BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708620.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,575,942 number of mapped reads = 2,584,359 (72.27%) number of supplementary alignments = 836 (0.02%) number of secondary alignments = 0 number of mapped bases = 126,028,860 bp number of sequenced bases = 126,003,926 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 96,675 duplication rate = 2.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.551 >>>>>>> ACTG content number of A's = 37,077,714 bp (29.43%) number of C's = 23,902,397 bp (18.97%) number of T's = 39,594,734 bp (31.42%) number of G's = 25,418,035 bp (20.17%) number of N's = 11,046 bp (0.01%) GC percentage = 39.14% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 802,667 number of insertions = 6,014 mapped reads with insertion percentage = 0.23% number of deletions = 16,465 mapped reads with deletion percentage = 0.64% homopolymer indels = 48.08% >>>>>>> Coverage mean coverageData = 0.0407X std coverageData = 0.4083X There is a 3.41% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.09% 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 9952859 0.039931130201677614 0.6887398092566797 chr2 243199373 10733095 0.04413290572093703 0.4354234838086366 chr3 198022430 8630269 0.043582280047770344 0.24496264770145143 chr4 191154276 8369365 0.04378329993517906 0.24845305411774365 chr5 180915260 7766836 0.04293079533478823 0.24543555008421067 chr6 171115067 7605151 0.04444466015374321 0.34215408431679895 chr7 159138663 7164364 0.04501963171576979 0.6980709256421356 chr8 146364022 6679217 0.04563428162694245 0.6772971026339464 chr9 141213431 5313152 0.037624976338121834 0.323141674761883 chr10 135534747 5724563 0.04223686638821851 0.3286494558224898 chr11 135006516 5769113 0.04273210783396558 0.3301269366577377 chr12 133851895 5675954 0.04240473397855144 0.2495248989018435 chr13 115169878 4242193 0.03683422326799721 0.23054870035183245 chr14 107349540 3896070 0.03629330875567795 0.24674174570363136 chr15 102531392 3552817 0.0346510169295273 0.21747924471591432 chr16 90354753 3208198 0.03550668773340568 0.23398090489215903 chr17 81195210 3098589 0.038162214248845465 0.26231697774002616 chr18 78077248 3480667 0.0445797859063885 0.6747143122142926 chr19 59128983 2178471 0.03684269353998529 0.515724871804035 chr20 63025520 2402935 0.03812638118654158 0.23787965406300113 chr21 48129895 1638100 0.03403497971479057 0.23399641100259755 chr22 51304566 1304810 0.025432629134802542 0.18429524655441043 chrMT 16571 18370 1.1085631524953232 1.230418928045853 chrX 155270560 7325920 0.04718164216062594 0.28027496973852645 chrY 59373566 297782 0.0050153969192283316 0.08944862975544221