BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714206.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 122,072 number of mapped reads = 24,085 (19.73%) number of supplementary alignments = 1,044 (0.86%) number of secondary alignments = 0 number of mapped bases = 2,693,476 bp number of sequenced bases = 2,656,763 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,060 duplication rate = 46.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 31.8907 >>>>>>> ACTG content number of A's = 424,935 bp (15.99%) number of C's = 348,014 bp (13.1%) number of T's = 383,209 bp (14.42%) number of G's = 1,500,516 bp (56.48%) number of N's = 89 bp (0%) GC percentage = 69.58% >>>>>>> Mismatches and indels general error rate = 0.0374 number of mismatches = 84,362 number of insertions = 2,498 mapped reads with insertion percentage = 7.07% number of deletions = 5,038 mapped reads with deletion percentage = 20.42% homopolymer indels = 40.46% >>>>>>> Coverage mean coverageData = 0.0009X std coverageData = 1.4241X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% 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 39984 1.6041685208078178E-4 0.08207709067604885 chr2 243199373 1224858 0.005036435681929164 5.026761815582033 chr3 198022430 23888 1.2063279902180778E-4 0.03613574654808417 chr4 191154276 27865 1.4577230801784418E-4 0.04544690152132152 chr5 180915260 25903 1.4317752963459245E-4 0.040267610518653435 chr6 171115067 44691 2.611751307674151E-4 0.11377856450770593 chr7 159138663 51373 3.22819100220793E-4 0.169079574591726 chr8 146364022 92434 6.315349820053455E-4 0.38753637572696165 chr9 141213431 13854 9.81068153495966E-5 0.03870436567184637 chr10 135534747 21834 1.6109522084399507E-4 0.10560425491576243 chr11 135006516 22933 1.6986587521449704E-4 0.07278759661561149 chr12 133851895 34143 2.550804379721333E-4 0.06834554454290974 chr13 115169878 8788 7.630467403985615E-5 0.021313429175414882 chr14 107349540 19833 1.8475160676049475E-4 0.05885549121357465 chr15 102531392 15229 1.4853012041424348E-4 0.04113010759843203 chr16 90354753 13262 1.4677700463638034E-4 0.03903425946012605 chr17 81195210 24053 2.962366868685973E-4 0.07490747743782582 chr18 78077248 6280 8.043316280819734E-5 0.01878939448248807 chr19 59128983 17792 3.0090150544277077E-4 0.10626137096425085 chr20 63025520 33679 5.343708389871278E-4 0.18923363387503467 chr21 48129895 3615 7.51092434338367E-5 0.015671663963789502 chr22 51304566 3895 7.591916867594202E-5 0.025592287506233134 chrMT 16571 1404 0.08472632912920161 0.4059915115243102 chrX 155270560 917465 0.005908814909922396 0.7791422390787542 chrY 59373566 4421 7.446074571299963E-5 0.014866701425709224