BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618607.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 = 38,481,152 number of mapped reads = 36,183,650 (94.03%) number of supplementary alignments = 54,593 (0.14%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 18,280,415 number of mapped paired reads (second in pair) = 17,903,235 number of mapped paired reads (both in pair) = 35,386,692 number of mapped paired reads (singletons) = 796,958 number of mapped bases = 3,449,529,826 bp number of sequenced bases = 3,447,211,364 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,267,611 duplication rate = 12.94% >>>>>>> Insert size mean insert size = 29,361.9606 std insert size = 1,703,703.652 median insert size = 210 >>>>>>> Mapping quality mean mapping quality = 52.5326 >>>>>>> ACTG content number of A's = 929,881,931 bp (26.97%) number of C's = 775,223,621 bp (22.49%) number of T's = 935,543,148 bp (27.14%) number of G's = 806,410,130 bp (23.39%) number of N's = 152,534 bp (0%) GC percentage = 45.88% >>>>>>> Mismatches and indels general error rate = 0.0133 number of mismatches = 44,823,838 number of insertions = 628,583 mapped reads with insertion percentage = 1.71% number of deletions = 1,681,010 mapped reads with deletion percentage = 4.53% homopolymer indels = 52.26% >>>>>>> Coverage mean coverageData = 1.1143X std coverageData = 4.718X There is a 23.54% of reference with a coverageData >= 1X There is a 15.36% of reference with a coverageData >= 2X There is a 11.02% of reference with a coverageData >= 3X There is a 8.41% of reference with a coverageData >= 4X There is a 6.65% of reference with a coverageData >= 5X There is a 5.4% of reference with a coverageData >= 6X There is a 4.47% of reference with a coverageData >= 7X There is a 3.76% of reference with a coverageData >= 8X There is a 3.2% of reference with a coverageData >= 9X There is a 2.75% of reference with a coverageData >= 10X There is a 2.39% of reference with a coverageData >= 11X There is a 2.09% of reference with a coverageData >= 12X There is a 1.84% of reference with a coverageData >= 13X There is a 1.62% of reference with a coverageData >= 14X There is a 1.44% of reference with a coverageData >= 15X There is a 1.29% of reference with a coverageData >= 16X There is a 1.16% of reference with a coverageData >= 17X There is a 1.04% of reference with a coverageData >= 18X There is a 0.94% of reference with a coverageData >= 19X There is a 0.86% of reference with a coverageData >= 20X There is a 0.78% of reference with a coverageData >= 21X There is a 0.71% of reference with a coverageData >= 22X There is a 0.65% of reference with a coverageData >= 23X There is a 0.6% of reference with a coverageData >= 24X There is a 0.55% of reference with a coverageData >= 25X There is a 0.5% of reference with a coverageData >= 26X There is a 0.47% of reference with a coverageData >= 27X There is a 0.43% of reference with a coverageData >= 28X There is a 0.4% of reference with a coverageData >= 29X There is a 0.37% of reference with a coverageData >= 30X There is a 0.34% of reference with a coverageData >= 31X There is a 0.32% of reference with a coverageData >= 32X There is a 0.3% of reference with a coverageData >= 33X There is a 0.28% of reference with a coverageData >= 34X There is a 0.26% of reference with a coverageData >= 35X There is a 0.24% of reference with a coverageData >= 36X There is a 0.23% of reference with a coverageData >= 37X There is a 0.21% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.13% of reference with a coverageData >= 46X There is a 0.12% of reference with a coverageData >= 47X There is a 0.12% of reference with a coverageData >= 48X There is a 0.11% of reference with a coverageData >= 49X There is a 0.1% of reference with a coverageData >= 50X There is a 0.1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 318186260 1.2765715837474283 5.09492337169966 chr2 243199373 296140146 1.2176846607248448 5.545786265737716 chr3 198022430 223162035 1.1269533203890085 3.940773866439967 chr4 191154276 168464352 0.8813004632969863 3.765403107269049 chr5 180915260 204022869 1.1277261464842712 3.9164480304064804 chr6 171115067 191172751 1.1172175212367477 4.158452471002919 chr7 159138663 186054009 1.1691314071175778 4.108968304307129 chr8 146364022 172344700 1.1775072701951304 4.126340228569963 chr9 141213431 156521719 1.1084053258361806 5.2815844333553175 chr10 135534747 177108019 1.3067351577378161 4.688297958343311 chr11 135006516 181723666 1.3460362609461014 4.937162461189282 chr12 133851895 158419172 1.1835407485265712 4.330727309890266 chr13 115169878 91907276 0.7980148767718587 3.0594863206117298 chr14 107349540 113733343 1.0594674462508176 4.227022948875721 chr15 102531392 126422224 1.2330099253894846 4.524326937442838 chr16 90354753 134054681 1.4836483588195963 9.533852662530972 chr17 81195210 117470478 1.4467661084933459 5.05085079069793 chr18 78077248 90722613 1.161959665893962 4.965628016094472 chr19 59128983 79967420 1.352423396154133 5.174887098143123 chr20 63025520 111121956 1.763126365319953 5.775017437693075 chr21 48129895 44942252 0.9337699988749196 5.9052966952033685 chr22 51304566 69173625 1.3482937366627368 5.361480885362819 chrMT 16571 5330 0.3216462494719691 0.9657036536778554 chrX 155270560 5269676 0.033938668090074516 0.8739149647220366 chrY 59373566 31419254 0.5291791636702434 4.0558497653323755