BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238654.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 = 3,583,041 number of mapped reads = 3,196,537 (89.21%) number of supplementary alignments = 27,580 (0.77%) number of secondary alignments = 0 number of mapped bases = 197,077,392 bp number of sequenced bases = 196,994,715 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,148,095 duplication rate = 21.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 31.3243 >>>>>>> ACTG content number of A's = 49,274,127 bp (25.01%) number of C's = 33,965,063 bp (17.24%) number of T's = 67,267,827 bp (34.15%) number of G's = 46,483,265 bp (23.6%) number of N's = 4,433 bp (0%) GC percentage = 40.84% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 1,055,897 number of insertions = 12,048 mapped reads with insertion percentage = 0.37% number of deletions = 49,170 mapped reads with deletion percentage = 1.53% homopolymer indels = 42.54% >>>>>>> Coverage mean coverageData = 0.0637X std coverageData = 1.0212X There is a 2.14% of reference with a coverageData >= 1X There is a 1.2% of reference with a coverageData >= 2X There is a 0.83% of reference with a coverageData >= 3X There is a 0.58% of reference with a coverageData >= 4X There is a 0.41% of reference with a coverageData >= 5X There is a 0.29% of reference with a coverageData >= 6X There is a 0.21% of reference with a coverageData >= 7X There is a 0.15% of reference with a coverageData >= 8X There is a 0.11% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% 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 4472008 0.01794181287115028 0.41813333613738707 chr2 243199373 2558977 0.01052213650238317 2.121854938335875 chr3 198022430 5423282 0.027387210630634116 0.4008797591033961 chr4 191154276 27137058 0.14196416929747363 0.8861492866345034 chr5 180915260 27857269 0.1539796532365484 0.9445866825737476 chr6 171115067 66770920 0.39021064112372994 2.2136946866889327 chr7 159138663 5647090 0.03548534274163156 0.6746504664888157 chr8 146364022 3711345 0.025356948717902818 0.873961577603299 chr9 141213431 4502812 0.031886570336216814 0.5222287111801295 chr10 135534747 5331324 0.039335477565764006 0.5280181995828134 chr11 135006516 1356357 0.010046603972803802 0.2778002960643442 chr12 133851895 17828533 0.1331959700682609 0.8844741238333622 chr13 115169878 733890 0.006372239102311109 0.49217769581520077 chr14 107349540 738682 0.006881091432715967 0.24515550966050337 chr15 102531392 751226 0.007326790218550822 0.45386584316271755 chr16 90354753 5961279 0.06597637425891696 0.645749933153083 chr17 81195210 1191455 0.014673956751882284 0.25929212520852946 chr18 78077248 7663085 0.09814747825128263 2.105584734130003 chr19 59128983 692058 0.011704209422982973 0.503297822172776 chr20 63025520 1870257 0.02967459848010774 0.4257373940614588 chr21 48129895 327311 0.006800575816755886 0.17193759758698401 chr22 51304566 1879744 0.03663892215753272 0.45778036421944335 chrMT 16571 56897 3.4335284533220687 4.1126911624707905 chrX 155270560 2358932 0.015192397064839594 0.3251230596226355 chrY 59373566 255601 0.004304962919020225 0.3165918374276352