BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818983.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,209,869 number of mapped reads = 2,141,994 (96.93%) number of supplementary alignments = 32,187 (1.46%) number of secondary alignments = 0 number of mapped bases = 198,290,013 bp number of sequenced bases = 198,169,530 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 944,398 duplication rate = 37.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.0466 >>>>>>> ACTG content number of A's = 55,424,122 bp (27.97%) number of C's = 43,071,138 bp (21.73%) number of T's = 57,769,474 bp (29.15%) number of G's = 41,895,572 bp (21.14%) number of N's = 9,224 bp (0%) GC percentage = 42.88% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 1,270,413 number of insertions = 32,084 mapped reads with insertion percentage = 1.45% number of deletions = 63,307 mapped reads with deletion percentage = 2.89% homopolymer indels = 41% >>>>>>> Coverage mean coverageData = 0.0641X std coverageData = 0.7852X There is a 3.01% of reference with a coverageData >= 1X There is a 1.43% of reference with a coverageData >= 2X There is a 0.77% of reference with a coverageData >= 3X There is a 0.43% of reference with a coverageData >= 4X There is a 0.24% of reference with a coverageData >= 5X There is a 0.14% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 20406767 0.08187248207497946 1.4812850048625426 chr2 243199373 15962331 0.06563475391854731 1.079112885243084 chr3 198022430 9758361 0.049279069042835195 0.4004393268458895 chr4 191154276 10747105 0.05622215325175357 0.5218810045047123 chr5 180915260 11015950 0.060890109546314665 0.4609391848411577 chr6 171115067 8058283 0.04709277295844439 0.4762249338982946 chr7 159138663 9324495 0.0585935235612731 0.8867209472277471 chr8 146364022 17699894 0.12093063416909929 0.716249198065015 chr9 141213431 8785484 0.0622142238014173 0.776125410407279 chr10 135534747 10360158 0.07643912892684265 0.9337168726659928 chr11 135006516 6678224 0.049465938369967266 0.5048788742715475 chr12 133851895 9022908 0.06740963958709736 0.4813064678941986 chr13 115169878 4295735 0.037299119132521784 0.3433812905468075 chr14 107349540 4491480 0.04183976941121499 0.4023551769509018 chr15 102531392 5053114 0.049283579413415164 0.40753967947911507 chr16 90354753 6634939 0.07343209714711964 0.881540542570745 chr17 81195210 6984240 0.08601788208934985 0.6171664442833669 chr18 78077248 4743278 0.06075109102206061 0.814292713562946 chr19 59128983 4170709 0.07053578107372488 1.3391361869749139 chr20 63025520 6671649 0.10585631026923698 0.6452049353974209 chr21 48129895 2817857 0.058546917669361216 0.49446280790111863 chr22 51304566 1681260 0.032770182677307906 0.37045723483955034 chrMT 16571 139340 8.40866574135538 7.519460783747818 chrX 155270560 12000463 0.07728743298150016 0.5776394866159097 chrY 59373566 785989 0.013238029192991373 0.8351589051374847