BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083628.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 = 1,430,365 number of mapped reads = 1,317,539 (92.11%) number of supplementary alignments = 10,338 (0.72%) number of secondary alignments = 0 number of mapped bases = 88,228,181 bp number of sequenced bases = 88,195,050 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,759 duplication rate = 2.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3767 >>>>>>> ACTG content number of A's = 24,165,408 bp (27.4%) number of C's = 16,200,797 bp (18.37%) number of T's = 27,949,702 bp (31.69%) number of G's = 19,874,633 bp (22.53%) number of N's = 4,510 bp (0.01%) GC percentage = 40.9% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 613,651 number of insertions = 6,775 mapped reads with insertion percentage = 0.51% number of deletions = 20,411 mapped reads with deletion percentage = 1.53% homopolymer indels = 48.28% >>>>>>> Coverage mean coverageData = 0.0285X std coverageData = 0.2595X There is a 2.51% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 9782703 0.0392484598864851 0.46402899105509937 chr2 243199373 7378024 0.03033734795031729 0.3434969210531721 chr3 198022430 7616810 0.038464380019980565 0.21980235896149025 chr4 191154276 4350799 0.02276066793295275 0.16799284285633087 chr5 180915260 4072919 0.02251285491339979 0.16568514594407877 chr6 171115067 5747651 0.03358939163434392 0.229410755110135 chr7 159138663 5906533 0.03711563795153915 0.3884641240225151 chr8 146364022 6533607 0.04463943331647446 0.30790105144883045 chr9 141213431 3915595 0.02772820525832277 0.2080127695949943 chr10 135534747 4462796 0.03292732010633406 0.24100429743189658 chr11 135006516 2545975 0.018858163853365417 0.1662553328311406 chr12 133851895 3632475 0.027138016985116274 0.18217874322560518 chr13 115169878 3197075 0.02775964562539521 0.18465767756183468 chr14 107349540 895958 0.008346174562089415 0.10417822881758566 chr15 102531392 2407352 0.023479170164782313 0.17514892855034572 chr16 90354753 2218383 0.024551923682421 0.1787825321386797 chr17 81195210 1779975 0.0219221675761415 0.16933549658050462 chr18 78077248 2178751 0.027905069092599166 0.30387225833238335 chr19 59128983 2248830 0.03803261760818717 0.3422619412525156 chr20 63025520 2147237 0.03406932620309995 0.20650591080326272 chr21 48129895 1470018 0.030542721940282645 0.19368418169120172 chr22 51304566 721287 0.014058924112134582 0.13023701710738705 chrMT 16571 6232 0.37607869169030234 0.6671819179413561 chrX 155270560 2853113 0.01837510600850541 0.15354476697833047 chrY 59373566 158083 0.002662514830252911 0.06520882372814756