BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240056.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 = 1,822,803 number of mapped reads = 1,496,274 (82.09%) number of supplementary alignments = 6,791 (0.37%) number of secondary alignments = 0 number of mapped bases = 93,661,673 bp number of sequenced bases = 93,611,918 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 101,609 duplication rate = 5.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8891 >>>>>>> ACTG content number of A's = 25,594,961 bp (27.34%) number of C's = 16,256,560 bp (17.37%) number of T's = 30,431,981 bp (32.51%) number of G's = 21,265,533 bp (22.72%) number of N's = 62,883 bp (0.07%) GC percentage = 40.08% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 905,575 number of insertions = 6,421 mapped reads with insertion percentage = 0.43% number of deletions = 28,573 mapped reads with deletion percentage = 1.89% homopolymer indels = 49.34% >>>>>>> Coverage mean coverageData = 0.0303X std coverageData = 0.2981X There is a 2.42% of reference with a coverageData >= 1X There is a 0.44% 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 6847753 0.027473363847707325 0.44982490214860227 chr2 243199373 9112888 0.037470853183490735 0.3535310503743393 chr3 198022430 6649108 0.03357754977554815 0.2215153480051866 chr4 191154276 5980586 0.03128669745268999 0.2204136350275237 chr5 180915260 5491314 0.03035296193366994 0.21348091309665088 chr6 171115067 5464893 0.03193694801872707 0.2612076794056787 chr7 159138663 5316290 0.03340665241104859 0.46217080911774955 chr8 146364022 5479105 0.03743478024947962 0.4425904738401627 chr9 141213431 3566793 0.025258171087139722 0.26784408999320947 chr10 135534747 4402374 0.03248151560721178 0.25268251195085656 chr11 135006516 4416080 0.03271012489500877 0.2841141741543143 chr12 133851895 4613392 0.03446639287400451 0.22784387360302652 chr13 115169878 2160355 0.018757986354730704 0.16413844239944614 chr14 107349540 3456818 0.0322015166529824 0.22544522997848565 chr15 102531392 2202037 0.021476710274254348 0.18870425403418498 chr16 90354753 2594139 0.02871059810212751 0.20979805664498555 chr17 81195210 2113918 0.0260350087154156 0.2183285245558057 chr18 78077248 2433186 0.03116382893003606 0.4196727340875999 chr19 59128983 1540455 0.026052452145168808 0.31482706967979807 chr20 63025520 1971262 0.03127720326623247 0.2186618981286869 chr21 48129895 1690510 0.03512390791627532 0.23557091459344684 chr22 51304566 729815 0.014225147134077696 0.13888610049826544 chrMT 16571 29754 1.7955464365457727 2.245333699202286 chrX 155270560 5206936 0.03353459921829354 0.2424737573468452 chrY 59373566 191912 0.003232280169932862 0.0747224171399977