BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6432732.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP127755/SRP127755.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 = 376,241,972 number of mapped reads = 376,105,455 (99.96%) number of supplementary alignments = 6,232,223 (1.66%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 188,056,048 number of mapped paired reads (second in pair) = 188,049,407 number of mapped paired reads (both in pair) = 376,057,492 number of mapped paired reads (singletons) = 47,963 number of mapped bases = 51,439,690,564 bp number of sequenced bases = 51,391,238,327 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 182,114,109 duplication rate = 31.45% >>>>>>> Insert size mean insert size = 84,899.9718 std insert size = 2,963,291.1823 median insert size = 317 >>>>>>> Mapping quality mean mapping quality = 57.3716 >>>>>>> ACTG content number of A's = 14,253,065,272 bp (27.73%) number of C's = 10,854,088,498 bp (21.12%) number of T's = 14,041,729,176 bp (27.32%) number of G's = 12,230,690,536 bp (23.8%) number of N's = 11,664,845 bp (0.02%) GC percentage = 44.92% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 405,033,385 number of insertions = 10,773,745 mapped reads with insertion percentage = 2.81% number of deletions = 33,566,593 mapped reads with deletion percentage = 8.53% homopolymer indels = 52.5% >>>>>>> Coverage mean coverageData = 16.6165X std coverageData = 44.8671X There is a 64.03% of reference with a coverageData >= 1X There is a 55.22% of reference with a coverageData >= 2X There is a 49.2% of reference with a coverageData >= 3X There is a 44.65% of reference with a coverageData >= 4X There is a 41% of reference with a coverageData >= 5X There is a 37.99% of reference with a coverageData >= 6X There is a 35.43% of reference with a coverageData >= 7X There is a 33.23% of reference with a coverageData >= 8X There is a 31.3% of reference with a coverageData >= 9X There is a 29.59% of reference with a coverageData >= 10X There is a 28.07% of reference with a coverageData >= 11X There is a 26.7% of reference with a coverageData >= 12X There is a 25.45% of reference with a coverageData >= 13X There is a 24.32% of reference with a coverageData >= 14X There is a 23.28% of reference with a coverageData >= 15X There is a 22.32% of reference with a coverageData >= 16X There is a 21.44% of reference with a coverageData >= 17X There is a 20.61% of reference with a coverageData >= 18X There is a 19.85% of reference with a coverageData >= 19X There is a 19.13% of reference with a coverageData >= 20X There is a 18.46% of reference with a coverageData >= 21X There is a 17.84% of reference with a coverageData >= 22X There is a 17.25% of reference with a coverageData >= 23X There is a 16.69% of reference with a coverageData >= 24X There is a 16.16% of reference with a coverageData >= 25X There is a 15.67% of reference with a coverageData >= 26X There is a 15.2% of reference with a coverageData >= 27X There is a 14.75% of reference with a coverageData >= 28X There is a 14.32% of reference with a coverageData >= 29X There is a 13.92% of reference with a coverageData >= 30X There is a 13.54% of reference with a coverageData >= 31X There is a 13.17% of reference with a coverageData >= 32X There is a 12.82% of reference with a coverageData >= 33X There is a 12.48% of reference with a coverageData >= 34X There is a 12.16% of reference with a coverageData >= 35X There is a 11.86% of reference with a coverageData >= 36X There is a 11.56% of reference with a coverageData >= 37X There is a 11.28% of reference with a coverageData >= 38X There is a 11.01% of reference with a coverageData >= 39X There is a 10.75% of reference with a coverageData >= 40X There is a 10.49% of reference with a coverageData >= 41X There is a 10.25% of reference with a coverageData >= 42X There is a 10.02% of reference with a coverageData >= 43X There is a 9.8% of reference with a coverageData >= 44X There is a 9.58% of reference with a coverageData >= 45X There is a 9.37% of reference with a coverageData >= 46X There is a 9.17% of reference with a coverageData >= 47X There is a 8.98% of reference with a coverageData >= 48X There is a 8.79% of reference with a coverageData >= 49X There is a 8.61% of reference with a coverageData >= 50X There is a 8.43% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4676917903 18.763916752688854 49.302084378610864 chr2 243199373 4103971245 16.874925269646972 46.39026166461635 chr3 198022430 3628700195 18.324692788589655 45.82967352245868 chr4 191154276 2544606707 13.311795897257355 36.43252283455786 chr5 180915260 2898240588 16.019879074877377 41.87697113477532 chr6 171115067 2897448077 16.932746647026704 44.38671313201051 chr7 159138663 2452409449 15.410519372027148 40.56050326516782 chr8 146364022 2439541273 16.667629378208805 42.578935805885145 chr9 141213431 2122970267 15.033770173036869 42.916253533014874 chr10 135534747 2763790037 20.39174527695101 50.38782063811051 chr11 135006516 2995989706 22.191445233650796 54.32978860996171 chr12 133851895 2301935659 17.197632196391393 43.92494896626309 chr13 115169878 1372504001 11.917213292524282 35.23789769820787 chr14 107349540 1593535204 14.84435987336322 41.330444690042825 chr15 102531392 1483298813 14.466777287096619 40.847444644963744 chr16 90354753 1818882420 20.130456446491532 54.55926948724037 chr17 81195210 1961376755 24.156311129683637 58.53166999272261 chr18 78077248 1382476060 17.70651624401516 45.94181242620524 chr19 59128983 1344843819 22.74424065436742 56.83385756033317 chr20 63025520 1576534918 25.01423102895462 57.89096260194986 chr21 48129895 662413609 13.763038730917655 41.62603809852572 chr22 51304566 881511751 17.18193563902285 48.277767126376794 chrMT 16571 6603088 398.47251222014364 572.9687617868283 chrX 155270560 1443956948 9.299618343619034 26.480925976014692 chrY 59373566 85232072 1.4355221985487616 13.163364116940452