BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013336.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 = 1,876,358 number of mapped reads = 1,581,434 (84.28%) number of supplementary alignments = 19,372 (1.03%) number of secondary alignments = 0 number of mapped bases = 101,286,643 bp number of sequenced bases = 101,225,266 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 202,409 duplication rate = 9.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.0996 >>>>>>> ACTG content number of A's = 27,401,736 bp (27.07%) number of C's = 19,007,711 bp (18.78%) number of T's = 31,690,376 bp (31.31%) number of G's = 23,113,346 bp (22.83%) number of N's = 12,097 bp (0.01%) GC percentage = 41.61% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 843,189 number of insertions = 6,402 mapped reads with insertion percentage = 0.4% number of deletions = 36,051 mapped reads with deletion percentage = 2.25% homopolymer indels = 44.02% >>>>>>> Coverage mean coverageData = 0.0327X std coverageData = 0.3665X There is a 1.89% of reference with a coverageData >= 1X There is a 0.72% of reference with a coverageData >= 2X There is a 0.32% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% 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% 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 9839802 0.03947754256548071 0.5309027574096167 chr2 243199373 3567163 0.014667648834768994 0.4049216508342906 chr3 198022430 10852926 0.05480654893488581 0.3784022488420765 chr4 191154276 4843120 0.02533618447541294 0.24842965054156074 chr5 180915260 1642625 0.009079527066981525 0.1341194174579732 chr6 171115067 12343167 0.07213372391105688 0.586866970857608 chr7 159138663 3329875 0.020924362045193254 0.2974722372795578 chr8 146364022 4871398 0.033282755785434756 0.3289356017965481 chr9 141213431 2460871 0.017426607246728534 0.27537135831023196 chr10 135534747 4777688 0.03525065052137516 0.3337891884907238 chr11 135006516 10303221 0.07631647201383969 0.5499936564076836 chr12 133851895 902422 0.0067419441465509326 0.11746376855682097 chr13 115169878 1300387 0.011291033928159583 0.15707744474789573 chr14 107349540 1558516 0.014518143254270116 0.19804717130670835 chr15 102531392 2789924 0.02721043717030585 0.26314234762617283 chr16 90354753 5078982 0.05621156421068408 0.39327771070794776 chr17 81195210 1773693 0.021844798480107386 0.26258404571537874 chr18 78077248 5342952 0.06843161275356427 0.5453069361417917 chr19 59128983 2345592 0.03966907396327111 0.5057421238214703 chr20 63025520 1145410 0.01817374930028344 0.2025383916875162 chr21 48129895 2470763 0.05133530833591056 0.373838216100495 chr22 51304566 1229087 0.023956678631683583 0.24619503072332327 chrMT 16571 14829 0.8948765916359905 1.320464017409745 chrX 155270560 6276937 0.040425802547501596 0.34622513608989436 chrY 59373566 225293 0.0037945000642204984 0.08752083027120182