BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004082.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 = 2,225,438 number of mapped reads = 2,023,019 (90.9%) number of supplementary alignments = 20,371 (0.92%) number of secondary alignments = 0 number of mapped bases = 131,496,885 bp number of sequenced bases = 131,437,526 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 56,590 duplication rate = 1.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8964 >>>>>>> ACTG content number of A's = 37,453,127 bp (28.5%) number of C's = 24,950,920 bp (18.98%) number of T's = 39,580,039 bp (30.11%) number of G's = 29,437,209 bp (22.4%) number of N's = 16,231 bp (0.01%) GC percentage = 41.38% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,020,384 number of insertions = 9,844 mapped reads with insertion percentage = 0.48% number of deletions = 34,533 mapped reads with deletion percentage = 1.69% homopolymer indels = 44.28% >>>>>>> Coverage mean coverageData = 0.0425X std coverageData = 0.4102X There is a 3.8% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.04% 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% 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 10390872 0.04168844979527654 0.7332752777967898 chr2 243199373 10558115 0.04341341373441781 0.47570519064672384 chr3 198022430 8766503 0.04427025261734239 0.22758966833627353 chr4 191154276 8470653 0.0443131756048188 0.2513559143575941 chr5 180915260 7338193 0.040561492712112845 0.2212846508331706 chr6 171115067 7606214 0.044450872347786885 0.262412680709445 chr7 159138663 8397686 0.05276961513746034 0.6639357495151333 chr8 146364022 8111855 0.05542246577509328 0.458405425689702 chr9 141213431 5223524 0.036990277504127776 0.37750574647379836 chr10 135534747 6178231 0.04558411135706772 0.3355507641248045 chr11 135006516 6095952 0.04515302061420502 0.4252446429904077 chr12 133851895 5436525 0.04061597334875237 0.2236820331280099 chr13 115169878 4125213 0.03581850629380714 0.2049689633103973 chr14 107349540 3737630 0.03481738254304583 0.23071389907361295 chr15 102531392 3801714 0.037078536883611214 0.22797913923547072 chr16 90354753 3336403 0.03692559482731362 0.24584326449680446 chr17 81195210 2988918 0.03681150649157752 0.24990432859900413 chr18 78077248 3498204 0.04480439679431324 0.7200713206752797 chr19 59128983 2183978 0.036935828914899486 0.5157085161253453 chr20 63025520 2939997 0.04664772301759668 0.2453074807718569 chr21 48129895 1596832 0.033177550044520145 0.22494920208892852 chr22 51304566 1252844 0.02441973683200049 0.1663675749444619 chrMT 16571 426980 25.766700862953353 17.578857937086664 chrX 155270560 8677234 0.05588460555561853 0.2999343041005569 chrY 59373566 356615 0.006006292429866854 0.11799618762740953