BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549094.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 8,359,423 number of mapped reads = 7,237,636 (86.58%) number of secondary alignments = 0 number of mapped bases = 287,445,940 bp number of sequenced bases = 287,419,929 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 282,378 duplication rate = 2.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6125 >>>>>>> ACTG content number of A's = 86,621,795 bp (30.14%) number of C's = 57,276,078 bp (19.93%) number of T's = 87,632,304 bp (30.49%) number of G's = 55,820,244 bp (19.42%) number of N's = 69,508 bp (0.02%) GC percentage = 39.35% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 1,150,778 number of insertions = 6,653 mapped reads with insertion percentage = 0.09% number of deletions = 20,741 mapped reads with deletion percentage = 0.29% homopolymer indels = 45.05% >>>>>>> Coverage mean coverageData = 0.0929X std coverageData = 0.9189X There is a 7.74% of reference with a coverageData >= 1X There is a 1.11% of reference with a coverageData >= 2X There is a 0.18% 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 0.01% 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 22934509 0.09201384898455278 2.247056662666045 chr2 243199373 25207804 0.10365077709308075 0.6118080771906834 chr3 198022430 20691418 0.10449027415732652 0.38105286024873214 chr4 191154276 21505932 0.11250562869961643 0.39887713307127076 chr5 180915260 18950366 0.10474719490218791 0.3913132130101081 chr6 171115067 17695224 0.1034112560058782 0.4797120608256833 chr7 159138663 16241324 0.10205768789197381 0.9050426708442371 chr8 146364022 15697551 0.10725006586659665 1.6222511574008078 chr9 141213431 12356462 0.08750203087976809 0.6028851441874326 chr10 135534747 13331355 0.0983611604779105 0.7484136223734262 chr11 135006516 13196865 0.09774983749673238 0.5887465188097681 chr12 133851895 13347396 0.09971764688127875 0.39569769641445207 chr13 115169878 10486567 0.09105303558626675 0.33975314721004046 chr14 107349540 9103495 0.08480236617688348 0.4123797651209734 chr15 102531392 7677047 0.07487508801206952 0.31119310188196647 chr16 90354753 7043941 0.0779587212196795 0.43856140522244824 chr17 81195210 5989518 0.07376688846546489 0.38970520889632776 chr18 78077248 8233815 0.1054572901954741 1.2433168363738 chr19 59128983 4049259 0.0684817968203512 1.7623166254335563 chr20 63025520 5471508 0.08681416670580425 0.3553849711372266 chr21 48129895 3813828 0.07924031415402008 0.3872423832533479 chr22 51304566 2218262 0.043237126301779845 0.29064315648881245 chrMT 16571 39833 2.403777683905618 2.996358969913582 chrX 155270560 9815343 0.06321444966772838 0.39712136099074063 chrY 59373566 2347318 0.039534731668298316 0.34073134181225373