BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230378.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 = 3,235,788 number of mapped reads = 2,844,317 (87.9%) number of supplementary alignments = 42,509 (1.31%) number of secondary alignments = 0 number of mapped bases = 187,513,051 bp number of sequenced bases = 187,437,189 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 318,060 duplication rate = 8.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2448 >>>>>>> ACTG content number of A's = 50,711,602 bp (27.06%) number of C's = 35,582,947 bp (18.98%) number of T's = 58,161,699 bp (31.03%) number of G's = 42,942,342 bp (22.91%) number of N's = 38,599 bp (0.02%) GC percentage = 41.89% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,580,572 number of insertions = 15,820 mapped reads with insertion percentage = 0.55% number of deletions = 46,487 mapped reads with deletion percentage = 1.62% homopolymer indels = 46.39% >>>>>>> Coverage mean coverageData = 0.0606X std coverageData = 0.494X There is a 3.61% of reference with a coverageData >= 1X There is a 1.39% of reference with a coverageData >= 2X There is a 0.57% of reference with a coverageData >= 3X There is a 0.23% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% 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% 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 12552057 0.05035918044914319 0.5733475340315054 chr2 243199373 14818546 0.060931678471062505 0.6718450488410649 chr3 198022430 16533942 0.08349529899213942 0.44081136092313533 chr4 191154276 12071615 0.06315116382748351 0.4261316395395792 chr5 180915260 8305414 0.04590775814046864 0.32501012032959214 chr6 171115067 6929219 0.04049449952878784 0.33176739678986444 chr7 159138663 11953361 0.07511286556429093 0.7308002784930586 chr8 146364022 11830011 0.08082594915299608 0.6564373735014133 chr9 141213431 9961779 0.07054413259033412 0.5049290338417588 chr10 135534747 12922915 0.09534761591431605 0.555937561579429 chr11 135006516 7840986 0.05807857451858101 0.5181441051410738 chr12 133851895 6668783 0.049822103751314094 0.34596371972504786 chr13 115169878 2939149 0.025520119071412058 0.24048630140410931 chr14 107349540 7744804 0.07214566545883662 0.4347258473718616 chr15 102531392 5619122 0.054803918003961165 0.35893480152215257 chr16 90354753 4866588 0.0538608965042492 0.3788431368947373 chr17 81195210 6484735 0.07986597977885641 0.4915765525223844 chr18 78077248 4941130 0.06328514550102995 0.6941870111048284 chr19 59128983 3530474 0.059708011551627735 0.46757738401430265 chr20 63025520 4137068 0.06564115615388814 0.4008097981540761 chr21 48129895 1807389 0.037552315457991335 0.3299117031297091 chr22 51304566 2380698 0.04640323826148339 0.3235615593312847 chrMT 16571 44773 2.701888841952809 3.111658410840983 chrX 155270560 10092728 0.06500091195652286 0.4055835569421831 chrY 59373566 535765 0.009023628461190961 0.24309993321481385