BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927034.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 = 36,794,008 number of mapped reads = 36,056,457 (98%) number of supplementary alignments = 790,103 (2.15%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 18,086,661 number of mapped paired reads (second in pair) = 17,969,796 number of mapped paired reads (both in pair) = 35,633,504 number of mapped paired reads (singletons) = 422,953 number of mapped bases = 3,313,030,507 bp number of sequenced bases = 3,310,575,243 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,504,766 duplication rate = 7.67% >>>>>>> Insert size mean insert size = 228,175.1911 std insert size = 4,730,554.1938 median insert size = 183 >>>>>>> Mapping quality mean mapping quality = 53.0914 >>>>>>> ACTG content number of A's = 927,935,482 bp (28.03%) number of C's = 665,575,559 bp (20.1%) number of T's = 948,368,340 bp (28.65%) number of G's = 768,242,896 bp (23.21%) number of N's = 452,966 bp (0.01%) GC percentage = 43.31% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 33,381,105 number of insertions = 546,544 mapped reads with insertion percentage = 1.49% number of deletions = 1,693,249 mapped reads with deletion percentage = 4.58% homopolymer indels = 52.06% >>>>>>> Coverage mean coverageData = 1.0702X std coverageData = 3.3224X There is a 37.03% of reference with a coverageData >= 1X There is a 22.14% of reference with a coverageData >= 2X There is a 13.81% of reference with a coverageData >= 3X There is a 9.14% of reference with a coverageData >= 4X There is a 6.24% of reference with a coverageData >= 5X There is a 4.39% of reference with a coverageData >= 6X There is a 3.15% of reference with a coverageData >= 7X There is a 2.3% of reference with a coverageData >= 8X There is a 1.71% of reference with a coverageData >= 9X There is a 1.29% of reference with a coverageData >= 10X There is a 0.98% of reference with a coverageData >= 11X There is a 0.75% of reference with a coverageData >= 12X There is a 0.58% of reference with a coverageData >= 13X There is a 0.45% of reference with a coverageData >= 14X There is a 0.36% of reference with a coverageData >= 15X There is a 0.28% of reference with a coverageData >= 16X There is a 0.23% of reference with a coverageData >= 17X There is a 0.18% of reference with a coverageData >= 18X There is a 0.15% of reference with a coverageData >= 19X There is a 0.12% of reference with a coverageData >= 20X There is a 0.1% of reference with a coverageData >= 21X There is a 0.08% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% 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 0.01% 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 276910385 1.1109716954326063 4.040176220340245 chr2 243199373 280850323 1.154815160645994 5.292013662884972 chr3 198022430 213187917 1.0765846929562475 2.1860323182709522 chr4 191154276 177041112 0.9261687245751176 2.6197223670181895 chr5 180915260 186658880 1.0317475706582186 2.122920431735078 chr6 171115067 180485711 1.0547622378571724 2.17691443483447 chr7 159138663 171023883 1.0746846792347375 2.443156762768272 chr8 146364022 158680146 1.084147209346297 2.3571706742957397 chr9 141213431 141553971 1.002411526988534 3.690261509241234 chr10 135534747 164221241 1.2116541671782513 4.13174868417219 chr11 135006516 164053736 1.215154207816162 3.1244741553230817 chr12 133851895 149758480 1.1188372043593406 2.2680176897665087 chr13 115169878 94409438 0.8197407138001831 1.8943957730963215 chr14 107349540 107234800 0.9989311551777492 2.211023490736419 chr15 102531392 116869115 1.1398373973114497 2.4354890382931065 chr16 90354753 112197291 1.241741992255792 4.459559130059714 chr17 81195210 103580271 1.275694354383713 2.9248123319969306 chr18 78077248 87921507 1.126083580712271 3.3264871166010206 chr19 59128983 67977682 1.1496507896981756 3.0356010438259866 chr20 63025520 85262362 1.3528228247858962 2.69798612101664 chr21 48129895 43369904 0.9011011555292194 2.909438776800308 chr22 51304566 53242004 1.0377634614431783 2.454889902225162 chrMT 16571 5956160 359.4327439502746 287.0060340658379 chrX 155270560 165497999 1.0658685007640856 2.3393917374694246 chrY 59373566 5086189 0.08566419945199182 2.4167757961123986