BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717063.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,453,248 number of mapped reads = 920,158 (63.32%) number of supplementary alignments = 2,612 (0.18%) number of secondary alignments = 0 number of mapped bases = 50,342,212 bp number of sequenced bases = 50,328,360 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,889 duplication rate = 1.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.0441 >>>>>>> ACTG content number of A's = 12,375,749 bp (24.59%) number of C's = 9,944,995 bp (19.76%) number of T's = 14,881,989 bp (29.57%) number of G's = 13,124,146 bp (26.08%) number of N's = 1,481 bp (0%) GC percentage = 45.84% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 266,227 number of insertions = 3,510 mapped reads with insertion percentage = 0.38% number of deletions = 8,258 mapped reads with deletion percentage = 0.89% homopolymer indels = 35.1% >>>>>>> Coverage mean coverageData = 0.0163X std coverageData = 0.1579X There is a 1.49% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 4970760 0.019942818918794188 0.1864986271319124 chr2 243199373 4333724 0.01781963475703533 0.18836286555803908 chr3 198022430 3451440 0.017429540683850813 0.1482872351248029 chr4 191154276 3255407 0.017030259893323026 0.15440130531931656 chr5 180915260 3083214 0.017042310305941024 0.14093374250210514 chr6 171115067 2179570 0.012737452278238012 0.12402952740562927 chr7 159138663 2953529 0.018559468480641942 0.18302576317727423 chr8 146364022 3016017 0.020606273036142722 0.16280478734582796 chr9 141213431 2194099 0.015537466829199837 0.14509116833826136 chr10 135534747 2601798 0.019196538582095114 0.23375207275706017 chr11 135006516 2096044 0.015525502487598451 0.1585151089697993 chr12 133851895 2491659 0.01861504463571472 0.148496320013833 chr13 115169878 842347 0.007313952351325752 0.09330616823588256 chr14 107349540 1607122 0.014970925818592237 0.13493464121175708 chr15 102531392 994692 0.00970134102929179 0.11018029748693768 chr16 90354753 1355751 0.015004755754243499 0.14354967010792327 chr17 81195210 2001578 0.024651429560930995 0.17741151254432905 chr18 78077248 1335853 0.01710937608866542 0.17161750154699076 chr19 59128983 1346230 0.022767683996864956 0.18380503930161712 chr20 63025520 1293554 0.020524289208561867 0.1638456172360669 chr21 48129895 664261 0.013801422172227885 0.1374545175130614 chr22 51304566 560791 0.010930625550949988 0.11579230909544694 chrMT 16571 8229 0.4965904290628206 0.8134318874957124 chrX 155270560 1552578 0.009999178208670079 0.11731693733163136 chrY 59373566 151965 0.0025594723416141117 0.07922311614197448