BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083647.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 = 1,727,825 number of mapped reads = 1,347,846 (78.01%) number of supplementary alignments = 8,111 (0.47%) number of secondary alignments = 0 number of mapped bases = 81,584,567 bp number of sequenced bases = 81,557,876 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,941 duplication rate = 2.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5927 >>>>>>> ACTG content number of A's = 23,565,054 bp (28.89%) number of C's = 15,815,023 bp (19.39%) number of T's = 23,663,264 bp (29.01%) number of G's = 18,503,844 bp (22.69%) number of N's = 10,691 bp (0.01%) GC percentage = 42.08% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 707,901 number of insertions = 5,998 mapped reads with insertion percentage = 0.44% number of deletions = 16,705 mapped reads with deletion percentage = 1.23% homopolymer indels = 44.5% >>>>>>> Coverage mean coverageData = 0.0264X std coverageData = 0.2374X There is a 2.42% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0% 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 7976340 0.03200128436189533 0.47253381263630134 chr2 243199373 8735505 0.035919109873691984 0.23619050613881376 chr3 198022430 6782223 0.034249771604156154 0.19777632551215713 chr4 191154276 3955574 0.020693097129566695 0.15405180439909205 chr5 180915260 4169475 0.02304656334683984 0.16179400634278887 chr6 171115067 5499909 0.032141582248861815 0.21312735119963078 chr7 159138663 4587941 0.028829832509023906 0.30437134539816113 chr8 146364022 5540992 0.03785760957019888 0.26694717870607837 chr9 141213431 3708348 0.02626058990097054 0.19572178453625125 chr10 135534747 3780552 0.027893599860410703 0.2419100595321207 chr11 135006516 2347571 0.017388575526236082 0.16094353981753173 chr12 133851895 2852070 0.02130765500182123 0.15572717675317466 chr13 115169878 2446092 0.021238990979915773 0.15342245616016179 chr14 107349540 1857655 0.017304731813475867 0.14154656160595613 chr15 102531392 2222321 0.021674542368448485 0.15767045966778392 chr16 90354753 2653809 0.029370995015613622 0.18860818487536316 chr17 81195210 1884427 0.023208598142673686 0.16855903687196108 chr18 78077248 1990511 0.025494123460908867 0.3115468716978022 chr19 59128983 2115045 0.035770021615288056 0.3398624935674835 chr20 63025520 1541751 0.02446232891057464 0.1661533647977506 chr21 48129895 1307491 0.027165880997662678 0.1772344336005224 chr22 51304566 575350 0.011214401462824966 0.11096650327092404 chrMT 16571 5984 0.3611127873996741 0.6220992587939217 chrX 155270560 2887305 0.01859531517114384 0.15183566278191818 chrY 59373566 160326 0.0027002925847505943 0.06377175893627342