BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717040.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 = 8,230,669 number of mapped reads = 7,634,299 (92.75%) number of supplementary alignments = 218,183 (2.65%) number of secondary alignments = 0 number of mapped bases = 568,289,981 bp number of sequenced bases = 568,086,804 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 557,712 duplication rate = 5.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8269 >>>>>>> ACTG content number of A's = 143,104,378 bp (25.19%) number of C's = 118,357,445 bp (20.83%) number of T's = 167,894,821 bp (29.55%) number of G's = 138,665,058 bp (24.41%) number of N's = 65,102 bp (0.01%) GC percentage = 45.24% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 4,266,071 number of insertions = 46,749 mapped reads with insertion percentage = 0.6% number of deletions = 115,013 mapped reads with deletion percentage = 1.48% homopolymer indels = 40.78% >>>>>>> Coverage mean coverageData = 0.1836X std coverageData = 1.2339X There is a 12.18% of reference with a coverageData >= 1X There is a 3.51% of reference with a coverageData >= 2X There is a 1.26% of reference with a coverageData >= 3X There is a 0.52% of reference with a coverageData >= 4X There is a 0.24% of reference with a coverageData >= 5X There is a 0.13% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% 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 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% 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 56657027 0.2273094717786079 1.8015515716133272 chr2 243199373 45539972 0.18725365710543998 2.1969680512975067 chr3 198022430 41035287 0.2072254491574515 0.6843748256821071 chr4 191154276 25967902 0.13584787399681292 0.6623290302635446 chr5 180915260 31895069 0.1762983896438587 0.6182137953361551 chr6 171115067 37117897 0.21691775979025857 0.8896212309155117 chr7 159138663 27655047 0.17377956103602554 1.8563285100579368 chr8 146364022 38519289 0.2631745730518392 1.641883775647912 chr9 141213431 31301040 0.22165766937565592 1.1508463683886807 chr10 135534747 31519856 0.23255922704456003 1.2432623335399806 chr11 135006516 26806600 0.19855782368311764 0.9866759340126108 chr12 133851895 20968710 0.15665605630760776 0.5634390877732863 chr13 115169878 16538227 0.14359854579337142 0.5225390967491369 chr14 107349540 12629295 0.11764647524339648 0.5979693521958183 chr15 102531392 11305743 0.11026616121626438 0.47089340227144355 chr16 90354753 15121897 0.1673613893892223 0.7144940584013479 chr17 81195210 17987248 0.22153090065288333 0.8334040283901837 chr18 78077248 17496333 0.22409003196424138 1.8711794904692174 chr19 59128983 11475697 0.19407905256885613 1.659532489000591 chr20 63025520 12419744 0.1970589691286958 0.7285127924682142 chr21 48129895 8480705 0.1762045190416476 0.6907305661760328 chr22 51304566 8552896 0.16670828089648004 0.6065229249913487 chrMT 16571 561718 33.89765252549635 22.99406855113855 chrX 155270560 19420296 0.12507390969672552 0.6810169598977858 chrY 59373566 1316486 0.02217293130077449 0.6292185787781959