BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231836.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 5,464,576 number of mapped reads = 5,082,685 (93.01%) number of supplementary alignments = 28,847 (0.53%) number of secondary alignments = 0 number of mapped bases = 324,218,110 bp number of sequenced bases = 324,108,262 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 530,790 duplication rate = 8.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6809 >>>>>>> ACTG content number of A's = 85,307,720 bp (26.32%) number of C's = 57,234,597 bp (17.66%) number of T's = 105,411,578 bp (32.52%) number of G's = 76,032,400 bp (23.46%) number of N's = 121,967 bp (0.04%) GC percentage = 41.12% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 1,995,515 number of insertions = 19,692 mapped reads with insertion percentage = 0.38% number of deletions = 61,852 mapped reads with deletion percentage = 1.21% homopolymer indels = 44.83% >>>>>>> Coverage mean coverageData = 0.1047X std coverageData = 1.357X There is a 8.17% of reference with a coverageData >= 1X There is a 1.5% of reference with a coverageData >= 2X There is a 0.31% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 35370592 0.141907738717329 3.355312641001797 chr2 243199373 25758065 0.10591336927501042 1.2505229459614335 chr3 198022430 27305851 0.1378927175067996 0.4679830287204088 chr4 191154276 13128483 0.06868003831627602 0.37980820446183544 chr5 180915260 11501078 0.06357163016541556 0.36052456165222996 chr6 171115067 23695218 0.13847534536511621 0.9481933654782344 chr7 159138663 21908143 0.1376670042778982 1.9758552193033816 chr8 146364022 22968195 0.15692514243698497 1.282495813627364 chr9 141213431 18942629 0.13414183669257354 1.1492703071341994 chr10 135534747 18094876 0.13350728429809958 1.1495690993967116 chr11 135006516 12452880 0.09223910348149418 0.702293730959165 chr12 133851895 9794696 0.07317562444670657 0.4345301897056459 chr13 115169878 10770103 0.09351492931163824 0.3732310160799664 chr14 107349540 11334020 0.10558051762494744 0.5496597638296006 chr15 102531392 5631220 0.05492191113527455 0.33679197986909704 chr16 90354753 7090590 0.07847500839275162 0.6267636406511911 chr17 81195210 7316075 0.09010476110598149 0.5060960135524402 chr18 78077248 8035272 0.10291438550703016 2.498459770923781 chr19 59128983 6063337 0.10254424636391937 1.8606559462062335 chr20 63025520 7577669 0.12023175691370734 0.5995569580241457 chr21 48129895 6087294 0.1264763615212541 0.514633552469013 chr22 51304566 2251995 0.04389463113283133 0.2447809641997914 chrMT 16571 738601 44.57190272162211 26.138556563038396 chrX 155270560 9684461 0.0623715210404342 0.5544864890738026 chrY 59373566 716767 0.012072156824806514 0.25646049770091633