BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080783.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,588,033 number of mapped reads = 2,260,570 (87.35%) number of supplementary alignments = 25,481 (0.98%) number of secondary alignments = 0 number of mapped bases = 150,475,662 bp number of sequenced bases = 150,423,410 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 92,980 duplication rate = 3.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3143 >>>>>>> ACTG content number of A's = 43,067,522 bp (28.63%) number of C's = 28,870,027 bp (19.19%) number of T's = 46,075,303 bp (30.63%) number of G's = 32,407,634 bp (21.54%) number of N's = 2,924 bp (0%) GC percentage = 40.74% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 1,123,338 number of insertions = 11,212 mapped reads with insertion percentage = 0.49% number of deletions = 32,876 mapped reads with deletion percentage = 1.44% homopolymer indels = 48.1% >>>>>>> Coverage mean coverageData = 0.0486X std coverageData = 0.325X There is a 3.89% of reference with a coverageData >= 1X There is a 0.72% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 19684707 0.07897555850021333 0.5239537332284373 chr2 243199373 10797860 0.04439920986144977 0.3753010724758536 chr3 198022430 9081706 0.04586200664237885 0.2583292794056895 chr4 191154276 9643536 0.050448968245941826 0.2740277610574613 chr5 180915260 12108085 0.06692683082676387 0.31220526235022994 chr6 171115067 10795803 0.06309089660701825 0.3542571801689684 chr7 159138663 10477307 0.06583759598382449 0.3476655553097196 chr8 146364022 6964884 0.04758603859628837 0.42731443832020816 chr9 141213431 5176184 0.03665504027021339 0.26641108734346 chr10 135534747 5654158 0.04171740550045074 0.2934192773745482 chr11 135006516 5213295 0.0386151361760939 0.25053072582202307 chr12 133851895 6418965 0.0479557274852179 0.2649613776496186 chr13 115169878 6310186 0.054790246456629915 0.2839148909600166 chr14 107349540 4016603 0.037416117479404196 0.2426492867559753 chr15 102531392 3997127 0.03898442147357172 0.24680905820134608 chr16 90354753 3256959 0.03604634943775454 0.23997438073418143 chr17 81195210 3489462 0.04297620512343031 0.26016042533348566 chr18 78077248 1937374 0.024813553879358043 0.3283870277292306 chr19 59128983 2040957 0.03451703202810033 0.34071494440102434 chr20 63025520 2376340 0.03770440926151819 0.2385244035399105 chr21 48129895 2237446 0.04648765595686423 0.26591579377370905 chr22 51304566 705902 0.013759048268725243 0.13774126979751147 chrMT 16571 202454 12.217367690543721 6.716184798253878 chrX 155270560 7581400 0.04882702812432698 0.27576512353211174 chrY 59373566 306962 0.00517001117972264 0.10093577306176406