BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472813.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 1,931,969 number of mapped reads = 1,500,402 (77.66%) number of supplementary alignments = 15,266 (0.79%) number of secondary alignments = 0 number of mapped bases = 95,085,171 bp number of sequenced bases = 95,044,310 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 50,843 duplication rate = 2.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.0319 >>>>>>> ACTG content number of A's = 25,405,520 bp (26.73%) number of C's = 19,453,033 bp (20.47%) number of T's = 27,680,976 bp (29.12%) number of G's = 22,502,856 bp (23.68%) number of N's = 1,925 bp (0%) GC percentage = 44.14% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 824,095 number of insertions = 7,399 mapped reads with insertion percentage = 0.49% number of deletions = 22,791 mapped reads with deletion percentage = 1.5% homopolymer indels = 44.03% >>>>>>> Coverage mean coverageData = 0.0307X std coverageData = 0.2549X There is a 2.66% of reference with a coverageData >= 1X There is a 0.28% of reference with a coverageData >= 2X There is a 0.06% 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% 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 8185411 0.0328400826732544 0.3274472076648633 chr2 243199373 8379923 0.034457009064739655 0.3452615661286678 chr3 198022430 6853599 0.03461021562052339 0.20998108467149917 chr4 191154276 4485737 0.023466579424045945 0.18992494867088863 chr5 180915260 5492172 0.030357704485514378 0.1977609535274649 chr6 171115067 4684502 0.0273763268315817 0.2056566076047333 chr7 159138663 5405819 0.033969237255688144 0.3229938610134219 chr8 146364022 4698675 0.032102663863664525 0.24223750296874194 chr9 141213431 4300316 0.030452599087405503 0.2667388379754839 chr10 135534747 4616006 0.03405773133586179 0.25777099139557796 chr11 135006516 3759908 0.02784982615209476 0.2607030061279149 chr12 133851895 4567872 0.034126315507150645 0.21216918933446252 chr13 115169878 4299300 0.037330073406867725 0.22325125433068554 chr14 107349540 2468910 0.022998794405639744 0.18763667940858395 chr15 102531392 2305251 0.02248336782553386 0.18488693812368087 chr16 90354753 3038201 0.033625248247870256 0.22346344381500266 chr17 81195210 2600855 0.03203212356985098 0.21639924253405524 chr18 78077248 2087145 0.026731795157534242 0.41827095502670936 chr19 59128983 2441841 0.04129685437004726 0.28746517188354787 chr20 63025520 3211516 0.05095580329999657 0.2622754824878291 chr21 48129895 1344772 0.02794047234052765 0.20841533523958294 chr22 51304566 1086328 0.021174099786751922 0.16946069265076832 chrMT 16571 68907 4.158288576428701 3.5918391906565574 chrX 155270560 4226652 0.027221206647287163 0.20774521438344584 chrY 59373566 475553 0.008009507126454221 0.12679455033307208