BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004002.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 = 3,683,337 number of mapped reads = 3,357,832 (91.16%) number of supplementary alignments = 29,759 (0.81%) number of secondary alignments = 0 number of mapped bases = 220,726,524 bp number of sequenced bases = 220,632,998 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 126,885 duplication rate = 2.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.9079 >>>>>>> ACTG content number of A's = 59,387,631 bp (26.92%) number of C's = 42,547,824 bp (19.28%) number of T's = 66,928,273 bp (30.33%) number of G's = 51,726,453 bp (23.44%) number of N's = 42,817 bp (0.02%) GC percentage = 42.73% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,831,402 number of insertions = 17,635 mapped reads with insertion percentage = 0.52% number of deletions = 56,812 mapped reads with deletion percentage = 1.67% homopolymer indels = 45.55% >>>>>>> Coverage mean coverageData = 0.0713X std coverageData = 0.5954X There is a 5.95% of reference with a coverageData >= 1X There is a 0.82% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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% 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 15842815 0.06356178747494474 0.9688705397499647 chr2 243199373 21057023 0.08658337700566358 0.8484063562645208 chr3 198022430 15533730 0.07844429542653325 0.32456787455468933 chr4 191154276 12428917 0.06502034513734864 0.3201010029593047 chr5 180915260 11620312 0.0642306901032008 0.2914362024886069 chr6 171115067 13068849 0.0763746245676893 0.3949286697336151 chr7 159138663 15385945 0.09668263330828662 1.1175335051696402 chr8 146364022 16021156 0.10946102587970696 0.6081726413252264 chr9 141213431 7384343 0.052292072699515385 0.5287217258466113 chr10 135534747 9551958 0.07047608241744827 0.5804023137849561 chr11 135006516 9426734 0.06982428907357331 0.47862067267035496 chr12 133851895 10076253 0.07527912100161152 0.32188938892217317 chr13 115169878 7521951 0.06531179098757055 0.2928096159674425 chr14 107349540 5883991 0.05481151572703526 0.3405054058360815 chr15 102531392 6539087 0.06377643834192752 0.31469024522124256 chr16 90354753 5925291 0.0655780775583549 0.3632381525822561 chr17 81195210 6059225 0.07462539970030252 0.3632701102484499 chr18 78077248 6509472 0.08337220082347165 1.0837473416721748 chr19 59128983 3379773 0.05715932912291084 0.7830324170552254 chr20 63025520 5309333 0.08424100269224276 0.36846939639496257 chr21 48129895 3119107 0.0648060212888476 0.326923303388177 chr22 51304566 1981630 0.038624827271709114 0.22552971894752016 chrMT 16571 110654 6.677569247480538 4.576974360350951 chrX 155270560 10445512 0.06727297177262709 0.3604841847953108 chrY 59373566 543463 0.0091532821188473 0.17168669078242954