BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240189.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 = 1,223,758 number of mapped reads = 957,406 (78.23%) number of supplementary alignments = 8,294 (0.68%) number of secondary alignments = 0 number of mapped bases = 62,482,501 bp number of sequenced bases = 62,451,167 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 86,248 duplication rate = 7.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5385 >>>>>>> ACTG content number of A's = 17,573,995 bp (28.14%) number of C's = 11,483,145 bp (18.39%) number of T's = 19,833,851 bp (31.76%) number of G's = 13,524,978 bp (21.66%) number of N's = 35,198 bp (0.06%) GC percentage = 40.04% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 565,311 number of insertions = 4,431 mapped reads with insertion percentage = 0.46% number of deletions = 18,104 mapped reads with deletion percentage = 1.87% homopolymer indels = 46.87% >>>>>>> Coverage mean coverageData = 0.0202X std coverageData = 0.2463X There is a 1.3% of reference with a coverageData >= 1X There is a 0.43% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 5246862 0.02105054735249787 0.3387744842134585 chr2 243199373 6067169 0.02494730527121877 0.28026229577347456 chr3 198022430 4091774 0.020663184468547327 0.2105782471109936 chr4 191154276 4346136 0.02273627402402445 0.2218522982791524 chr5 180915260 3719349 0.020558514522213328 0.20787473966005623 chr6 171115067 2974455 0.017382776701948755 0.21344315385164617 chr7 159138663 3492184 0.021944283897873392 0.3062989946574506 chr8 146364022 3374098 0.023052782739189825 0.32219467403786006 chr9 141213431 2649304 0.018760991650999544 0.23500585978042499 chr10 135534747 2750788 0.020295813884538407 0.2403207076045015 chr11 135006516 2568369 0.019024037328687158 0.23224628993048765 chr12 133851895 2941947 0.021979121027759823 0.2172293028169525 chr13 115169878 1989459 0.01727412613912815 0.18936074866981498 chr14 107349540 2198662 0.020481336016903287 0.21402547490573864 chr15 102531392 1655496 0.01614623548659127 0.19733483278592603 chr16 90354753 1691010 0.01871523017721049 0.20028613193223188 chr17 81195210 1459642 0.017976947162277185 0.2038165549689609 chr18 78077248 1363023 0.017457364788267128 0.3139713093897022 chr19 59128983 971196 0.016425041506294806 0.258323868409347 chr20 63025520 1358297 0.0215515397572285 0.21416237046386513 chr21 48129895 1017961 0.021150285077497052 0.21785969342605624 chr22 51304566 530183 0.01033403147782207 0.14245348591383997 chrMT 16571 14161 0.8545652042725242 1.3304731739126359 chrX 155270560 3827889 0.024653025016461588 0.23539420024151478 chrY 59373566 183087 0.0030836450012114817 0.07921469164477116