BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006040.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 24,488,990 number of mapped reads = 17,402,452 (71.06%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,733,929 number of mapped paired reads (second in pair) = 8,668,523 number of mapped paired reads (both in pair) = 15,705,052 number of mapped paired reads (singletons) = 1,697,400 number of mapped bases = 670,320,608 bp number of sequenced bases = 670,230,178 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,024,214 duplication rate = 4.91% >>>>>>> Insert size mean insert size = 60,268.289 std insert size = 2,380,886.4083 median insert size = 68 >>>>>>> Mapping quality mean mapping quality = 46.29 >>>>>>> ACTG content number of A's = 191,413,882 bp (28.56%) number of C's = 142,179,899 bp (21.21%) number of T's = 193,430,264 bp (28.86%) number of G's = 143,122,413 bp (21.35%) number of N's = 83,720 bp (0.01%) GC percentage = 42.57% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 3,930,193 number of insertions = 24,430 mapped reads with insertion percentage = 0.14% number of deletions = 69,345 mapped reads with deletion percentage = 0.4% homopolymer indels = 42.18% >>>>>>> Coverage mean coverageData = 0.2165X std coverageData = 1.2438X There is a 13.38% of reference with a coverageData >= 1X There is a 5.13% of reference with a coverageData >= 2X There is a 1.7% of reference with a coverageData >= 3X There is a 0.66% of reference with a coverageData >= 4X There is a 0.27% of reference with a coverageData >= 5X There is a 0.12% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 55304457 0.22188292561967177 1.8545764171962553 chr2 243199373 57286118 0.2355520793221782 0.965650798881116 chr3 198022430 45649175 0.23052527433382167 0.6876280230233389 chr4 191154276 44683653 0.23375701519750466 0.8102138580287225 chr5 180915260 41374518 0.22869556719538198 0.6816935129847107 chr6 171115067 39269694 0.22949290608056155 0.9361778253927371 chr7 159138663 36574879 0.22983025187285883 1.3387384407720804 chr8 146364022 33716393 0.23035984212021723 2.592642245497913 chr9 141213431 27648984 0.19579571011202185 0.8109419800996223 chr10 135534747 31213020 0.23029533526188675 1.262135104980806 chr11 135006516 30377077 0.2250045249667801 0.8722860845348253 chr12 133851895 30086827 0.2247769969935801 0.6920784061680755 chr13 115169878 21662360 0.1880905005386912 0.615809739860842 chr14 107349540 20169177 0.18788321775761685 0.7164437712327694 chr15 102531392 19413873 0.18934564937926524 0.6239456975296648 chr16 90354753 19057715 0.21092100157697294 0.8621190514648676 chr17 81195210 17589968 0.21663800118258209 0.7191358803854163 chr18 78077248 17192979 0.22020472596575125 1.2724874049321826 chr19 59128983 13172552 0.22277656965620396 3.954289324917686 chr20 63025520 13450572 0.21341469296881643 0.6995798440545173 chr21 48129895 8529301 0.17721420335531585 0.7258114321717367 chr22 51304566 7632795 0.1487741851280839 0.7601161365862911 chrMT 16571 113176 6.829762838694104 5.222138967381957 chrX 155270560 37364254 0.2406396550640379 0.7916299559059051 chrY 59373566 1787091 0.03009910167767252 0.5946208262535814