BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234073.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 = 4,836,247 number of mapped reads = 4,556,365 (94.21%) number of supplementary alignments = 33,627 (0.7%) number of secondary alignments = 0 number of mapped bases = 293,019,421 bp number of sequenced bases = 292,909,056 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 567,518 duplication rate = 10.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5848 >>>>>>> ACTG content number of A's = 75,311,270 bp (25.71%) number of C's = 52,990,134 bp (18.09%) number of T's = 95,181,776 bp (32.5%) number of G's = 69,398,050 bp (23.69%) number of N's = 27,826 bp (0.01%) GC percentage = 41.78% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 1,598,761 number of insertions = 18,873 mapped reads with insertion percentage = 0.41% number of deletions = 63,361 mapped reads with deletion percentage = 1.38% homopolymer indels = 44.34% >>>>>>> Coverage mean coverageData = 0.0947X std coverageData = 1.0234X There is a 6.97% of reference with a coverageData >= 1X There is a 1.64% of reference with a coverageData >= 2X There is a 0.43% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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 0.01% 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 30048923 0.120557063727436 2.135660309521169 chr2 243199373 13600834 0.05592462608857137 1.8235779692299257 chr3 198022430 28317820 0.14300309313444948 0.4940042304065761 chr4 191154276 9886080 0.05171780724382017 0.3692406805807557 chr5 180915260 19444925 0.10748084489942972 0.4346913696093701 chr6 171115067 18800740 0.10987191443521452 0.6944312676731577 chr7 159138663 17582302 0.11048416311000427 1.350559568805804 chr8 146364022 16573850 0.11323718611668106 0.9915625758904509 chr9 141213431 8956224 0.06342331559099361 0.6171017978826426 chr10 135534747 9997490 0.07376329849938776 0.6524401352967627 chr11 135006516 14532785 0.10764506359085661 0.7739692659132107 chr12 133851895 11537405 0.08619530563986412 0.39859298826344264 chr13 115169878 10489623 0.09107957030222781 0.4538450274118458 chr14 107349540 14692683 0.1368676847613879 0.5061253365102493 chr15 102531392 8031804 0.07833507224792188 0.40080845458475695 chr16 90354753 8307110 0.09193882694804113 0.458627905363633 chr17 81195210 8530725 0.10506438741891301 0.506921974729011 chr18 78077248 7193626 0.09213472790434417 1.5675636772536097 chr19 59128983 7993961 0.13519530684300793 1.1412005388650923 chr20 63025520 7683399 0.1219093313311814 0.4880475533971306 chr21 48129895 5588963 0.11612248478830049 0.47599995020638747 chr22 51304566 3037006 0.059195627929100894 0.3047441374811965 chrMT 16571 408517 24.652525496349043 13.934594843463547 chrX 155270560 11072765 0.07131271375591097 0.4441480446965188 chrY 59373566 709861 0.011955842436683017 0.26506025318814624