BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013339.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 = 2,321,519 number of mapped reads = 2,065,943 (88.99%) number of supplementary alignments = 15,035 (0.65%) number of secondary alignments = 0 number of mapped bases = 136,861,778 bp number of sequenced bases = 136,801,610 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 91,248 duplication rate = 3.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6939 >>>>>>> ACTG content number of A's = 37,002,558 bp (27.05%) number of C's = 26,153,436 bp (19.12%) number of T's = 42,392,093 bp (30.99%) number of G's = 31,221,644 bp (22.82%) number of N's = 31,879 bp (0.02%) GC percentage = 41.94% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,093,369 number of insertions = 9,258 mapped reads with insertion percentage = 0.44% number of deletions = 34,554 mapped reads with deletion percentage = 1.65% homopolymer indels = 45.08% >>>>>>> Coverage mean coverageData = 0.0442X std coverageData = 0.3757X There is a 3.61% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 10021141 0.04020507936868892 0.6187034891630242 chr2 243199373 13884424 0.05709070639750375 0.481028796319189 chr3 198022430 8555836 0.04320639838628382 0.244068778608842 chr4 191154276 8318162 0.04351543776085867 0.2512840822231421 chr5 180915260 7205877 0.03983012267732418 0.23567570633565435 chr6 171115067 7140192 0.04172743011578285 0.29231326096226257 chr7 159138663 8465978 0.05319875032505457 0.6038967774843443 chr8 146364022 7646858 0.0522454760091247 0.3656607374440291 chr9 141213431 5076394 0.03594837944274578 0.3087291248011147 chr10 135534747 6435013 0.04747869562924702 0.3782085730388574 chr11 135006516 5719357 0.04236356265944971 0.28518973059836644 chr12 133851895 6794979 0.05076490698917636 0.26825283847066256 chr13 115169878 3484859 0.030258423995204717 0.20578373319343787 chr14 107349540 4664732 0.04345367478985005 0.2613292868220269 chr15 102531392 3830926 0.037363444748706814 0.2271539600702792 chr16 90354753 4590885 0.050809557301318725 0.297650340227767 chr17 81195210 3726489 0.045895429053019264 0.2748660663359196 chr18 78077248 3312826 0.04243010716771165 0.5237896876588517 chr19 59128983 3002278 0.050775065757515225 0.47837327768533255 chr20 63025520 3224660 0.051164353741151206 0.2727746689695383 chr21 48129895 2308994 0.047974216440738134 0.27269349094779083 chr22 51304566 1499498 0.02922737909916244 0.20028195813058522 chrMT 16571 451039 27.218574618309095 15.493254113190925 chrX 155270560 7201278 0.04637890144789843 0.2737889106881066 chrY 59373566 299103 0.005037645877628438 0.11344998724957991