number of mapped paired reads (singletons) = 422,180 number of mapped bases = 11,116,197,493 bp number of sequenced bases = 11,114,414,343 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 28,578,793 duplication rate = 36.12% >>>>>>> Insert size mean insert size = 18,938.174 std insert size = 1,440,363.2556 median insert size = 233 >>>>>>> Mapping quality mean mapping quality = 55.7343 >>>>>>> ACTG content number of A's = 2,784,330,023 bp (25.05%) number of C's = 2,772,728,877 bp (24.95%) number of T's = 2,803,903,383 bp (25.23%) number of G's = 2,752,592,185 bp (24.77%) number of N's = 859,875 bp (0.01%) GC percentage = 49.71% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 65,768,312 number of insertions = 531,359 mapped reads with insertion percentage = 0.68% number of deletions = 644,209 mapped reads with deletion percentage = 0.84% homopolymer indels = 46.39% >>>>>>> Coverage mean coverageData = 3.5909X std coverageData = 22.7396X There is a 22.31% of reference with a coverageData >= 1X There is a 14.03% of reference with a coverageData >= 2X There is a 8.97% of reference with a coverageData >= 3X There is a 6.98% of reference with a coverageData >= 4X There is a 5.59% of reference with a coverageData >= 5X There is a 4.88% of reference with a coverageData >= 6X There is a 4.39% of reference with a coverageData >= 7X There is a 4.09% of reference with a coverageData >= 8X There is a 3.87% of reference with a coverageData >= 9X There is a 3.72% of reference with a coverageData >= 10X There is a 3.59% of reference with a coverageData >= 11X There is a 3.49% of reference with a coverageData >= 12X There is a 3.41% of reference with a coverageData >= 13X There is a 3.33% of reference with a coverageData >= 14X There is a 3.27% of reference with a coverageData >= 15X There is a 3.2% of reference with a coverageData >= 16X There is a 3.15% of reference with a coverageData >= 17X There is a 3.09% of reference with a coverageData >= 18X There is a 3.04% of reference with a coverageData >= 19X There is a 3% of reference with a coverageData >= 20X There is a 2.95% of reference with a coverageData >= 21X There is a 2.91% of reference with a coverageData >= 22X There is a 2.87% of reference with a coverageData >= 23X There is a 2.83% of reference with a coverageData >= 24X There is a 2.79% of reference with a coverageData >= 25X There is a 2.75% of reference with a coverageData >= 26X There is a 2.71% of reference with a coverageData >= 27X There is a 2.68% of reference with a coverageData >= 28X There is a 2.64% of reference with a coverageData >= 29X There is a 2.61% of reference with a coverageData >= 30X There is a 2.58% of reference with a coverageData >= 31X There is a 2.54% of reference with a coverageData >= 32X There is a 2.51% of reference with a coverageData >= 33X There is a 2.48% of reference with a coverageData >= 34X There is a 2.45% of reference with a coverageData >= 35X There is a 2.42% of reference with a coverageData >= 36X There is a 2.39% of reference with a coverageData >= 37X There is a 2.37% of reference with a coverageData >= 38X There is a 2.34% of reference with a coverageData >= 39X There is a 2.31% of reference with a coverageData >= 40X There is a 2.29% of reference with a coverageData >= 41X There is a 2.26% of reference with a coverageData >= 42X There is a 2.23% of reference with a coverageData >= 43X There is a 2.21% of reference with a coverageData >= 44X There is a 2.18% of reference with a coverageData >= 45X There is a 2.16% of reference with a coverageData >= 46X There is a 2.13% of reference with a coverageData >= 47X There is a 2.11% of reference with a coverageData >= 48X There is a 2.09% of reference with a coverageData >= 49X There is a 2.06% of reference with a coverageData >= 50X There is a 2.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1139428958 4.571418732794251 26.537875703750384 chr2 243199373 819613070 3.370128219861817 22.327433437458996 chr3 198022430 643585462 3.250063449882925 21.106587860009842 chr4 191154276 374690177 1.9601454115522898 14.84571888244114 chr5 180915260 544888320 3.011842782084828 21.15502651140598 chr6 171115067 556141984 3.250105287338607 21.121005086321635 chr7 159138663 528779212 3.322757663233604 21.33794043686041 chr8 146364022 430907625 2.9440816063390223 20.86794363964795 chr9 141213431 457578789 3.240334759658945 21.382916388867606 chr10 135534747 459576710 3.390840505276481 21.10870645655424 chr11 135006516 656229267 4.860722922440277 27.77180586304272 chr12 133851895 586586762 4.3823567981611316 24.80869705227536 chr13 115169878 209888077 1.82242163180897 15.093776098729924 chr14 107349540 380914193 3.548354217447043 22.519384528839986 chr15 102531392 400698360 3.9080553982920665 22.876307315892518 chr16 90354753 485481359 5.373058338170655 28.88486685954797 chr17 81195210 618463304 7.616992480221432 32.6827439658352 chr18 78077248 214935341 2.752854980237008 23.513492505779528 chr19 59128983 641796013 10.85416965483746 39.15178488246905 chr20 63025520 309871203 4.9165989110442885 27.885154307387843 chr21 48129895 117858626 2.4487613363793956 21.9542397670771 chr22 51304566 191885580 3.7401267559694396 19.72819265326677 chrMT 16571 1086684 65.57745458934282 25.671522969143314 chrX 155270560 340770245 2.194686777712401 15.697371314928334 chrY 59373566 4542172 0.07650158658147634 2.2041590333273833