BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618615.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 37,830,542 number of mapped reads = 36,551,903 (96.62%) number of supplementary alignments = 103,202 (0.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 18,452,477 number of mapped paired reads (second in pair) = 18,099,426 number of mapped paired reads (both in pair) = 35,934,686 number of mapped paired reads (singletons) = 617,217 number of mapped bases = 3,431,682,727 bp number of sequenced bases = 3,429,300,425 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,784,068 duplication rate = 23.01% >>>>>>> Insert size mean insert size = 65,334.2431 std insert size = 2,562,615.8854 median insert size = 204 >>>>>>> Mapping quality mean mapping quality = 52.1042 >>>>>>> ACTG content number of A's = 934,872,015 bp (27.26%) number of C's = 739,961,186 bp (21.58%) number of T's = 949,270,825 bp (27.68%) number of G's = 805,075,056 bp (23.48%) number of N's = 121,343 bp (0%) GC percentage = 45.05% >>>>>>> Mismatches and indels general error rate = 0.0122 number of mismatches = 40,814,072 number of insertions = 612,959 mapped reads with insertion percentage = 1.65% number of deletions = 1,758,389 mapped reads with deletion percentage = 4.69% homopolymer indels = 53.16% >>>>>>> Coverage mean coverageData = 1.1085X std coverageData = 4.0727X There is a 24.1% of reference with a coverageData >= 1X There is a 16.18% of reference with a coverageData >= 2X There is a 11.75% of reference with a coverageData >= 3X There is a 9.04% of reference with a coverageData >= 4X There is a 7.12% of reference with a coverageData >= 5X There is a 5.75% of reference with a coverageData >= 6X There is a 4.72% of reference with a coverageData >= 7X There is a 3.93% of reference with a coverageData >= 8X There is a 3.3% of reference with a coverageData >= 9X There is a 2.8% of reference with a coverageData >= 10X There is a 2.4% of reference with a coverageData >= 11X There is a 2.07% of reference with a coverageData >= 12X There is a 1.79% of reference with a coverageData >= 13X There is a 1.56% of reference with a coverageData >= 14X There is a 1.37% of reference with a coverageData >= 15X There is a 1.2% of reference with a coverageData >= 16X There is a 1.06% of reference with a coverageData >= 17X There is a 0.94% of reference with a coverageData >= 18X There is a 0.83% of reference with a coverageData >= 19X There is a 0.74% of reference with a coverageData >= 20X There is a 0.67% of reference with a coverageData >= 21X There is a 0.6% of reference with a coverageData >= 22X There is a 0.54% of reference with a coverageData >= 23X There is a 0.48% of reference with a coverageData >= 24X There is a 0.43% of reference with a coverageData >= 25X There is a 0.39% of reference with a coverageData >= 26X There is a 0.36% of reference with a coverageData >= 27X There is a 0.32% of reference with a coverageData >= 28X There is a 0.29% of reference with a coverageData >= 29X There is a 0.27% of reference with a coverageData >= 30X There is a 0.24% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.14% of reference with a coverageData >= 37X There is a 0.13% of reference with a coverageData >= 38X There is a 0.12% of reference with a coverageData >= 39X There is a 0.11% of reference with a coverageData >= 40X There is a 0.1% of reference with a coverageData >= 41X There is a 0.1% of reference with a coverageData >= 42X There is a 0.09% of reference with a coverageData >= 43X There is a 0.08% of reference with a coverageData >= 44X There is a 0.08% of reference with a coverageData >= 45X There is a 0.07% of reference with a coverageData >= 46X There is a 0.07% of reference with a coverageData >= 47X There is a 0.06% of reference with a coverageData >= 48X There is a 0.06% of reference with a coverageData >= 49X There is a 0.05% of reference with a coverageData >= 50X There is a 0.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 312331474 1.2530820294325364 4.797840455392915 chr2 243199373 300488331 1.2355637569838636 4.452254131344794 chr3 198022430 229693838 1.1599384877763594 3.5238106270471072 chr4 191154276 183930376 0.9622090588232513 3.452053421952647 chr5 180915260 205852047 1.1378368358755364 3.518867077672875 chr6 171115067 193817992 1.132676364495711 3.7056596726661235 chr7 159138663 180614689 1.1349516553372074 3.691866987950248 chr8 146364022 176781480 1.20782059405282 3.7557712008298494 chr9 141213431 157664500 1.11649790592511 5.28875088700702 chr10 135534747 177844363 1.3121680376176892 4.067215398139965 chr11 135006516 176592032 1.308025991871385 4.562753560335689 chr12 133851895 159340350 1.1904228176971272 3.8600502530424885 chr13 115169878 97454168 0.8461775743133113 2.929537430266173 chr14 107349540 110237096 1.0268986341254933 3.597825130972179 chr15 102531392 117000617 1.1411199508536858 3.7867859909597006 chr16 90354753 123048849 1.3618414628392599 5.428780694221867 chr17 81195210 114598041 1.4113891817017286 4.52113515726993 chr18 78077248 92554234 1.1854187534888525 5.221097830603639 chr19 59128983 75164634 1.2711978151222387 4.475843543702922 chr20 63025520 100791295 1.5992140167982747 4.668104839829462 chr21 48129895 45539991 0.9461892863053202 5.510549306167433 chr22 51304566 62156602 1.2115218360876496 4.33953253100282 chrMT 16571 170108 10.265403415605576 22.918288629843964 chrX 155270560 5548176 0.03573231139244941 0.9092562347023544 chrY 59373566 32467444 0.5468333163616954 3.0224423236330296