BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231847.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 = 4,417,674 number of mapped reads = 2,319,291 (52.5%) number of supplementary alignments = 13,608 (0.31%) number of secondary alignments = 0 number of mapped bases = 153,896,485 bp number of sequenced bases = 153,832,693 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 92,363 duplication rate = 2.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8409 >>>>>>> ACTG content number of A's = 44,984,659 bp (29.24%) number of C's = 31,997,113 bp (20.8%) number of T's = 42,514,323 bp (27.64%) number of G's = 34,323,734 bp (22.31%) number of N's = 12,864 bp (0.01%) GC percentage = 43.11% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 901,790 number of insertions = 11,090 mapped reads with insertion percentage = 0.47% number of deletions = 37,699 mapped reads with deletion percentage = 1.61% homopolymer indels = 44.51% >>>>>>> Coverage mean coverageData = 0.0497X std coverageData = 2.3256X There is a 4.29% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% 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 14584154 0.05851200667620403 1.140207510721316 chr2 243199373 8865102 0.036451993648848754 8.104394495559498 chr3 198022430 17614125 0.08895015074807434 0.3294167586620294 chr4 191154276 5450641 0.02851435559830218 0.19902259404426303 chr5 180915260 8477035 0.04685638458580001 0.2419681480513256 chr6 171115067 9432805 0.05512550803021922 0.3498225160709027 chr7 159138663 10129039 0.06364913974424932 0.8391522105473498 chr8 146364022 9211519 0.06293567827754828 0.5115161117808693 chr9 141213431 4724864 0.03345902699581033 0.3917175529776089 chr10 135534747 7151602 0.052765819528183426 0.40355384254135984 chr11 135006516 5500500 0.0407424779408425 0.362874846234925 chr12 133851895 5009883 0.03742855489643983 0.22261020355579378 chr13 115169878 7795841 0.06768993017427699 0.2862826142884121 chr14 107349540 7528316 0.07012900101854186 0.33410230147131437 chr15 102531392 4599801 0.044862367615178776 0.23401053275178998 chr16 90354753 3566984 0.039477546908904725 0.2976719248057506 chr17 81195210 4120061 0.050742660804744516 0.28667547933933996 chr18 78077248 3700044 0.04738952889323148 0.9938369239165799 chr19 59128983 3739134 0.06323690701732516 0.656936751439695 chr20 63025520 3898156 0.06185043772744755 0.2913738122146446 chr21 48129895 2850615 0.059227534155227225 0.2833561894243863 chr22 51304566 1017337 0.019829365674782242 0.1527950172407388 chrMT 16571 62689 3.7830547341741596 2.835694343447117 chrX 155270560 4552526 0.029319956081822595 0.24453722277473122 chrY 59373566 313712 0.005283698135968454 0.1215763825135131