BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013191.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 = 1,558,899 number of mapped reads = 1,215,205 (77.95%) number of supplementary alignments = 7,534 (0.48%) number of secondary alignments = 0 number of mapped bases = 76,247,932 bp number of sequenced bases = 76,209,341 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 81,524 duplication rate = 5.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6801 >>>>>>> ACTG content number of A's = 20,285,781 bp (26.62%) number of C's = 13,267,461 bp (17.41%) number of T's = 25,142,710 bp (32.99%) number of G's = 17,512,462 bp (22.98%) number of N's = 927 bp (0%) GC percentage = 40.39% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 623,148 number of insertions = 5,264 mapped reads with insertion percentage = 0.43% number of deletions = 22,389 mapped reads with deletion percentage = 1.82% homopolymer indels = 48.03% >>>>>>> Coverage mean coverageData = 0.0246X std coverageData = 0.2335X There is a 1.91% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 4438912 0.017809030854932153 0.3028641450036276 chr2 243199373 9253680 0.038049769149692665 0.30986454285646525 chr3 198022430 4584388 0.023150852153465646 0.18934880133341045 chr4 191154276 5581327 0.029198023276235788 0.2152772881115726 chr5 180915260 3255590 0.017995109975797507 0.16707982807806115 chr6 171115067 3413264 0.019947185597630628 0.19750445224311158 chr7 159138663 4843951 0.03043855533711503 0.2838495108069225 chr8 146364022 4679984 0.031974961715659875 0.28469155434556015 chr9 141213431 2728640 0.019322807899200465 0.20528851571040446 chr10 135534747 3378953 0.0249305294383292 0.237998566864595 chr11 135006516 3024553 0.02240301497744005 0.2057163267965794 chr12 133851895 4176673 0.03120368971989526 0.22075525837242901 chr13 115169878 2347199 0.020380320277842093 0.1788592267564647 chr14 107349540 3138625 0.029237433155279473 0.2153514010170924 chr15 102531392 1899803 0.018528988663296407 0.17085123603026162 chr16 90354753 2615236 0.028944088862707645 0.2139443769933379 chr17 81195210 2304286 0.028379580519589765 0.22164752361104187 chr18 78077248 1333929 0.017084733826684056 0.30964740926874273 chr19 59128983 1450288 0.024527531616770747 0.2568432211987248 chr20 63025520 1655866 0.026272944673840056 0.20560624935830196 chr21 48129895 1356475 0.028183626829021754 0.2136418952211578 chr22 51304566 952282 0.018561349880632457 0.16663433946406195 chrMT 16571 25644 1.5475227807615715 2.0963154379807034 chrX 155270560 3655118 0.02354031569152581 0.20231820432566694 chrY 59373566 153266 0.00258138444977349 0.07355921550591879