BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927047.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 32,316,992 number of mapped reads = 31,609,885 (97.81%) number of supplementary alignments = 517,199 (1.6%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,865,147 number of mapped paired reads (second in pair) = 15,744,738 number of mapped paired reads (both in pair) = 31,193,784 number of mapped paired reads (singletons) = 416,101 number of mapped bases = 2,922,952,879 bp number of sequenced bases = 2,920,814,578 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,564,740 duplication rate = 6.26% >>>>>>> Insert size mean insert size = 181,293.8422 std insert size = 4,199,703.3658 median insert size = 184 >>>>>>> Mapping quality mean mapping quality = 52.946 >>>>>>> ACTG content number of A's = 830,326,848 bp (28.43%) number of C's = 579,978,123 bp (19.86%) number of T's = 846,763,445 bp (28.99%) number of G's = 663,304,240 bp (22.71%) number of N's = 441,922 bp (0.02%) GC percentage = 42.57% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 29,887,790 number of insertions = 480,129 mapped reads with insertion percentage = 1.49% number of deletions = 1,483,097 mapped reads with deletion percentage = 4.57% homopolymer indels = 52.15% >>>>>>> Coverage mean coverageData = 0.9442X std coverageData = 3.6148X There is a 37.32% of reference with a coverageData >= 1X There is a 21.05% of reference with a coverageData >= 2X There is a 12.22% of reference with a coverageData >= 3X There is a 7.53% of reference with a coverageData >= 4X There is a 4.78% of reference with a coverageData >= 5X There is a 3.11% of reference with a coverageData >= 6X There is a 2.07% of reference with a coverageData >= 7X There is a 1.4% of reference with a coverageData >= 8X There is a 0.96% of reference with a coverageData >= 9X There is a 0.67% of reference with a coverageData >= 10X There is a 0.47% of reference with a coverageData >= 11X There is a 0.34% of reference with a coverageData >= 12X There is a 0.24% of reference with a coverageData >= 13X There is a 0.18% of reference with a coverageData >= 14X There is a 0.13% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% 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 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 238154655 0.9554826946649814 4.136306975081799 chr2 243199373 254761018 1.047539781280604 6.329243027264966 chr3 198022430 197025795 0.9949670600446626 1.8559713130526627 chr4 191154276 177762824 0.9299442718194805 2.683015966540154 chr5 180915260 177493487 0.9810863218503514 1.835030102354704 chr6 171115067 167713489 0.9801211076287046 1.8947296416882051 chr7 159138663 152019493 0.9552643596107125 2.4117401374449625 chr8 146364022 148444212 1.0142124408141777 2.2858469545993607 chr9 141213431 124771916 0.8835697505288997 4.324942473739306 chr10 135534747 142626951 1.0523275702871973 6.1626606421013825 chr11 135006516 137570895 1.018994483199611 2.740908669528183 chr12 133851895 131452404 0.9820735373227253 1.8682616647832482 chr13 115169878 89016669 0.7729162394354537 1.6230493095960998 chr14 107349540 88342092 0.8229387103102631 1.7539247004832514 chr15 102531392 85909399 0.8378838648752569 1.7479200920726488 chr16 90354753 89443209 0.9899114991770273 3.7814874723612 chr17 81195210 76022114 0.9362881628115747 2.7455426237484044 chr18 78077248 77290835 0.9899277571873435 4.385583411379372 chr19 59128983 47341578 0.8006492856472772 2.6733592759660967 chr20 63025520 67409547 1.069559553019158 2.094739620299892 chr21 48129895 37571037 0.7806174727786129 2.5371419629614507 chr22 51304566 36045313 0.7025751470151799 1.716328234530598 chrMT 16571 7206051 434.85915152978095 333.32958920104414 chrX 155270560 166247177 1.070693484972296 2.28428438958985 chrY 59373566 5310719 0.08944584867952853 3.7903950341898858