BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716324.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 = 3,572,748 number of mapped reads = 3,248,058 (90.91%) number of supplementary alignments = 12,325 (0.34%) number of secondary alignments = 0 number of mapped bases = 184,228,099 bp number of sequenced bases = 184,179,401 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 138,879 duplication rate = 3.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9278 >>>>>>> ACTG content number of A's = 43,302,995 bp (23.51%) number of C's = 35,825,824 bp (19.45%) number of T's = 57,638,589 bp (31.29%) number of G's = 47,408,116 bp (25.74%) number of N's = 3,877 bp (0%) GC percentage = 45.19% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 902,954 number of insertions = 10,805 mapped reads with insertion percentage = 0.33% number of deletions = 28,767 mapped reads with deletion percentage = 0.88% homopolymer indels = 41.37% >>>>>>> Coverage mean coverageData = 0.0595X std coverageData = 0.421X There is a 5% of reference with a coverageData >= 1X There is a 0.67% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% 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 14922748 0.05987045464572784 0.6666438659604613 chr2 243199373 15455872 0.06355226910885169 0.5154577729047943 chr3 198022430 12184240 0.06152959540997452 0.29015080209527794 chr4 191154276 11591531 0.06063966364006422 0.3268909726404789 chr5 180915260 10982902 0.060707438388558264 0.29391148057120814 chr6 171115067 10517432 0.06146409071037561 0.31839149017427504 chr7 159138663 10098718 0.06345860779287808 0.48374471117053597 chr8 146364022 9171916 0.06266509948735899 0.36637855628137617 chr9 141213431 7834660 0.055480983250098925 0.4662364901075047 chr10 135534747 8722980 0.06435973204716279 0.4213145353036935 chr11 135006516 8454445 0.06262249593938118 0.43841853678135934 chr12 133851895 8370977 0.06253909965189511 0.30391694293603305 chr13 115169878 5734672 0.04979315858960969 0.25671368490457963 chr14 107349540 5619279 0.05234562719132285 0.29645140127711683 chr15 102531392 5398363 0.05265083107425285 0.2695489252255293 chr16 90354753 5637484 0.06239277750003921 0.3356369368213606 chr17 81195210 5197089 0.06400733491544637 0.320830922355702 chr18 78077248 4900156 0.06276035753719189 0.8587521828242262 chr19 59128983 3949077 0.06678750080988202 0.4998342169252032 chr20 63025520 3947592 0.06263481840371964 0.3045706454134433 chr21 48129895 2432177 0.05053360286782259 0.31339754220299676 chr22 51304566 2265099 0.0441500469958171 0.24331307193319276 chrMT 16571 9334 0.5632731880996922 0.809200746199529 chrX 155270560 10301397 0.06634481771689366 0.3775261965732916 chrY 59373566 527959 0.00889215581223469 0.17964965733325744