BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10251080.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP224945/SRP224945.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 = 3,940,513 number of mapped reads = 3,737,877 (94.86%) number of supplementary alignments = 31,680 (0.8%) number of secondary alignments = 0 number of mapped bases = 289,593,563 bp number of sequenced bases = 289,396,397 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 758,433 duplication rate = 17.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.9688 >>>>>>> ACTG content number of A's = 84,863,573 bp (29.32%) number of C's = 57,759,586 bp (19.96%) number of T's = 85,595,248 bp (29.58%) number of G's = 61,175,561 bp (21.14%) number of N's = 2,429 bp (0%) GC percentage = 41.1% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,764,999 number of insertions = 37,310 mapped reads with insertion percentage = 0.98% number of deletions = 110,288 mapped reads with deletion percentage = 2.9% homopolymer indels = 44.78% >>>>>>> Coverage mean coverageData = 0.0935X std coverageData = 1.0849X There is a 6.37% of reference with a coverageData >= 1X There is a 1.83% of reference with a coverageData >= 2X There is a 0.58% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.03% 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 0.01% 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 24275645 0.09739452163691902 2.366377743864884 chr2 243199373 25077097 0.10311332916142016 1.46020479811778 chr3 198022430 19780320 0.09988929031928352 0.4321234280262462 chr4 191154276 18486874 0.09671179942634399 0.5037203721033472 chr5 180915260 17231413 0.09524576865434127 0.44560959996035526 chr6 171115067 16680982 0.09748400472531153 0.5515786814269803 chr7 159138663 15926996 0.1000825047776102 1.492354426730301 chr8 146364022 14227033 0.09720307494692924 0.7044616771709638 chr9 141213431 12528943 0.08872345152494737 1.144920488844489 chr10 135534747 16788702 0.12387009509819648 1.0291928346467716 chr11 135006516 12995528 0.09625852429226453 0.6494406737882166 chr12 133851895 13070613 0.09764981661260753 0.4490516906781827 chr13 115169878 8768435 0.0761347945510544 0.37015045493362453 chr14 107349540 8649095 0.08056946494600722 0.6820739536531116 chr15 102531392 8477019 0.08267730335700504 0.3949847386244095 chr16 90354753 8034077 0.08891703793379857 0.8689436846412059 chr17 81195210 7703256 0.09487328131794967 0.552008549213837 chr18 78077248 7398190 0.09475474852802189 1.3322740173009437 chr19 59128983 6110907 0.10334875876353226 2.0841012380564092 chr20 63025520 5910738 0.09378324843650636 0.47822400632799517 chr21 48129895 3730984 0.07751905546438445 0.42492495290454974 chr22 51304566 3395524 0.06618366092405889 0.3778698821882047 chrMT 16571 305941 18.46243437330276 10.926635636781796 chrX 155270560 13228750 0.08519805686280774 0.5185300408065711 chrY 59373566 810501 0.013650872848028026 1.0524721379082358