BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006159.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 = 16,902,882 number of mapped reads = 14,552,968 (86.1%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,347,178 number of mapped paired reads (second in pair) = 7,205,790 number of mapped paired reads (both in pair) = 13,516,212 number of mapped paired reads (singletons) = 1,036,756 number of mapped bases = 562,632,277 bp number of sequenced bases = 562,570,996 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 842,748 duplication rate = 4.64% >>>>>>> Insert size mean insert size = 57,928.0828 std insert size = 2,312,456.0657 median insert size = 96 >>>>>>> Mapping quality mean mapping quality = 47.9084 >>>>>>> ACTG content number of A's = 158,813,456 bp (28.23%) number of C's = 119,530,829 bp (21.25%) number of T's = 161,510,902 bp (28.71%) number of G's = 122,693,226 bp (21.81%) number of N's = 22,583 bp (0%) GC percentage = 43.06% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 2,759,516 number of insertions = 17,245 mapped reads with insertion percentage = 0.12% number of deletions = 47,651 mapped reads with deletion percentage = 0.33% homopolymer indels = 45.45% >>>>>>> Coverage mean coverageData = 0.1817X std coverageData = 1.2008X There is a 11.43% of reference with a coverageData >= 1X There is a 4.03% of reference with a coverageData >= 2X There is a 1.44% of reference with a coverageData >= 3X There is a 0.56% of reference with a coverageData >= 4X There is a 0.23% of reference with a coverageData >= 5X There is a 0.1% of reference with a coverageData >= 6X There is a 0.05% 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 0.01% 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% of reference with a coverageData >= 17X There is a 0% 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 46121953 0.18504247979386176 2.5420848056579928 chr2 243199373 51523264 0.2118560725072264 0.9931817128286449 chr3 198022430 40974140 0.2069166609055348 0.6567447080633372 chr4 191154276 38376311 0.20076093406354142 0.7022707120028133 chr5 180915260 34578127 0.19112885778678923 0.6356578165826902 chr6 171115067 34062776 0.19906356931152064 0.7989272627599765 chr7 159138663 30911496 0.19424252672023518 1.584701575449986 chr8 146364022 29716081 0.20302858990852274 2.061943480372096 chr9 141213431 23451563 0.16607175984556313 0.8548978187892934 chr10 135534747 26351178 0.1944237812315391 0.8531116624389505 chr11 135006516 25503766 0.18890766724177965 1.3223522253922877 chr12 133851895 25799116 0.19274374860363389 0.6485474498546198 chr13 115169878 18639393 0.16184260436570055 0.570701351233066 chr14 107349540 17793124 0.16574942007203758 0.6491365921240096 chr15 102531392 15755162 0.1536618365622111 0.5646546507143774 chr16 90354753 14982268 0.1658160473306811 0.6431516433885754 chr17 81195210 14067749 0.17325836093040464 0.817364025467482 chr18 78077248 15262956 0.19548532243349562 1.464767257125907 chr19 59128983 9598050 0.16232394864630093 1.7609267362450025 chr20 63025520 11939838 0.18944449803825497 0.6555548979701241 chr21 48129895 7434863 0.154474947431321 0.6798363445536711 chr22 51304566 5563397 0.10843863292791522 0.6869417957936502 chrMT 16571 175996 10.620722949731459 6.376462992956726 chrX 155270560 19825916 0.12768625295097796 0.6690705854629747 chrY 59373566 4223794 0.07113930128434597 0.698417639143168