BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085048.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,412,474 number of mapped reads = 2,211,982 (91.69%) number of supplementary alignments = 15,666 (0.65%) number of secondary alignments = 0 number of mapped bases = 148,448,192 bp number of sequenced bases = 148,395,020 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 76,109 duplication rate = 2.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.326 >>>>>>> ACTG content number of A's = 42,937,480 bp (28.93%) number of C's = 28,076,113 bp (18.92%) number of T's = 46,008,208 bp (31%) number of G's = 31,356,163 bp (21.13%) number of N's = 17,056 bp (0.01%) GC percentage = 40.05% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,277,354 number of insertions = 10,524 mapped reads with insertion percentage = 0.47% number of deletions = 30,877 mapped reads with deletion percentage = 1.38% homopolymer indels = 47.32% >>>>>>> Coverage mean coverageData = 0.048X std coverageData = 0.3731X There is a 4.03% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 12346542 0.04953464890264005 0.537783008302112 chr2 243199373 13501276 0.05551525825685414 0.45523034163434545 chr3 198022430 9946814 0.050230744062680174 0.261187086664992 chr4 191154276 9227605 0.04827307655937553 0.25598595344108466 chr5 180915260 7697865 0.04254956160138178 0.236196011832532 chr6 171115067 10024402 0.05858281316630055 0.338994357749969 chr7 159138663 13052639 0.08202053953412942 0.40272587888353506 chr8 146364022 8732281 0.05966139001017613 0.7679171363128527 chr9 141213431 4710517 0.03335742901112572 0.30982251350146844 chr10 135534747 11115631 0.08201314604586232 0.4913250450456831 chr11 135006516 5447723 0.04035155606859746 0.3038909086741859 chr12 133851895 6516089 0.04868133544168351 0.25835633857437307 chr13 115169878 2754096 0.023913336089493815 0.1760271140848331 chr14 107349540 5334153 0.049689574822584244 0.26642733676137753 chr15 102531392 2576818 0.025131990795560447 0.18288713374047494 chr16 90354753 3945405 0.04366571617986715 0.25539973560222795 chr17 81195210 2448629 0.03015730854073781 0.2211139514014587 chr18 78077248 3584722 0.04591250449810936 0.47525116918127186 chr19 59128983 2292160 0.03876542236486631 0.4134542523460669 chr20 63025520 3447452 0.05469930275862857 0.27205170435678344 chr21 48129895 1764556 0.036662369614560764 0.228661064751658 chr22 51304566 887368 0.017296082379880184 0.14691633838324966 chrMT 16571 24005 1.448615050389234 1.6118878619141894 chrX 155270560 6790928 0.043736095239174766 0.2646413081136339 chrY 59373566 278516 0.0046909090823347216 0.09822007179297455