BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818879.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,876,299 number of mapped reads = 1,735,885 (92.52%) number of supplementary alignments = 23,480 (1.25%) number of secondary alignments = 0 number of mapped bases = 160,842,753 bp number of sequenced bases = 160,743,611 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 298,176 duplication rate = 14.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2937 >>>>>>> ACTG content number of A's = 46,558,811 bp (28.96%) number of C's = 33,576,133 bp (20.89%) number of T's = 46,293,570 bp (28.8%) number of G's = 34,312,798 bp (21.35%) number of N's = 2,299 bp (0%) GC percentage = 42.23% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 964,620 number of insertions = 22,229 mapped reads with insertion percentage = 1.24% number of deletions = 50,008 mapped reads with deletion percentage = 2.82% homopolymer indels = 40.36% >>>>>>> Coverage mean coverageData = 0.052X std coverageData = 0.6685X There is a 3.83% of reference with a coverageData >= 1X There is a 0.84% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 13410122 0.053801759635335074 1.0742362769325218 chr2 243199373 11742816 0.04828472974722677 0.8386772700980045 chr3 198022430 9460129 0.047773017430399176 0.27845692408998657 chr4 191154276 9400094 0.04917543147190702 0.3829876835500961 chr5 180915260 8409583 0.0464835470484911 0.2884747989217638 chr6 171115067 7652841 0.04472336150270157 0.3050761957435427 chr7 159138663 13901124 0.08735227340699726 1.56831718467497 chr8 146364022 15464092 0.10565500857854261 0.5574805135359597 chr9 141213431 5675958 0.04019417954656169 0.5648390832212575 chr10 135534747 7295011 0.053823917198148455 0.8895210786119667 chr11 135006516 6787680 0.05027668442314295 0.3743874161696573 chr12 133851895 6017196 0.04495413382081741 0.2726336302202383 chr13 115169878 3915612 0.03399857730161006 0.2311404822751343 chr14 107349540 5220969 0.04863522470613288 0.3081045474103504 chr15 102531392 4231855 0.04127374960441384 0.256921340592543 chr16 90354753 3871579 0.04284864792890309 0.5744263405063007 chr17 81195210 4206532 0.051807637420975945 0.4110790630741542 chr18 78077248 2809318 0.03598126306910817 0.6524842622559098 chr19 59128983 3015758 0.05100304194306877 0.9923295051354655 chr20 63025520 6404069 0.10161072847951115 0.4396220819628104 chr21 48129895 1913006 0.039746731215598956 0.3201972146664248 chr22 51304566 1882051 0.036683888915462225 0.26494289289274586 chrMT 16571 242235 14.61800736225937 9.357370908332799 chrX 155270560 7317036 0.047124425905335825 0.3664702603418233 chrY 59373566 596087 0.010039602472251708 0.6675933257234218