BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124980.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 5,932,968 number of mapped reads = 5,801,136 (97.78%) number of supplementary alignments = 58,267 (0.98%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,907,943 number of mapped paired reads (second in pair) = 2,893,193 number of mapped paired reads (both in pair) = 5,768,568 number of mapped paired reads (singletons) = 32,568 number of mapped bases = 491,895,475 bp number of sequenced bases = 491,580,962 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 878,324 duplication rate = 10.43% >>>>>>> Insert size mean insert size = 83,350.5401 std insert size = 2,717,580.768 median insert size = 168 >>>>>>> Mapping quality mean mapping quality = 52.356 >>>>>>> ACTG content number of A's = 142,186,610 bp (28.92%) number of C's = 89,534,163 bp (18.21%) number of T's = 149,011,780 bp (30.31%) number of G's = 110,843,051 bp (22.55%) number of N's = 5,358 bp (0%) GC percentage = 40.76% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 3,978,784 number of insertions = 82,778 mapped reads with insertion percentage = 1.38% number of deletions = 165,858 mapped reads with deletion percentage = 2.79% homopolymer indels = 45.37% >>>>>>> Coverage mean coverageData = 0.1589X std coverageData = 2.4728X There is a 9.63% of reference with a coverageData >= 1X There is a 3.2% of reference with a coverageData >= 2X There is a 1.07% of reference with a coverageData >= 3X There is a 0.48% of reference with a coverageData >= 4X There is a 0.22% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 38827744 0.155777922816088 1.5817195939994189 chr2 243199373 44539933 0.18314164403705102 2.6073057664415944 chr3 198022430 32568067 0.16446655563210694 0.688204098750276 chr4 191154276 33975038 0.17773621762978506 1.9750871707013031 chr5 180915260 29758939 0.16449103851162142 0.636998580746877 chr6 171115067 28400106 0.16597080840344702 0.917214841140187 chr7 159138663 29324960 0.18427300724526008 1.3191296950495184 chr8 146364022 24369992 0.16650261223349 0.7708233374282697 chr9 141213431 20464884 0.14492165408827154 1.994836020278981 chr10 135534747 29512036 0.21774516611596287 9.063905928168246 chr11 135006516 22025964 0.163147414307025 1.0780660161805815 chr12 133851895 20946036 0.1564866601253572 0.5784168459072525 chr13 115169878 15285371 0.13272021526323055 0.5283904800549246 chr14 107349540 14280683 0.13302975494818142 0.6539964380717027 chr15 102531392 13158970 0.12834088900304796 0.5358293535380378 chr16 90354753 16746906 0.18534615439654845 3.8118887234383947 chr17 81195210 11663904 0.14365261201984697 1.5183433140704474 chr18 78077248 13532518 0.17332216934695238 2.2587048171186788 chr19 59128983 6639985 0.11229662110034938 0.9447608802008471 chr20 63025520 9410784 0.14931703855834907 0.7693204943782626 chr21 48129895 6297693 0.1308478441517481 0.9439559244576115 chr22 51304566 4308952 0.08398769029641533 0.514527654974525 chrMT 16571 2160392 130.37185444451148 74.51070202723014 chrX 155270560 15643862 0.1007522739661659 0.6905890998079487 chrY 59373566 8051756 0.1356117973442929 3.510307098986699