BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8751176.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP188831/SRP188831.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 = 5,833,031 number of mapped reads = 5,343,659 (91.61%) number of supplementary alignments = 201,030 (3.45%) number of secondary alignments = 0 number of mapped bases = 527,356,781 bp number of sequenced bases = 527,192,843 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 159,588 duplication rate = 1.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.3425 >>>>>>> ACTG content number of A's = 156,588,707 bp (29.7%) number of C's = 106,754,497 bp (20.25%) number of T's = 157,424,371 bp (29.86%) number of G's = 106,422,412 bp (20.19%) number of N's = 2,856 bp (0%) GC percentage = 40.44% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 1,981,752 number of insertions = 187,140 mapped reads with insertion percentage = 3.41% number of deletions = 75,192 mapped reads with deletion percentage = 1.38% homopolymer indels = 50.69% >>>>>>> Coverage mean coverageData = 0.1704X std coverageData = 1.525X There is a 13.64% of reference with a coverageData >= 1X There is a 2.38% of reference with a coverageData >= 2X There is a 0.46% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% 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 62053058 0.248958489054276 4.242401989769956 chr2 243199373 41005280 0.16860767153375844 0.672526400587496 chr3 198022430 34635726 0.1749080950072171 0.5508189854707383 chr4 191154276 24444311 0.12787739574290244 0.4759325158756193 chr5 180915260 41905915 0.2316328373847513 0.551416789198862 chr6 171115067 29656253 0.1733117575204526 1.060106304704326 chr7 159138663 29358329 0.184482692304635 0.9262413443618958 chr8 146364022 26208986 0.1790671344082086 0.6246151285562371 chr9 141213431 23210670 0.16436588103294508 0.8337875815493185 chr10 135534747 25974679 0.19164590317197405 2.2454805948300702 chr11 135006516 23727738 0.17575253923299525 0.7846543986329271 chr12 133851895 27586230 0.20609517706118394 0.5212994530445834 chr13 115169878 21463433 0.18636325203018797 0.4903280317112458 chr14 107349540 10949195 0.10199573281823099 0.3987307657643913 chr15 102531392 12224624 0.11922810918240533 0.38890730075583124 chr16 90354753 14185498 0.1569978061917783 1.0939831454240678 chr17 81195210 13443085 0.16556500069400645 0.7824501185173128 chr18 78077248 10828271 0.13868663762329328 1.6682643031923288 chr19 59128983 9252753 0.15648422365052347 3.001610345450945 chr20 63025520 8735433 0.13860152205011558 0.442400200043097 chr21 48129895 6486634 0.13477349161056762 0.45771872826069293 chr22 51304566 5269990 0.10271970724788901 0.36578762335068965 chrMT 16571 1099122 66.32804296662844 24.066518479960905 chrX 155270560 22511087 0.1449797501857403 0.5166374572041608 chrY 59373566 1140481 0.019208564969804914 0.7257372777300096