BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548971.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 = 8,924,237 number of mapped reads = 3,921,914 (43.95%) number of secondary alignments = 0 number of mapped bases = 154,916,143 bp number of sequenced bases = 154,894,750 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 103,688 duplication rate = 1.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7919 >>>>>>> ACTG content number of A's = 47,467,547 bp (30.65%) number of C's = 29,702,969 bp (19.18%) number of T's = 47,827,723 bp (30.88%) number of G's = 29,888,278 bp (19.3%) number of N's = 8,233 bp (0.01%) GC percentage = 38.47% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 486,326 number of insertions = 6,620 mapped reads with insertion percentage = 0.17% number of deletions = 16,946 mapped reads with deletion percentage = 0.43% homopolymer indels = 44.61% >>>>>>> Coverage mean coverageData = 0.05X std coverageData = 0.3665X There is a 4.26% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 12326174 0.04945293195478137 0.5919268008076218 chr2 243199373 13490032 0.05546902458502637 0.3394985480236864 chr3 198022430 11063833 0.05587161514985954 0.27076405124863095 chr4 191154276 10894568 0.05699358773433873 0.27871287544043327 chr5 180915260 10001065 0.05528038375535596 0.27156760112688244 chr6 171115067 9553720 0.05583213779766103 0.301986141209798 chr7 159138663 8828770 0.05547847288373913 0.5233287503253942 chr8 146364022 8170136 0.05582065789364547 0.5986269821603903 chr9 141213431 6540892 0.0463191918338136 0.3085931481646939 chr10 135534747 7232435 0.05336222009548592 0.3098342090723132 chr11 135006516 7125042 0.05277554158941484 0.3417045260768851 chr12 133851895 7087983 0.052953923439036855 0.2689039180796586 chr13 115169878 5345377 0.046412977879511166 0.24494994966430164 chr14 107349540 4794517 0.04466266925782821 0.27509946577584093 chr15 102531392 4441258 0.04331608021082948 0.2354904785863328 chr16 90354753 4039722 0.04470956829465297 0.2510397926559723 chr17 81195210 3765111 0.04637109750686032 0.25626686945637345 chr18 78077248 4349810 0.05571162036858676 0.5225279093359645 chr19 59128983 2595782 0.043900332261760704 0.554229073492782 chr20 63025520 3051290 0.04841356326770489 0.25465060397778977 chr21 48129895 2039694 0.04237894140429768 0.2554051866192189 chr22 51304566 1583567 0.03086600518168305 0.23066703517048442 chrMT 16571 3841 0.23179047733993122 0.5087308910002695 chrX 155270560 5324357 0.034290834012577785 0.2486387833632235 chrY 59373566 1267167 0.02134227544965044 0.23516303282330853