BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714205.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 = 87,638 number of mapped reads = 45,458 (51.87%) number of supplementary alignments = 1,206 (1.38%) number of secondary alignments = 0 number of mapped bases = 5,769,264 bp number of sequenced bases = 5,663,730 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,053 duplication rate = 41.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.7094 >>>>>>> ACTG content number of A's = 1,450,608 bp (25.61%) number of C's = 1,106,594 bp (19.54%) number of T's = 1,377,964 bp (24.33%) number of G's = 1,728,512 bp (30.52%) number of N's = 52 bp (0%) GC percentage = 50.06% >>>>>>> Mismatches and indels general error rate = 0.0406 number of mismatches = 211,300 number of insertions = 5,542 mapped reads with insertion percentage = 11.44% number of deletions = 17,249 mapped reads with deletion percentage = 36.58% homopolymer indels = 30.73% >>>>>>> Coverage mean coverageData = 0.0019X std coverageData = 0.77X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 0.01% 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 341701 0.0013709133346552424 0.1788566882370105 chr2 243199373 1030734 0.00423822638720372 2.615087551267771 chr3 198022430 308374 0.0015572680327173038 0.1861355690894897 chr4 191154276 245407 0.0012838164289874425 0.17786336767370012 chr5 180915260 221659 0.001225208973527164 0.1634960828027929 chr6 171115067 194903 0.0011390171737477683 0.1575636207637994 chr7 159138663 212783 0.0013370917914523387 0.18402108615777338 chr8 146364022 299866 0.002048768514983826 0.29110495817085325 chr9 141213431 164242 0.001163076336556117 0.1544563486010538 chr10 135534747 231548 0.0017084032333051834 0.21184670376057962 chr11 135006516 246007 0.0018221861232238599 0.24270248330930363 chr12 133851895 166205 0.0012417082328195653 0.1837957035367607 chr13 115169878 158727 0.001378198907183005 0.19678035533248223 chr14 107349540 150851 0.0014052319180873993 0.1962467087023392 chr15 102531392 143340 0.0013980108648090918 0.17503723039798702 chr16 90354753 143741 0.0015908515626178515 0.19954452827888217 chr17 81195210 183442 0.002259271205776794 0.27953492871412994 chr18 78077248 108070 0.001384142023038517 0.17863170100021886 chr19 59128983 82422 0.0013939356947844004 0.19257877860634384 chr20 63025520 109545 0.0017381054531561183 0.20484429716399208 chr21 48129895 38491 7.997316428801683E-4 0.1228820279901971 chr22 51304566 41913 8.169448309922356E-4 0.13112503418895186 chrMT 16571 79227 4.781063303361294 44.30056254624625 chrX 155270560 853746 0.005498440915006683 0.49920178499194673 chrY 59373566 12320 2.074997482886576E-4 0.05240030443441922