BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068181.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 4,720,252 number of mapped reads = 4,467,680 (94.65%) number of supplementary alignments = 32,474 (0.69%) number of secondary alignments = 0 number of mapped bases = 286,419,757 bp number of sequenced bases = 286,298,866 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 583,694 duplication rate = 10.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7913 >>>>>>> ACTG content number of A's = 74,380,846 bp (25.98%) number of C's = 51,504,019 bp (17.99%) number of T's = 93,197,880 bp (32.55%) number of G's = 67,183,929 bp (23.47%) number of N's = 32,192 bp (0.01%) GC percentage = 41.46% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 1,624,999 number of insertions = 17,733 mapped reads with insertion percentage = 0.39% number of deletions = 69,023 mapped reads with deletion percentage = 1.53% homopolymer indels = 44.26% >>>>>>> Coverage mean coverageData = 0.0925X std coverageData = 1.0306X There is a 6.58% of reference with a coverageData >= 1X There is a 1.71% of reference with a coverageData >= 2X There is a 0.5% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% 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 34996548 0.14040706442211834 2.327779955054716 chr2 243199373 15781934 0.06489298802591896 1.2428913088530873 chr3 198022430 21920405 0.11069657614038975 0.44295585711768776 chr4 191154276 7539867 0.039443883536249016 0.31100291722380635 chr5 180915260 13234356 0.07315223713024539 0.3653731239091713 chr6 171115067 15520480 0.09070200697171804 0.5919828137315134 chr7 159138663 28790952 0.18091739277714053 2.060013267914289 chr8 146364022 13159723 0.08991091403596438 0.7032939836660264 chr9 141213431 11376170 0.0805601132940393 0.6995988433815515 chr10 135534747 14550988 0.10735983444894762 0.7614003196343487 chr11 135006516 17445853 0.12922230361088646 0.6665023905391596 chr12 133851895 12235894 0.09141367778170044 0.43504295083348704 chr13 115169878 7578477 0.06580259640459114 0.3711120448937363 chr14 107349540 7488478 0.0697578955624775 0.40772007511110875 chr15 102531392 5546433 0.054094974151916324 0.3572891242484441 chr16 90354753 7099751 0.07857639763566174 0.42704169601420305 chr17 81195210 7384041 0.09094183018924393 0.4468742791522171 chr18 78077248 6575119 0.08421299633921524 1.3585017746865673 chr19 59128983 7319837 0.12379440045501881 1.4836997128177933 chr20 63025520 5030027 0.07980936928406145 0.39474615643981603 chr21 48129895 5953390 0.12369422372519201 0.4927764047008084 chr22 51304566 5585722 0.10887377938252124 0.4416319629727336 chrMT 16571 249513 15.057208376078691 8.495064648432505 chrX 155270560 13459917 0.08668685808822998 0.49846592874413687 chrY 59373566 595882 0.010036149757284243 0.34754412840609006