BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082905.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 = 2,501,993 number of mapped reads = 2,198,671 (87.88%) number of supplementary alignments = 26,837 (1.07%) number of secondary alignments = 0 number of mapped bases = 145,152,548 bp number of sequenced bases = 145,098,347 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 147,251 duplication rate = 5.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8472 >>>>>>> ACTG content number of A's = 39,247,153 bp (27.05%) number of C's = 27,103,891 bp (18.68%) number of T's = 45,776,423 bp (31.55%) number of G's = 32,963,751 bp (22.72%) number of N's = 7,129 bp (0%) GC percentage = 41.4% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 1,068,645 number of insertions = 11,710 mapped reads with insertion percentage = 0.53% number of deletions = 33,071 mapped reads with deletion percentage = 1.49% homopolymer indels = 47.43% >>>>>>> Coverage mean coverageData = 0.0469X std coverageData = 0.3677X There is a 3.57% of reference with a coverageData >= 1X There is a 0.77% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.06% 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 0.01% 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 13825921 0.05546995608087171 0.5708147301339823 chr2 243199373 15094017 0.06206437464787378 0.6053764178096351 chr3 198022430 9709773 0.049033702899211974 0.2790516002751612 chr4 191154276 7569229 0.039597487214986495 0.25524125609327913 chr5 180915260 9091014 0.05025012262647164 0.28343787268061943 chr6 171115067 8406952 0.04913040182487262 0.36174674600867207 chr7 159138663 6459286 0.040589042777115704 0.2955192937796615 chr8 146364022 13938665 0.09523286398893849 0.47799412839318517 chr9 141213431 3343358 0.023675920741561756 0.25852922525822003 chr10 135534747 4899261 0.036147638214132645 0.2878999174278208 chr11 135006516 6085821 0.04507797979173094 0.3025073505866019 chr12 133851895 5271964 0.03938654734772339 0.252488087257991 chr13 115169878 3325084 0.028871125486474858 0.21621754216891972 chr14 107349540 3321426 0.030940290941162858 0.23249350327977586 chr15 102531392 3229157 0.0314943251721385 0.228165401027942 chr16 90354753 6363699 0.07043015213599223 0.34726262572783173 chr17 81195210 3253868 0.04007463001819935 0.2627088196356709 chr18 78077248 5373404 0.06882163674621318 0.5441695353388607 chr19 59128983 2633423 0.044536923626777074 0.46037447804457776 chr20 63025520 3274736 0.051958889034156325 0.2919315996649269 chr21 48129895 2284170 0.047458445525385 0.27661294796348945 chr22 51304566 2021526 0.03940245786310716 0.2505062392008346 chrMT 16571 128102 7.730493029992155 5.751627200677706 chrX 155270560 5976652 0.03849185576454416 0.2617697735226152 chrY 59373566 272040 0.004581836974386884 0.09386452864506911