BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1505992.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 5,139,615 number of mapped reads = 3,607,738 (70.19%) number of supplementary alignments = 202 (0%) number of secondary alignments = 0 number of mapped bases = 169,079,501 bp number of sequenced bases = 169,041,366 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 223,664 duplication rate = 4.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8282 >>>>>>> ACTG content number of A's = 50,453,585 bp (29.85%) number of C's = 33,170,186 bp (19.62%) number of T's = 50,794,756 bp (30.05%) number of G's = 34,074,183 bp (20.16%) number of N's = 548,656 bp (0.32%) GC percentage = 39.78% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,338,170 number of insertions = 8,066 mapped reads with insertion percentage = 0.22% number of deletions = 27,213 mapped reads with deletion percentage = 0.75% homopolymer indels = 46.34% >>>>>>> Coverage mean coverageData = 0.0546X std coverageData = 0.5472X There is a 4.3% of reference with a coverageData >= 1X There is a 0.81% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.05% 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% of reference with a coverageData >= 7X There is a 0% 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 16404662 0.0658159323101546 1.0450583236698383 chr2 243199373 10473009 0.04306347039800962 0.3586438946016129 chr3 198022430 10423960 0.052640299384266724 0.28007042861045106 chr4 191154276 7366854 0.03853878738239682 0.24459440762289048 chr5 180915260 11813186 0.0652967914370518 0.3154089845267177 chr6 171115067 11425001 0.06676794276684005 0.37814852638203406 chr7 159138663 10373754 0.06518688673411815 0.6729769004616905 chr8 146364022 9997510 0.06830578897319452 0.6876142487233384 chr9 141213431 8206751 0.058115937994594864 0.3909467859722324 chr10 135534747 5369325 0.039615855851341204 0.4468821366490914 chr11 135006516 8574032 0.06350828281503094 0.40453917318812505 chr12 133851895 4877700 0.0364410231173791 0.2549368932914706 chr13 115169878 5347947 0.046435292742083134 0.2616974644449708 chr14 107349540 6341413 0.059072567986784105 1.3483774099309034 chr15 102531392 5511213 0.05375146959869617 0.28155292561848844 chr16 90354753 5099828 0.05644227703217782 0.32483987824632504 chr17 81195210 2683793 0.03305358776706163 0.24365275605967568 chr18 78077248 5317176 0.06810147816685343 0.6577007185796969 chr19 59128983 3988787 0.06745908347518847 0.7774454832699667 chr20 63025520 4044517 0.06417268750817129 0.34519113487667785 chr21 48129895 2552520 0.0530339823097474 0.3073511151645682 chr22 51304566 1007700 0.019641526643067207 0.16440053018455245 chrMT 16571 45617 2.75282119365156 2.433672467962517 chrX 155270560 11351193 0.07310589335157934 0.38253286795285407 chrY 59373566 482053 0.00811898345469093 0.13789686885031435