BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238278.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 = 913,694 number of mapped reads = 766,085 (83.84%) number of supplementary alignments = 6,139 (0.67%) number of secondary alignments = 0 number of mapped bases = 51,412,043 bp number of sequenced bases = 51,385,797 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,240 duplication rate = 1.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2874 >>>>>>> ACTG content number of A's = 15,159,714 bp (29.5%) number of C's = 9,325,176 bp (18.15%) number of T's = 15,337,756 bp (29.85%) number of G's = 11,548,875 bp (22.47%) number of N's = 14,276 bp (0.03%) GC percentage = 40.62% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 509,301 number of insertions = 4,515 mapped reads with insertion percentage = 0.58% number of deletions = 15,623 mapped reads with deletion percentage = 2.01% homopolymer indels = 44.86% >>>>>>> Coverage mean coverageData = 0.0166X std coverageData = 0.1827X There is a 1.56% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% 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 3411910 0.013688672013378856 0.2746893324956557 chr2 243199373 4571942 0.018799152084985022 0.20069961681828563 chr3 198022430 4278727 0.02160728458892258 0.15202740851740607 chr4 191154276 3188846 0.01668205423769856 0.14170800011963744 chr5 180915260 2824862 0.015614282620493152 0.129495477819667 chr6 171115067 3652982 0.021348102560717227 0.17498804067615037 chr7 159138663 2799182 0.01758957846717614 0.230816462108343 chr8 146364022 2641834 0.01804974995836067 0.2625337664134094 chr9 141213431 2259505 0.01600063806961818 0.16986308544280365 chr10 135534747 2323457 0.017142888089059553 0.19473185481588537 chr11 135006516 2058843 0.015249952824499226 0.1474958777447312 chr12 133851895 2603721 0.019452253552331104 0.14582459413108648 chr13 115169878 1718586 0.014922183038172533 0.1257678832135044 chr14 107349540 2033263 0.018940584188809752 0.15193914997195368 chr15 102531392 1154495 0.011259917352921532 0.11005566898472104 chr16 90354753 1513608 0.016751835954883304 0.1485271007865487 chr17 81195210 1359125 0.01673898004574408 0.14724427735241724 chr18 78077248 1458717 0.018682997126128215 0.30190799658668804 chr19 59128983 830777 0.014050250111692265 0.19496279857092402 chr20 63025520 1059190 0.016805732027280376 0.13761741328260432 chr21 48129895 623634 0.012957310627833283 0.13019850148684164 chr22 51304566 476667 0.009290927439089925 0.09916648776821228 chrMT 16571 8344 0.5035302637137168 0.7482049060652086 chrX 155270560 2421569 0.01559580257841538 0.13730887434777647 chrY 59373566 138257 0.002328595186618907 0.07781730758704831