BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046456.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 6,006,804 number of mapped reads = 5,966,799 (99.33%) number of supplementary alignments = 40,504 (0.67%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,986,187 number of mapped paired reads (second in pair) = 2,980,612 number of mapped paired reads (both in pair) = 5,939,178 number of mapped paired reads (singletons) = 27,621 number of mapped bases = 555,314,574 bp number of sequenced bases = 555,187,679 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,394,700 duplication rate = 43.61% >>>>>>> Insert size mean insert size = 24,964.6578 std insert size = 1,605,713.146 median insert size = 119 >>>>>>> Mapping quality mean mapping quality = 52.3205 >>>>>>> ACTG content number of A's = 163,850,443 bp (29.51%) number of C's = 114,380,518 bp (20.6%) number of T's = 161,223,254 bp (29.04%) number of G's = 115,688,985 bp (20.84%) number of N's = 44,479 bp (0.01%) GC percentage = 41.44% >>>>>>> Mismatches and indels general error rate = 0.0033 number of mismatches = 1,756,539 number of insertions = 48,297 mapped reads with insertion percentage = 0.8% number of deletions = 47,896 mapped reads with deletion percentage = 0.78% homopolymer indels = 47.16% >>>>>>> Coverage mean coverageData = 0.1794X std coverageData = 16.2907X There is a 1.72% of reference with a coverageData >= 1X There is a 1.05% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.04% of reference with a coverageData >= 31X There is a 0.04% of reference with a coverageData >= 32X There is a 0.04% of reference with a coverageData >= 33X There is a 0.04% of reference with a coverageData >= 34X There is a 0.04% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.03% of reference with a coverageData >= 39X There is a 0.03% of reference with a coverageData >= 40X There is a 0.03% of reference with a coverageData >= 41X There is a 0.03% of reference with a coverageData >= 42X There is a 0.03% of reference with a coverageData >= 43X There is a 0.03% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 129672159 0.5202480879676524 32.710827342190036 chr2 243199373 44602292 0.1833980550599528 14.47610268775593 chr3 198022430 23374226 0.11803827475503659 12.15920784108955 chr4 191154276 10743774 0.05620472753641148 6.32730108963475 chr5 180915260 38371260 0.21209520965782544 15.967266285421841 chr6 171115067 30822223 0.18012571037943725 15.678852862877605 chr7 159138663 43413263 0.2728014813094163 28.282148998394575 chr8 146364022 68860530 0.47047443120960425 25.47979124047725 chr9 141213431 4903041 0.03472078374754594 1.1974881220611768 chr10 135534747 25724605 0.18980081174313182 17.045152077781783 chr11 135006516 13500211 0.09999673645381679 6.2752480580565075 chr12 133851895 14247191 0.10643996485817403 9.557610442166098 chr13 115169878 18390430 0.15968090198029036 15.683595463729656 chr14 107349540 25114957 0.23395495686334566 17.66089222422049 chr15 102531392 4419238 0.043101316716737836 2.352336867685631 chr16 90354753 17219157 0.1905727859164199 11.991540255116997 chr17 81195210 17379715 0.21404852576894623 13.02786729794818 chr18 78077248 2143664 0.027455680814979545 0.7016996139983372 chr19 59128983 1397357 0.02363235302051449 1.6817783903986019 chr20 63025520 4294174 0.0681338924296063 3.01752952824632 chr21 48129895 2568541 0.053366852348213104 6.164637330312614 chr22 51304566 2171588 0.04232738271287589 2.524548331994695 chrMT 16571 83076 5.013336551807375 3.535419140541764 chrX 155270560 11769199 0.07579800704009826 6.7989831705795405 chrY 59373566 128703 0.002167681826622979 0.2239789052269663