BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053608.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 7,307,358 number of mapped reads = 4,650,384 (63.64%) number of supplementary alignments = 140 (0%) number of secondary alignments = 0 number of mapped bases = 217,541,408 bp number of sequenced bases = 217,493,457 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,007,725 duplication rate = 15.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8125 >>>>>>> ACTG content number of A's = 65,904,726 bp (30.3%) number of C's = 42,575,186 bp (19.58%) number of T's = 64,577,331 bp (29.69%) number of G's = 44,327,904 bp (20.38%) number of N's = 108,310 bp (0.05%) GC percentage = 39.96% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 1,665,257 number of insertions = 11,400 mapped reads with insertion percentage = 0.24% number of deletions = 32,948 mapped reads with deletion percentage = 0.71% homopolymer indels = 45.85% >>>>>>> Coverage mean coverageData = 0.0703X std coverageData = 0.8943X There is a 3.43% of reference with a coverageData >= 1X There is a 1.31% of reference with a coverageData >= 2X There is a 0.7% of reference with a coverageData >= 3X There is a 0.43% of reference with a coverageData >= 4X There is a 0.28% of reference with a coverageData >= 5X There is a 0.2% of reference with a coverageData >= 6X There is a 0.14% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 17118201 0.06867866941041643 0.6271765352030108 chr2 243199373 18656874 0.07671431784489016 2.451064443744375 chr3 198022430 15070865 0.07610685819783143 0.5887930916532584 chr4 191154276 14208655 0.0743308248045678 0.6016465349419433 chr5 180915260 13596738 0.07515528540820714 0.5904402732176973 chr6 171115067 13028129 0.07613665604326941 0.6288789632378754 chr7 159138663 11769189 0.07395556037818415 0.6664884058641075 chr8 146364022 11255378 0.07689989552213863 0.653689194041296 chr9 141213431 8943435 0.06333275055118517 0.556118112522079 chr10 135534747 10143064 0.07483736993289256 0.6084331753438714 chr11 135006516 9837392 0.0728660533688611 0.6358910891179687 chr12 133851895 9968969 0.07447760825500453 0.5927844133431215 chr13 115169878 7162791 0.06219326723607366 0.542693602078977 chr14 107349540 6639204 0.061846599435824316 0.590058209072971 chr15 102531392 6171940 0.06019561306648407 0.5122216138686084 chr16 90354753 5952547 0.06587973296767244 0.5556486097678147 chr17 81195210 5533944 0.06815604023931954 0.5613557253702358 chr18 78077248 5697079 0.07296721062709588 0.6407196909832651 chr19 59128983 3817994 0.06457060152717323 0.5959128936453064 chr20 63025520 4447554 0.07056750979603182 0.5665383256692734 chr21 48129895 2777781 0.05771425431117188 0.5342373309155987 chr22 51304566 2288597 0.0446080569125173 0.42981830806286536 chrMT 16571 54745 3.3036630257679076 5.531692839344185 chrX 155270560 12843624 0.08271770257027475 0.6613439480801868 chrY 59373566 556719 0.009376546458402043 0.19267785187675437