BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068074.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 = 4,212,730 number of mapped reads = 3,957,417 (93.94%) number of supplementary alignments = 33,145 (0.79%) number of secondary alignments = 0 number of mapped bases = 253,639,625 bp number of sequenced bases = 253,544,571 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 787,667 duplication rate = 15.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4196 >>>>>>> ACTG content number of A's = 65,192,165 bp (25.71%) number of C's = 46,033,214 bp (18.16%) number of T's = 82,037,844 bp (32.36%) number of G's = 60,252,588 bp (23.76%) number of N's = 28,760 bp (0.01%) GC percentage = 41.92% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 1,357,753 number of insertions = 16,698 mapped reads with insertion percentage = 0.42% number of deletions = 54,114 mapped reads with deletion percentage = 1.35% homopolymer indels = 44.35% >>>>>>> Coverage mean coverageData = 0.0819X std coverageData = 0.8605X There is a 4.86% of reference with a coverageData >= 1X There is a 1.82% of reference with a coverageData >= 2X There is a 0.75% of reference with a coverageData >= 3X There is a 0.32% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 30292885 0.12153584564188508 1.612354915149196 chr2 243199373 18736763 0.07704280964573046 1.4004887682165668 chr3 198022430 14796495 0.07472130808615973 0.41910830470660937 chr4 191154276 13992800 0.07320160601586542 0.4776051423422931 chr5 180915260 8329677 0.046041870652591715 0.33496705038555374 chr6 171115067 16284371 0.09516620181669917 0.6396646722158802 chr7 159138663 20840324 0.1309570132557919 1.4169090215803737 chr8 146364022 10232836 0.06991360212826073 0.9759725472385307 chr9 141213431 7903507 0.055968521861068585 0.5951132066028444 chr10 135534747 14815595 0.10931215299350505 0.6702491163409838 chr11 135006516 12956958 0.0959728343778607 0.5595394527352611 chr12 133851895 10151262 0.07583950903347315 0.4476281336948959 chr13 115169878 6143915 0.053346544310830996 0.3926624856721144 chr14 107349540 4152368 0.0386808178218556 0.3587037281586464 chr15 102531392 5030863 0.04906656295078877 0.3661611024337972 chr16 90354753 5866339 0.06492562710010397 0.4270127795095344 chr17 81195210 7459725 0.09187395414089082 0.4940362932433771 chr18 78077248 8074988 0.10342306122264965 1.165880579143276 chr19 59128983 5589728 0.09453448573603912 1.0379042111415955 chr20 63025520 3799478 0.06028475449310057 0.4185425025386295 chr21 48129895 5178705 0.10759851023984159 0.5303639391101809 chr22 51304566 3159326 0.06157982118004857 0.3782665942661941 chrMT 16571 141647 8.547884859091184 6.462038548797892 chrX 155270560 18969409 0.1221700301718497 0.6220763702331815 chrY 59373566 739661 0.012457749295368244 0.44582507996611703