BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004140.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 = 1,900,471 number of mapped reads = 1,484,711 (78.12%) number of supplementary alignments = 21,102 (1.11%) number of secondary alignments = 0 number of mapped bases = 94,040,497 bp number of sequenced bases = 93,957,524 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 144,983 duplication rate = 7.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3462 >>>>>>> ACTG content number of A's = 26,493,157 bp (28.2%) number of C's = 16,231,104 bp (17.27%) number of T's = 30,913,551 bp (32.9%) number of G's = 20,279,204 bp (21.58%) number of N's = 40,508 bp (0.04%) GC percentage = 38.86% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 944,112 number of insertions = 7,214 mapped reads with insertion percentage = 0.48% number of deletions = 48,433 mapped reads with deletion percentage = 3.2% homopolymer indels = 41.75% >>>>>>> Coverage mean coverageData = 0.0304X std coverageData = 0.3241X There is a 2.04% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% 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 5043355 0.02023407195442855 0.368922892512139 chr2 243199373 7208327 0.029639578881644566 0.3415704881276855 chr3 198022430 8772535 0.04430071381307663 0.2967353347496745 chr4 191154276 5731833 0.029985376837711963 0.25605810543042545 chr5 180915260 4462681 0.024667244764206182 0.2201864239521172 chr6 171115067 5677205 0.033177703749489224 0.2706930258213638 chr7 159138663 8295332 0.05212644019762815 0.4659990918530946 chr8 146364022 6911310 0.04722000602033197 0.6748789268907915 chr9 141213431 3278492 0.023216573500009358 0.254415502035864 chr10 135534747 2421447 0.017865876121051085 0.2631669459352352 chr11 135006516 4202954 0.031131489979342925 0.29404522423041257 chr12 133851895 4393243 0.03282167204282016 0.2550636612350769 chr13 115169878 3857656 0.03349535544354749 0.2585407889623993 chr14 107349540 2594565 0.024169316421849597 0.22527007392940662 chr15 102531392 2623745 0.025589675013872826 0.23067236214214842 chr16 90354753 3023970 0.03346774684891231 0.272769341376326 chr17 81195210 1239092 0.015260653922811456 0.18448089109159294 chr18 78077248 3908656 0.05006139560656646 0.472058071722242 chr19 59128983 1114068 0.018841318478283315 0.31854078989277224 chr20 63025520 1798060 0.02852907837967858 0.24564542732776712 chr21 48129895 1451738 0.030162916416086094 0.2519290756365906 chr22 51304566 627161 0.012224272592034012 0.1484953558099479 chrMT 16571 21170 1.277533039647577 1.8574968767731999 chrX 155270560 5076939 0.03269737031926722 0.26296011386707574 chrY 59373566 304963 0.005136342998161842 0.12159136389407757