BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714230.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 = 259,020 number of mapped reads = 41,058 (15.85%) number of supplementary alignments = 705 (0.27%) number of secondary alignments = 0 number of mapped bases = 4,332,661 bp number of sequenced bases = 4,323,262 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 40,182 duplication rate = 34.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 7.8072 >>>>>>> ACTG content number of A's = 84,310 bp (1.95%) number of C's = 30,915 bp (0.72%) number of T's = 38,267 bp (0.89%) number of G's = 4,169,684 bp (96.45%) number of N's = 86 bp (0%) GC percentage = 97.16% >>>>>>> Mismatches and indels general error rate = 0.0329 number of mismatches = 108,507 number of insertions = 4,908 mapped reads with insertion percentage = 8.22% number of deletions = 2,138 mapped reads with deletion percentage = 4.99% homopolymer indels = 63.01% >>>>>>> Coverage mean coverageData = 0.0014X std coverageData = 5.3831X 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 4594 1.843124796066205E-5 0.007469867927608902 chr2 243199373 4188076 0.017220751634092413 19.20532282174406 chr3 198022430 3237 1.6346633055659403E-5 0.0082215014275012 chr4 191154276 5288 2.766351928219487E-5 0.015273914789271174 chr5 180915260 2023 1.1182030747433908E-5 0.0038610111122432938 chr6 171115067 3719 2.1733913121747485E-5 0.009733891199407253 chr7 159138663 6127 3.8501014677998145E-5 0.04649487747508366 chr8 146364022 4472 3.055395676404684E-5 0.013613651141399157 chr9 141213431 1420 1.0055700721555303E-5 0.005383057941014059 chr10 135534747 4115 3.0361217998215616E-5 0.013931866601774172 chr11 135006516 3672 2.719868721003066E-5 0.015449881880098213 chr12 133851895 6241 4.662616095199848E-5 0.04127221165441576 chr13 115169878 673 5.8435418330477E-6 0.002529665698049804 chr14 107349540 5750 5.3563340839653344E-5 0.060814177346700235 chr15 102531392 2295 2.238338868938793E-5 0.01134381064218685 chr16 90354753 4696 5.19729161342514E-5 0.024489227261338273 chr17 81195210 5859 7.215942910918021E-5 0.06492101736157775 chr18 78077248 1088 1.3934917378235462E-5 0.006049113569522972 chr19 59128983 3836 6.487512223912257E-5 0.020323858087171274 chr20 63025520 2185 3.466849619011473E-5 0.014542508660798332 chr21 48129895 557 1.157284884997152E-5 0.005591906006210068 chr22 51304566 726 1.4150787280804598E-5 0.004266709163209625 chrMT 16571 0 0.0 0.0 chrX 155270560 71037 4.575046293386203E-4 0.08306115061820406 chrY 59373566 975 1.642144923550659E-5 0.0053540345885270185