BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080694.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 = 2,125,207 number of mapped reads = 1,869,414 (87.96%) number of supplementary alignments = 22,206 (1.04%) number of secondary alignments = 0 number of mapped bases = 130,912,312 bp number of sequenced bases = 130,863,349 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 89,840 duplication rate = 4.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.9959 >>>>>>> ACTG content number of A's = 39,864,989 bp (30.46%) number of C's = 24,171,875 bp (18.47%) number of T's = 40,715,820 bp (31.11%) number of G's = 26,108,589 bp (19.95%) number of N's = 2,076 bp (0%) GC percentage = 38.42% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,009,544 number of insertions = 9,783 mapped reads with insertion percentage = 0.52% number of deletions = 27,503 mapped reads with deletion percentage = 1.45% homopolymer indels = 47.89% >>>>>>> Coverage mean coverageData = 0.0423X std coverageData = 0.368X There is a 3.01% of reference with a coverageData >= 1X There is a 0.83% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 9852100 0.039526882462611795 0.3812156156027093 chr2 243199373 11280398 0.04638333504256197 0.3444910288515334 chr3 198022430 8528954 0.043070646087920446 0.2764719530955772 chr4 191154276 9191414 0.0480837478100673 0.29533112236530595 chr5 180915260 7880999 0.043561825575133904 0.2770698843441525 chr6 171115067 8048390 0.047034958061291 0.30030048704030576 chr7 159138663 6479760 0.040717697873332015 0.355574863388316 chr8 146364022 6941483 0.04742615640884752 0.9789343125277984 chr9 141213431 6003023 0.04251028360043175 0.3040987656686424 chr10 135534747 6342672 0.046797386946094345 0.3230445710092112 chr11 135006516 5911458 0.04378646435109843 0.3114711108036592 chr12 133851895 6651193 0.049690689847909884 0.294562156139973 chr13 115169878 4448073 0.038621843465007404 0.2614761116192748 chr14 107349540 3737216 0.034813525982505374 0.25362303429834376 chr15 102531392 3820463 0.03726139795312639 0.2535331425783669 chr16 90354753 3124891 0.03458468864388352 0.25142698493914944 chr17 81195210 2696851 0.03321441006187434 0.24752318659234696 chr18 78077248 3491500 0.044718533112232645 0.4113453895806725 chr19 59128983 1882888 0.031843740657606104 0.3129773675388555 chr20 63025520 2660644 0.042215343879749026 0.27488155939266123 chr21 48129895 1748567 0.036330164443533486 0.2572771350659511 chr22 51304566 1167571 0.022757643052667087 0.19503622926540978 chrMT 16571 196713 11.870919075493331 6.992190198796039 chrX 155270560 8502188 0.054757244386830314 0.3186074289072946 chrY 59373566 322903 0.005438497664095163 0.11308448833316262