BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472619.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 18,404,364 number of mapped reads = 18,284,118 (99.35%) number of supplementary alignments = 90,302 (0.49%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,161,390 number of mapped paired reads (second in pair) = 9,122,728 number of mapped paired reads (both in pair) = 18,200,540 number of mapped paired reads (singletons) = 83,578 number of mapped bases = 1,800,992,806 bp number of sequenced bases = 1,800,763,738 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,407,189 duplication rate = 50.44% >>>>>>> Insert size mean insert size = 21,646.9921 std insert size = 1,422,559.2786 median insert size = 220 >>>>>>> Mapping quality mean mapping quality = 54.9929 >>>>>>> ACTG content number of A's = 491,385,166 bp (27.29%) number of C's = 411,700,485 bp (22.86%) number of T's = 491,010,910 bp (27.27%) number of G's = 406,340,078 bp (22.56%) number of N's = 327,099 bp (0.02%) GC percentage = 45.43% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 10,957,447 number of insertions = 111,174 mapped reads with insertion percentage = 0.6% number of deletions = 93,483 mapped reads with deletion percentage = 0.5% homopolymer indels = 45.88% >>>>>>> Coverage mean coverageData = 0.5818X std coverageData = 21.9103X There is a 3.73% of reference with a coverageData >= 1X There is a 1.66% of reference with a coverageData >= 2X There is a 0.79% of reference with a coverageData >= 3X There is a 0.61% of reference with a coverageData >= 4X There is a 0.48% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.35% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.3% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.28% of reference with a coverageData >= 18X There is a 0.27% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.21% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.19% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 216604433 0.8690226412715738 26.156620449472907 chr2 243199373 117947207 0.48498154228382817 18.369462739280223 chr3 198022430 160887028 0.8124687087215322 23.170102964397817 chr4 191154276 38606029 0.20196267542558138 9.131449959769421 chr5 180915260 106657238 0.5895425184144223 21.934004150882753 chr6 171115067 194836318 1.1386274827569685 42.28182082227813 chr7 159138663 65247727 0.4100054994178253 19.102001019383987 chr8 146364022 79576686 0.5436902109727485 17.68474292297724 chr9 141213431 88561156 0.6271440002049097 18.30567224905308 chr10 135534747 25308346 0.18672957717624986 11.05147663240581 chr11 135006516 67723193 0.5016290695183927 15.072053252487919 chr12 133851895 98727351 0.7375865018571459 21.29174921214266 chr13 115169878 70665107 0.6135728215323802 21.500531918330353 chr14 107349540 38363903 0.35737370649189554 17.446002223559113 chr15 102531392 16261274 0.15859800284385098 6.470459229075131 chr16 90354753 70853264 0.7841675357133675 21.80309833273164 chr17 81195210 45223089 0.5569674491881972 16.319879195351234 chr18 78077248 21640439 0.27716703078469157 16.470775812042593 chr19 59128983 52691918 0.8911351984525084 26.615382734304085 chr20 63025520 39452674 0.6259793493175463 23.17697142492072 chr21 48129895 7229573 0.150209615042792 8.267573976740314 chr22 51304566 35912321 0.6999829410894929 22.553692220735435 chrMT 16571 3994 0.24102347474503652 0.6295825345970215 chrX 155270560 138778650 0.8937859823523532 33.73017962647189 chrY 59373566 3233888 0.054466797564424546 4.6653075097970795