BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081255.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 = 5,051,610 number of mapped reads = 4,402,115 (87.14%) number of supplementary alignments = 39,477 (0.78%) number of secondary alignments = 0 number of mapped bases = 299,093,137 bp number of sequenced bases = 298,972,446 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 263,636 duplication rate = 4.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.4474 >>>>>>> ACTG content number of A's = 83,230,671 bp (27.84%) number of C's = 54,571,467 bp (18.25%) number of T's = 95,836,019 bp (32.06%) number of G's = 65,252,526 bp (21.83%) number of N's = 81,763 bp (0.03%) GC percentage = 40.08% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 2,556,113 number of insertions = 26,039 mapped reads with insertion percentage = 0.59% number of deletions = 73,173 mapped reads with deletion percentage = 1.64% homopolymer indels = 48.84% >>>>>>> Coverage mean coverageData = 0.0966X std coverageData = 0.8039X There is a 7.33% of reference with a coverageData >= 1X There is a 1.59% of reference with a coverageData >= 2X There is a 0.38% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 23901035 0.09589157653492868 1.586319272262144 chr2 243199373 24195672 0.09948903938991652 0.8001141166806274 chr3 198022430 20895757 0.10552217241248883 0.40514746044957217 chr4 191154276 20181474 0.10557689015546794 0.4676207912261344 chr5 180915260 18705431 0.10339332900939369 0.4046656676874932 chr6 171115067 17727206 0.10359815947709619 0.5349222754216333 chr7 159138663 16482233 0.10357151863215038 1.1356263431835962 chr8 146364022 14325858 0.09787827503127784 1.1941095722465787 chr9 141213431 12820969 0.09079142762277335 0.7522266427819305 chr10 135534747 14478674 0.10682628861217412 0.7795162268699523 chr11 135006516 13633776 0.10098605907288208 0.696183286822135 chr12 133851895 13078901 0.09771173579574649 0.4027450760304071 chr13 115169878 8845022 0.07679978613852487 0.3430619657593829 chr14 107349540 9561835 0.08907196994043942 0.4172983294284518 chr15 102531392 8731787 0.08516208382306953 0.36281404875213674 chr16 90354753 8266071 0.09148462837367283 0.4452370923715395 chr17 81195210 7698840 0.09481889387317306 0.5408345966163893 chr18 78077248 8153810 0.10443259987852031 1.492923041281276 chr19 59128983 5563762 0.09409534407178963 1.0976247399159142 chr20 63025520 6376518 0.1011735880957428 0.41912665986924796 chr21 48129895 4051481 0.0841780560709721 0.44760667080378586 chr22 51304566 3264571 0.06363119804970185 0.3106501846068727 chrMT 16571 30546 1.843340776054553 1.8049667972688987 chrX 155270560 17358002 0.111791971382083 0.48864072641217565 chrY 59373566 763906 0.012866095999691176 0.2992712048264026