BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231805.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 9,860,469 number of mapped reads = 7,705,871 (78.15%) number of supplementary alignments = 99,677 (1.01%) number of secondary alignments = 0 number of mapped bases = 500,285,095 bp number of sequenced bases = 500,111,065 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 990,375 duplication rate = 8.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8442 >>>>>>> ACTG content number of A's = 148,252,260 bp (29.64%) number of C's = 99,249,476 bp (19.85%) number of T's = 146,044,648 bp (29.2%) number of G's = 106,526,530 bp (21.3%) number of N's = 38,151 bp (0.01%) GC percentage = 41.15% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 2,819,651 number of insertions = 36,180 mapped reads with insertion percentage = 0.47% number of deletions = 103,023 mapped reads with deletion percentage = 1.32% homopolymer indels = 47.15% >>>>>>> Coverage mean coverageData = 0.1616X std coverageData = 7.0542X There is a 8.42% of reference with a coverageData >= 1X There is a 3.8% of reference with a coverageData >= 2X There is a 1.78% of reference with a coverageData >= 3X There is a 0.84% of reference with a coverageData >= 4X There is a 0.41% of reference with a coverageData >= 5X There is a 0.21% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% 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 0.01% of reference with a coverageData >= 12X There is a 0.01% 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% 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 67224600 0.26970685059998306 2.8471041577694374 chr2 243199373 42975105 0.1767073017906177 24.628633680032955 chr3 198022430 37691530 0.19033970040666606 0.7984350707526132 chr4 191154276 31038641 0.1623748191748533 0.7967553384302184 chr5 180915260 29228584 0.1615595279248417 0.6723968784258509 chr6 171115067 32110640 0.18765524604563313 0.8560640019378961 chr7 159138663 33426442 0.21004601502778744 1.636886730327184 chr8 146364022 25614119 0.17500283642109807 3.9410925473570386 chr9 141213431 15291279 0.10828487695338271 0.786134324335979 chr10 135534747 18224289 0.13446211693596183 1.2684187879131752 chr11 135006516 19844712 0.1469907719120757 0.9501258262628529 chr12 133851895 20912996 0.15623982013851953 0.6607114819816833 chr13 115169878 13867711 0.12041092029289116 0.5891604024052863 chr14 107349540 16540149 0.1540775023348959 0.7185543525049742 chr15 102531392 10863511 0.10595302363592216 0.5236257931237851 chr16 90354753 9153417 0.10130531816073915 0.6284079986752238 chr17 81195210 10266382 0.12644073461969 0.6821662316338784 chr18 78077248 9005403 0.11533965695102369 1.548041001845237 chr19 59128983 11107244 0.18784770913445273 1.7803321277881696 chr20 63025520 11262045 0.1786902353205495 0.7508100914290344 chr21 48129895 8814856 0.18314721027336545 0.7867015784828605 chr22 51304566 6289251 0.12258657445810964 0.5707118914711041 chrMT 16571 1151676 69.49948705569972 55.302757066281416 chrX 155270560 17122445 0.11027489692830374 0.6417060671243506 chrY 59373566 1258068 0.02118902543263108 0.4873751514699858