BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080554.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 = 3,702,161 number of mapped reads = 3,135,616 (84.7%) number of supplementary alignments = 22,499 (0.61%) number of secondary alignments = 0 number of mapped bases = 208,824,668 bp number of sequenced bases = 208,736,585 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 152,035 duplication rate = 3.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7608 >>>>>>> ACTG content number of A's = 56,920,067 bp (27.27%) number of C's = 37,339,211 bp (17.89%) number of T's = 67,495,175 bp (32.34%) number of G's = 46,811,808 bp (22.43%) number of N's = 170,324 bp (0.08%) GC percentage = 40.31% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 1,936,558 number of insertions = 18,277 mapped reads with insertion percentage = 0.58% number of deletions = 53,227 mapped reads with deletion percentage = 1.68% homopolymer indels = 47.31% >>>>>>> Coverage mean coverageData = 0.0675X std coverageData = 0.4748X There is a 5.48% of reference with a coverageData >= 1X There is a 0.89% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.05% 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% 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 18314631 0.07347877781215237 0.6645503891778066 chr2 243199373 13199075 0.05427265225720792 0.5345190674339815 chr3 198022430 13117070 0.06624032439153484 0.3120320435992682 chr4 191154276 13183123 0.06896588073185451 0.34287752570423774 chr5 180915260 14139977 0.07815801165694923 0.33302352988164957 chr6 171115067 12636901 0.07385031149828554 0.4063146036348436 chr7 159138663 10985046 0.06902814057197401 0.6921981587463697 chr8 146364022 10638195 0.07268312837153382 0.7422916224834751 chr9 141213431 8864239 0.06277192571009764 0.4698795310999591 chr10 135534747 10557135 0.07789246103805396 0.5319231264405585 chr11 135006516 10028746 0.07428342199423915 0.46184954296796055 chr12 133851895 9496243 0.07094589882347202 0.33050465288849995 chr13 115169878 7763746 0.06741125487690454 0.3079905981065003 chr14 107349540 7259248 0.06762253475888207 0.34496119784056806 chr15 102531392 7359596 0.07177895331802381 0.318601247794988 chr16 90354753 5320521 0.05888479380824604 0.3455030423776597 chr17 81195210 6128665 0.07548062256381873 0.3645575785571002 chr18 78077248 6348838 0.08131482810459713 0.7790811561239611 chr19 59128983 2385894 0.04035066863910039 0.5353459849384045 chr20 63025520 5096815 0.08086906700650784 0.35108489100925505 chr21 48129895 2990273 0.062129223427559936 0.333478818551236 chr22 51304566 2508530 0.04889486834368699 0.2620376561779373 chrMT 16571 47430 2.8622291955826444 2.672230262047116 chrX 155270560 9943766 0.0640415414229201 0.3434659475927205 chrY 59373566 510965 0.008605934162687819 0.2195887794969681