BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618665.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 = 42,789,014 number of mapped reads = 40,969,892 (95.75%) number of supplementary alignments = 159,798 (0.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 20,532,077 number of mapped paired reads (second in pair) = 20,437,815 number of mapped paired reads (both in pair) = 40,334,830 number of mapped paired reads (singletons) = 635,062 number of mapped bases = 4,037,523,832 bp number of sequenced bases = 4,036,198,665 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,647,095 duplication rate = 4.99% >>>>>>> Insert size mean insert size = 49,367.3524 std insert size = 2,115,710.1242 median insert size = 170 >>>>>>> Mapping quality mean mapping quality = 53.6569 >>>>>>> ACTG content number of A's = 1,206,607,818 bp (29.89%) number of C's = 812,576,089 bp (20.13%) number of T's = 1,202,541,667 bp (29.79%) number of G's = 814,143,047 bp (20.17%) number of N's = 330,044 bp (0.01%) GC percentage = 40.3% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 25,781,356 number of insertions = 442,942 mapped reads with insertion percentage = 1.04% number of deletions = 531,153 mapped reads with deletion percentage = 1.25% homopolymer indels = 41.53% >>>>>>> Coverage mean coverageData = 1.3042X std coverageData = 14.4162X There is a 60.73% of reference with a coverageData >= 1X There is a 34.24% of reference with a coverageData >= 2X There is a 16.4% of reference with a coverageData >= 3X There is a 7.31% of reference with a coverageData >= 4X There is a 3.05% of reference with a coverageData >= 5X There is a 1.27% of reference with a coverageData >= 6X There is a 0.55% of reference with a coverageData >= 7X There is a 0.26% of reference with a coverageData >= 8X There is a 0.15% of reference with a coverageData >= 9X There is a 0.1% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 328411106 1.3175939328953568 32.04064444532589 chr2 243199373 350135233 1.439704505323704 9.44820364020893 chr3 198022430 271848661 1.3728175187023006 2.069324345563364 chr4 191154276 279495277 1.4621450424682103 8.875991578451721 chr5 180915260 247680430 1.3690411190299812 1.805412202009811 chr6 171115067 236907150 1.3844902973973647 6.029715988699222 chr7 159138663 219973093 1.3822730997809125 10.021607400284173 chr8 146364022 208419081 1.4239775468864884 18.458473022340243 chr9 141213431 173210615 1.2265873987581253 15.301141675958226 chr10 135534747 213192661 1.572974205647796 34.220301736536115 chr11 135006516 185717172 1.3756163591392878 7.369971425004117 chr12 133851895 180291104 1.346944725735859 1.719898099866754 chr13 115169878 132962342 1.154488867306085 1.5013500817987115 chr14 107349540 123052655 1.146280226259004 1.796856772044902 chr15 102531392 114157065 1.1133864738713388 1.4934709868611757 chr16 90354753 124132952 1.3738397580479247 10.615931099657525 chr17 81195210 106574185 1.3125673915985931 6.387926860497602 chr18 78077248 115416224 1.4782311999521294 18.38320606310575 chr19 59128983 75213410 1.2720227236108559 14.071773639202583 chr20 63025520 82621381 1.310919465638681 4.886908740180708 chr21 48129895 57159953 1.1876184853509446 7.241216305006943 chr22 51304566 47692269 0.9295911206031837 6.518202213485435 chrMT 16571 1988268 119.9847927101563 21.083373126479426 chrX 155270560 110851604 0.7139254472966414 3.360735584371517 chrY 59373566 50419941 0.8491984631679357 16.9005402975069