BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081976.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 = 2,884,460 number of mapped reads = 2,673,196 (92.68%) number of supplementary alignments = 16,397 (0.57%) number of secondary alignments = 0 number of mapped bases = 183,611,388 bp number of sequenced bases = 183,543,410 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 129,765 duplication rate = 3.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7551 >>>>>>> ACTG content number of A's = 52,584,939 bp (28.65%) number of C's = 33,779,577 bp (18.4%) number of T's = 58,353,365 bp (31.79%) number of G's = 38,801,778 bp (21.14%) number of N's = 23,751 bp (0.01%) GC percentage = 39.54% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 1,385,290 number of insertions = 13,196 mapped reads with insertion percentage = 0.49% number of deletions = 38,363 mapped reads with deletion percentage = 1.42% homopolymer indels = 48.39% >>>>>>> Coverage mean coverageData = 0.0593X std coverageData = 0.5264X There is a 4.98% of reference with a coverageData >= 1X There is a 0.68% of reference with a coverageData >= 2X There is a 0.11% 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 0.01% 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 16991372 0.06816982815059867 0.9252256488319476 chr2 243199373 16095886 0.06618391240671496 0.6550189437317099 chr3 198022430 11586512 0.05851110906981598 0.2779378602008072 chr4 191154276 9655126 0.05050959990034437 0.276776216608313 chr5 180915260 9210350 0.0509097463641265 0.26060319928071174 chr6 171115067 16028565 0.09367126624799206 0.4811007789104578 chr7 159138663 12050075 0.07572059971372262 0.7338478986460084 chr8 146364022 10542735 0.07203091890983974 0.8289250737238385 chr9 141213431 8936301 0.06328223127727843 0.5303672046422865 chr10 135534747 7447252 0.0549471789695376 0.5451021218395796 chr11 135006516 8266988 0.06123399258743926 0.37828333119098967 chr12 133851895 7807911 0.058332465147392945 0.2937894322598179 chr13 115169878 5077856 0.04409013961098405 0.2377615300362389 chr14 107349540 4551011 0.04239432232313245 0.26565624345348565 chr15 102531392 4229300 0.04124883040698404 0.23083669614308078 chr16 90354753 3921091 0.04339662131553832 0.29436606523696035 chr17 81195210 4749157 0.05849060554187864 0.3140271432094988 chr18 78077248 5236969 0.06707420066854815 0.8894913728148198 chr19 59128983 3682899 0.06228585057855637 0.7249777655109306 chr20 63025520 4529867 0.07187353630719746 0.3150595033805443 chr21 48129895 1952909 0.040575800134199334 0.25999254951179884 chr22 51304566 1423381 0.027743748967684476 0.1858282377648642 chrMT 16571 164496 9.926739484641844 5.648811663658766 chrX 155270560 9067063 0.05839524891260777 0.33461096840239946 chrY 59373566 406316 0.006843382120588815 0.16012104112806058