BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081032.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 = 2,712,602 number of mapped reads = 2,003,526 (73.86%) number of supplementary alignments = 9,055 (0.33%) number of secondary alignments = 0 number of mapped bases = 125,813,582 bp number of sequenced bases = 125,769,826 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 67,145 duplication rate = 2.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7739 >>>>>>> ACTG content number of A's = 35,318,068 bp (28.08%) number of C's = 25,388,892 bp (20.19%) number of T's = 36,378,527 bp (28.92%) number of G's = 28,682,748 bp (22.81%) number of N's = 1,591 bp (0%) GC percentage = 42.99% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 960,070 number of insertions = 8,428 mapped reads with insertion percentage = 0.42% number of deletions = 24,928 mapped reads with deletion percentage = 1.23% homopolymer indels = 45.77% >>>>>>> Coverage mean coverageData = 0.0406X std coverageData = 0.3204X There is a 3.48% of reference with a coverageData >= 1X There is a 0.43% of reference with a coverageData >= 2X There is a 0.07% 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 10085289 0.04046244281975129 0.4451444285773702 chr2 243199373 10832662 0.04454231055932862 0.3600439141841809 chr3 198022430 7640412 0.038583568538170146 0.22261492385586074 chr4 191154276 8200633 0.04290059930440688 0.25223526518774847 chr5 180915260 7817557 0.04321115311113059 0.2366649548769689 chr6 171115067 6531406 0.03816967210724933 0.2604248361105347 chr7 159138663 6263234 0.03935708571335678 0.5320322529199469 chr8 146364022 6824738 0.04662852186447842 0.3171621707717262 chr9 141213431 5769845 0.04085903840124103 0.3213090671521836 chr10 135534747 5985070 0.04415893438750434 0.30178855358171836 chr11 135006516 5731635 0.042454506418045775 0.30426196639402403 chr12 133851895 5392241 0.04028513006857318 0.23109479832910548 chr13 115169878 3816462 0.03313767511327918 0.2068695221232259 chr14 107349540 3971389 0.03699493262849566 0.23550196018311365 chr15 102531392 3983709 0.03885355423634549 0.24385184257338383 chr16 90354753 3977136 0.04401689859082455 0.2589675508362933 chr17 81195210 3659363 0.04506870540762195 0.2632692648824604 chr18 78077248 3276068 0.04195931700871424 0.6126516320293685 chr19 59128983 2680629 0.04533527999289282 0.34504042000970364 chr20 63025520 2705900 0.04293340221548351 0.24346599848455866 chr21 48129895 1620287 0.033664877099773435 0.23619800895598178 chr22 51304566 1513337 0.02949712117241183 0.19571168887884519 chrMT 16571 43057 2.598334439683785 2.1673330457558104 chrX 155270560 7173953 0.04620291831239612 0.2793212967322777 chrY 59373566 317570 0.005348676547404951 0.12975708990083734