BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080693.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 = 2,767,848 number of mapped reads = 2,471,762 (89.3%) number of supplementary alignments = 21,556 (0.78%) number of secondary alignments = 0 number of mapped bases = 174,837,560 bp number of sequenced bases = 174,769,445 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 129,869 duplication rate = 4.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.9952 >>>>>>> ACTG content number of A's = 52,600,650 bp (30.1%) number of C's = 32,463,993 bp (18.58%) number of T's = 54,456,972 bp (31.16%) number of G's = 35,245,279 bp (20.17%) number of N's = 2,551 bp (0%) GC percentage = 38.74% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,442,361 number of insertions = 14,285 mapped reads with insertion percentage = 0.57% number of deletions = 37,457 mapped reads with deletion percentage = 1.5% homopolymer indels = 47.4% >>>>>>> Coverage mean coverageData = 0.0565X std coverageData = 0.6205X There is a 3.95% of reference with a coverageData >= 1X There is a 1.11% of reference with a coverageData >= 2X There is a 0.33% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 13654466 0.0547820741437591 0.948670824579911 chr2 243199373 14804345 0.0608732860507827 0.4794420560791298 chr3 198022430 12256770 0.06189586704900046 0.3338306172099877 chr4 191154276 12399704 0.06486752093371953 0.37977299136887943 chr5 180915260 11130950 0.061525766262061035 0.33434256635507875 chr6 171115067 10572316 0.06178483394451758 0.38322625053484455 chr7 159138663 9547594 0.059995439323252325 0.7862504259113583 chr8 146364022 9330629 0.06374947116443684 1.7770222242749716 chr9 141213431 7169367 0.05076972458802449 0.4413563696154003 chr10 135534747 8143873 0.06008697533481949 0.4941892507865606 chr11 135006516 7971936 0.05904852770217402 0.40371408433112227 chr12 133851895 7825006 0.05846018093356093 0.3290242357295867 chr13 115169878 5925348 0.05144876510158324 0.3039258098152675 chr14 107349540 5256944 0.048970344912516624 0.3256445305954344 chr15 102531392 4681937 0.04566344910249536 0.2820173914522309 chr16 90354753 4368958 0.04835338324703295 0.32548964571774436 chr17 81195210 3924409 0.048333011269999795 0.3325323203400736 chr18 78077248 4887687 0.0626006567239665 0.7674183281694413 chr19 59128983 2654820 0.044898793540893475 0.6186631802479102 chr20 63025520 3286874 0.05215147768713372 0.3128578531347131 chr21 48129895 2313850 0.04807511007451813 0.32381713151591457 chr22 51304566 1602956 0.031243924761004703 0.2299577585090651 chrMT 16571 142783 8.616438356164384 6.098714781290228 chrX 155270560 10489031 0.06755325027487503 0.37146411502629406 chrY 59373566 495007 0.008337161355610677 0.27106823073199376