BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2093987.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 447,882 number of mapped reads = 438,132 (97.82%) number of supplementary alignments = 20,217 (4.51%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 219,858 number of mapped paired reads (second in pair) = 218,274 number of mapped paired reads (both in pair) = 434,688 number of mapped paired reads (singletons) = 3,444 number of mapped bases = 59,335,490 bp number of sequenced bases = 58,807,761 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 439,899 duplication rate = 45.01% >>>>>>> Insert size mean insert size = 694,111.9687 std insert size = 7,332,838.99 median insert size = 187 >>>>>>> Mapping quality mean mapping quality = 33.921 >>>>>>> ACTG content number of A's = 16,371,653 bp (27.84%) number of C's = 12,612,940 bp (21.45%) number of T's = 15,721,591 bp (26.73%) number of G's = 14,100,945 bp (23.98%) number of N's = 632 bp (0%) GC percentage = 45.43% >>>>>>> Mismatches and indels general error rate = 0.0259 number of mismatches = 1,476,635 number of insertions = 21,209 mapped reads with insertion percentage = 4.77% number of deletions = 118,760 mapped reads with deletion percentage = 26.4% homopolymer indels = 34.45% >>>>>>> Coverage mean coverageData = 0.0192X std coverageData = 10.1435X There is a 0.01% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% 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 765764 0.0030722651639852887 2.789567910785421 chr2 243199373 1711334 0.007036753338998123 6.492755194426689 chr3 198022430 2618710 0.01322430999356992 6.936389480327875 chr4 191154276 7051465 0.036888868758551865 19.596211675541714 chr5 180915260 116624 6.446332940626457E-4 0.3085266999240521 chr6 171115067 1059887 0.00619400160711739 4.322707379906991 chr7 159138663 702104 0.004411900833928711 2.655460588271214 chr8 146364022 784865 0.005362417548214137 2.5590782314290337 chr9 141213431 76107 5.389501512784574E-4 0.15690948123886256 chr10 135534747 72095 5.319300149650923E-4 0.23270417614672936 chr11 135006516 2365630 0.0175223394402682 9.271869757838862 chr12 133851895 941801 0.007036142446843954 3.229401373683181 chr13 115169878 784335 0.006810244255012582 5.841370107148365 chr14 107349540 184993 0.0017232770629478245 0.9801094180644685 chr15 102531392 137625 0.0013422718380727728 0.5026639264542586 chr16 90354753 186947 0.002069033380014884 0.5875014298618207 chr17 81195210 117303 0.001444703449870996 0.6686303250780228 chr18 78077248 15995 2.04861216419923E-4 0.035606430538117705 chr19 59128983 74890 0.001266553155497364 0.28459987507946766 chr20 63025520 661597 0.01049728744800519 3.997905976316167 chr21 48129895 19980 4.1512660686253314E-4 0.10080744280272877 chr22 51304566 21620 4.2140498761845095E-4 0.08250026819293652 chrMT 16571 5763772 347.8228230040432 1856.0718777892478 chrX 155270560 32960904 0.21228044775519583 30.10570817004643 chrY 59373566 139143 0.0023435176522831726 1.4551424097055354