BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004124.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 = 3,169,090 number of mapped reads = 2,467,861 (77.87%) number of supplementary alignments = 15,783 (0.5%) number of secondary alignments = 0 number of mapped bases = 163,947,510 bp number of sequenced bases = 163,872,135 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 115,379 duplication rate = 3.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5919 >>>>>>> ACTG content number of A's = 45,722,109 bp (27.9%) number of C's = 29,045,573 bp (17.72%) number of T's = 52,958,831 bp (32.32%) number of G's = 36,128,369 bp (22.05%) number of N's = 17,253 bp (0.01%) GC percentage = 39.77% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 1,673,267 number of insertions = 15,566 mapped reads with insertion percentage = 0.62% number of deletions = 45,415 mapped reads with deletion percentage = 1.82% homopolymer indels = 46.94% >>>>>>> Coverage mean coverageData = 0.053X std coverageData = 0.6072X There is a 4.56% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% 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% 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 12673227 0.050845317653190523 1.2307920602153393 chr2 243199373 14097035 0.05796493151320748 0.682125954832443 chr3 198022430 9089361 0.045900663879339325 0.24592691510309392 chr4 191154276 10217368 0.05345089952369153 0.2704749067602392 chr5 180915260 7984051 0.04413144032183908 0.24532091605346673 chr6 171115067 10124408 0.05916725030414768 0.3299187649442981 chr7 159138663 11597498 0.0728766836504087 1.0313765089990563 chr8 146364022 12960639 0.08855071637755349 0.9098560478780853 chr9 141213431 5780181 0.04093223257212694 0.5419264828825905 chr10 135534747 7894781 0.0582491292804789 0.494136049465991 chr11 135006516 8410569 0.062297504218240846 0.45007341403205525 chr12 133851895 7455844 0.05570219233728443 0.2784198752074161 chr13 115169878 5169879 0.04488915929910076 0.233817512390067 chr14 107349540 3715027 0.03460682737904606 0.2828637069199258 chr15 102531392 4188519 0.040851088806050734 0.2364615735135016 chr16 90354753 2695475 0.029832132903954704 0.28049172228336494 chr17 81195210 2714887 0.03343654139203532 0.24444450985092056 chr18 78077248 5399339 0.06915380777765118 1.063720341234873 chr19 59128983 2907464 0.04917155432894897 0.7495974089251031 chr20 63025520 4063495 0.06447380362748296 0.31642116447976043 chr21 48129895 2501152 0.05196670385422615 0.2831564707172507 chr22 51304566 1336860 0.026057329868066713 0.176421415157933 chrMT 16571 124627 7.5207893307585545 4.880933261377534 chrX 155270560 10438161 0.06722562860596368 0.3892528506376742 chrY 59373566 407663 0.0068660689843018695 0.1375592825511548