BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084365.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 = 2,200,837 number of mapped reads = 1,979,071 (89.92%) number of supplementary alignments = 12,096 (0.55%) number of secondary alignments = 0 number of mapped bases = 132,865,105 bp number of sequenced bases = 132,821,900 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 70,207 duplication rate = 3.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1006 >>>>>>> ACTG content number of A's = 36,444,756 bp (27.44%) number of C's = 25,689,735 bp (19.34%) number of T's = 40,814,247 bp (30.73%) number of G's = 29,700,609 bp (22.36%) number of N's = 172,553 bp (0.13%) GC percentage = 41.7% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 1,313,376 number of insertions = 8,997 mapped reads with insertion percentage = 0.45% number of deletions = 24,927 mapped reads with deletion percentage = 1.25% homopolymer indels = 46.87% >>>>>>> Coverage mean coverageData = 0.0429X std coverageData = 0.2951X There is a 3.66% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.08% 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 12847013 0.051542551623171284 0.4526791676179644 chr2 243199373 12647688 0.05200543012913113 0.33631828547448717 chr3 198022430 8846510 0.0446742826052584 0.24386438540130398 chr4 191154276 6191238 0.03238869738911831 0.21116644594572342 chr5 180915260 6696427 0.03701416342656778 0.2182854970780714 chr6 171115067 6301765 0.03682764534113177 0.2429777481514036 chr7 159138663 7403609 0.04652300616601259 0.4036110382120059 chr8 146364022 6485940 0.04431375901927592 0.2768777207615065 chr9 141213431 4789066 0.0339136721350535 0.24787150938126432 chr10 135534747 9598251 0.07081764058629186 0.40977888521086836 chr11 135006516 7418448 0.054948814470554885 0.30146456970723207 chr12 133851895 6951099 0.05193127075264792 0.26006096014562124 chr13 115169878 3240470 0.02813643685547709 0.19046924765725123 chr14 107349540 3458869 0.032220622463775814 0.20688905294631577 chr15 102531392 2900879 0.028292593550275802 0.19346398738448506 chr16 90354753 2961191 0.0327729411202087 0.2198200864431063 chr17 81195210 3812743 0.0469577330978022 0.2595664506434907 chr18 78077248 3628234 0.046469798730610995 0.3892738042986445 chr19 59128983 2608483 0.04411513385914315 0.3365821691190843 chr20 63025520 2675791 0.04245567509796032 0.23677825641769928 chr21 48129895 1361324 0.028284375023049604 0.1961530702858156 chr22 51304566 1555623 0.03032133631146982 0.19776841651371047 chrMT 16571 71265 4.300585359966206 3.237194392574965 chrX 155270560 8133549 0.052383072489723743 0.28099200574917765 chrY 59373566 279630 0.0047096716407432895 0.09876526056419246