BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083610.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 = 1,920,965 number of mapped reads = 1,730,532 (90.09%) number of supplementary alignments = 14,416 (0.75%) number of secondary alignments = 0 number of mapped bases = 114,288,138 bp number of sequenced bases = 114,246,477 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 81,173 duplication rate = 3.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1803 >>>>>>> ACTG content number of A's = 30,132,564 bp (26.38%) number of C's = 21,592,158 bp (18.9%) number of T's = 35,655,861 bp (31.21%) number of G's = 26,860,247 bp (23.51%) number of N's = 5,647 bp (0%) GC percentage = 42.41% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 797,737 number of insertions = 8,423 mapped reads with insertion percentage = 0.48% number of deletions = 25,799 mapped reads with deletion percentage = 1.48% homopolymer indels = 47.82% >>>>>>> Coverage mean coverageData = 0.0369X std coverageData = 0.3053X There is a 3.09% of reference with a coverageData >= 1X There is a 0.45% 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 10181105 0.04084685911374319 0.4487935845295901 chr2 243199373 10284972 0.04229028995070641 0.5007664553022123 chr3 198022430 8455111 0.04269774388689201 0.24127902596007292 chr4 191154276 4839310 0.025316252930695622 0.18909210071635105 chr5 180915260 5863653 0.03241104702831591 0.21063386423362743 chr6 171115067 8082677 0.04723533200030831 0.29473154653708217 chr7 159138663 7532106 0.04733045922347607 0.4338082252757595 chr8 146364022 8231659 0.056241000264395574 0.3176269387790743 chr9 141213431 4422794 0.031319924519077794 0.2517588664367211 chr10 135534747 4970606 0.036674034592767565 0.2518347761259009 chr11 135006516 4393143 0.0325402293915947 0.2515847517841369 chr12 133851895 4089709 0.03055398655357102 0.2033083620149234 chr13 115169878 3119208 0.02708354002076828 0.19133294627996422 chr14 107349540 2233837 0.0208090039323876 0.16992337866343343 chr15 102531392 3066681 0.029909678784035235 0.2112660433060106 chr16 90354753 3663513 0.04054588030360727 0.24333312156938694 chr17 81195210 2802772 0.03451893282867302 0.22057156976900336 chr18 78077248 3282954 0.04204751171557686 0.41293857238262843 chr19 59128983 3579333 0.06053432375117969 0.3776123453024498 chr20 63025520 2892771 0.04589840750223084 0.2548833963657025 chr21 48129895 2095713 0.04354285418657157 0.2481219934204383 chr22 51304566 1112593 0.021686042524947973 0.17259607586514944 chrMT 16571 3874 0.23378190815279706 0.5774893841140908 chrX 155270560 4859127 0.031294580247536945 0.21886814922243952 chrY 59373566 228917 0.0038555373278404735 0.08574125700613536