BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083785.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 = 3,973,435 number of mapped reads = 3,120,921 (78.54%) number of supplementary alignments = 19,096 (0.48%) number of secondary alignments = 0 number of mapped bases = 196,718,115 bp number of sequenced bases = 196,653,964 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 134,977 duplication rate = 3.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2357 >>>>>>> ACTG content number of A's = 55,877,181 bp (28.41%) number of C's = 37,789,604 bp (19.22%) number of T's = 59,366,783 bp (30.19%) number of G's = 43,618,191 bp (22.18%) number of N's = 2,205 bp (0%) GC percentage = 41.4% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,649,581 number of insertions = 14,704 mapped reads with insertion percentage = 0.47% number of deletions = 40,476 mapped reads with deletion percentage = 1.29% homopolymer indels = 45.53% >>>>>>> Coverage mean coverageData = 0.0635X std coverageData = 0.4206X There is a 5.3% of reference with a coverageData >= 1X There is a 0.77% of reference with a coverageData >= 2X There is a 0.14% 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 0.01% 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 15267284 0.06125274207441192 0.61688088433675 chr2 243199373 17103515 0.07032713443714347 0.5680602265878172 chr3 198022430 13255891 0.06694136113772566 0.30061536705101355 chr4 191154276 13184608 0.06897364932605536 0.31948591121279646 chr5 180915260 12511068 0.06915429909008229 0.3049210155731732 chr6 171115067 11574004 0.06763871938874909 0.36315032132683284 chr7 159138663 10907775 0.06854258289200281 0.5096164736975842 chr8 146364022 10047530 0.06864753962555087 0.4381776476025271 chr9 141213431 8248054 0.058408424337483875 0.40566256248237453 chr10 135534747 9490659 0.07002380725291057 0.4465475622568826 chr11 135006516 8678498 0.06428206768923657 0.3672749409692827 chr12 133851895 9204940 0.06876959044920507 0.3085789324103845 chr13 115169878 6573259 0.057074463515538326 0.2805998688102625 chr14 107349540 5897654 0.05493879154023389 0.29775096367381226 chr15 102531392 5483499 0.05348117189318955 0.28071971678738433 chr16 90354753 5036132 0.05573732241844544 0.3166918311334982 chr17 81195210 4895324 0.060290797942390936 0.32072585358888206 chr18 78077248 5568527 0.07132073866128068 0.8283674433008028 chr19 59128983 3656409 0.06183784693201978 0.5073576053057145 chr20 63025520 3677753 0.05835339399024395 0.2958237198924359 chr21 48129895 2558318 0.05315444797874585 0.28331913784771545 chr22 51304566 2056120 0.040076744826181745 0.23217765322338935 chrMT 16571 67085 4.048337457003198 3.0040539977300353 chrX 155270560 11299055 0.07277010529233617 0.35689207176121074 chrY 59373566 475154 0.00800278696415169 0.15024477050697171