BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716944.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,488,877 number of mapped reads = 1,322,065 (88.8%) number of supplementary alignments = 6,217 (0.42%) number of secondary alignments = 0 number of mapped bases = 77,376,766 bp number of sequenced bases = 77,355,855 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 39,246 duplication rate = 2.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6445 >>>>>>> ACTG content number of A's = 19,474,370 bp (25.18%) number of C's = 14,317,061 bp (18.51%) number of T's = 23,709,568 bp (30.65%) number of G's = 19,853,828 bp (25.67%) number of N's = 1,028 bp (0%) GC percentage = 44.17% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 374,903 number of insertions = 5,114 mapped reads with insertion percentage = 0.39% number of deletions = 13,382 mapped reads with deletion percentage = 1.01% homopolymer indels = 41.8% >>>>>>> Coverage mean coverageData = 0.025X std coverageData = 0.2381X There is a 2.28% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 9632875 0.03864734603810676 0.4382900023634021 chr2 243199373 6589861 0.02709653778589306 0.2782339715193227 chr3 198022430 6732516 0.03399875458552852 0.20333309243028755 chr4 191154276 3471896 0.01816279537476839 0.15102806818203912 chr5 180915260 3393979 0.018760048212627282 0.14858582309838736 chr6 171115067 5852088 0.03419972362807771 0.291105644850338 chr7 159138663 4436988 0.02788126980807926 0.28555944385812376 chr8 146364022 4883970 0.03336865121129289 0.21674099910289238 chr9 141213431 2870424 0.02032684837180962 0.188455628542954 chr10 135534747 4116921 0.030375391485402633 0.27194951119118244 chr11 135006516 2574846 0.019072012790849295 0.18347929018134512 chr12 133851895 3072835 0.022956977934455093 0.16562865279841407 chr13 115169878 1746092 0.015161012847473886 0.13188293575475998 chr14 107349540 1675506 0.015607947644675515 0.14559015125631283 chr15 102531392 2353201 0.0229510294759287 0.16362412423869366 chr16 90354753 1682173 0.01861742679989397 0.16674654047426996 chr17 81195210 1667769 0.02054023876531633 0.1589938071729438 chr18 78077248 1492592 0.019116862315638992 0.31685039752007726 chr19 59128983 1626472 0.027507187126827464 0.2965848903072195 chr20 63025520 1197269 0.018996574720843238 0.1477758323649932 chr21 48129895 706768 0.014684594678629571 0.14036345751950802 chr22 51304566 1261784 0.02459399032826825 0.16911761426265406 chrMT 16571 4413 0.26630861142960593 0.5103072962432728 chrX 155270560 4147215 0.026709602902185707 0.19054387084189994 chrY 59373566 186313 0.003137978945040963 0.07488375024728894