BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695941.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 16,672,416 number of mapped reads = 16,547,438 (99.25%) number of supplementary alignments = 38,125 (0.23%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,317,417 number of mapped paired reads (second in pair) = 8,230,021 number of mapped paired reads (both in pair) = 16,446,868 number of mapped paired reads (singletons) = 100,570 number of mapped bases = 1,641,432,888 bp number of sequenced bases = 1,641,132,466 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 250,740 duplication rate = 1.48% >>>>>>> Insert size mean insert size = 28,541.7173 std insert size = 1,684,969.2546 median insert size = 334 >>>>>>> Mapping quality mean mapping quality = 54.7744 >>>>>>> ACTG content number of A's = 480,772,252 bp (29.3%) number of C's = 338,153,534 bp (20.6%) number of T's = 481,362,344 bp (29.33%) number of G's = 340,128,178 bp (20.73%) number of N's = 716,158 bp (0.04%) GC percentage = 41.33% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 11,213,351 number of insertions = 104,891 mapped reads with insertion percentage = 0.63% number of deletions = 132,476 mapped reads with deletion percentage = 0.79% homopolymer indels = 44.99% >>>>>>> Coverage mean coverageData = 0.5302X std coverageData = 1.065X There is a 30.39% of reference with a coverageData >= 1X There is a 12.24% of reference with a coverageData >= 2X There is a 5.35% of reference with a coverageData >= 3X There is a 2.48% of reference with a coverageData >= 4X There is a 1.21% of reference with a coverageData >= 5X There is a 0.61% of reference with a coverageData >= 6X There is a 0.32% of reference with a coverageData >= 7X There is a 0.17% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% 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% 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 145806243 0.5849784542763486 1.1453886973532372 chr2 243199373 167159837 0.6873366281252707 1.2275857724155292 chr3 198022430 99832743 0.504148661341041 0.98465875517393 chr4 191154276 128416874 0.6717970253513973 1.1680320537090207 chr5 180915260 111946334 0.6187777305242245 1.092851363865128 chr6 171115067 105191953 0.6147439547214156 1.129255656313191 chr7 159138663 92823434 0.5832865015335714 1.1053529464100895 chr8 146364022 102537486 0.7005648286981345 1.242668849326236 chr9 141213431 53342240 0.3777419727164621 0.9451501558110489 chr10 135534747 69946369 0.5160770248827778 1.0050276576716743 chr11 135006516 63460789 0.47005723042286346 1.0027258247957844 chr12 133851895 75994860 0.5677533366262764 1.1220336871778194 chr13 115169878 57476852 0.49906149939656963 1.0089771791885358 chr14 107349540 61596309 0.573792016248975 1.1118291966289662 chr15 102531392 58790761 0.5733927907659734 1.1509041119282504 chr16 90354753 35223911 0.38984015594619575 0.8629978640820983 chr17 81195210 44109618 0.5432539431821163 1.0626488497882651 chr18 78077248 49473953 0.633653903887596 1.1178235482098413 chr19 59128983 20444950 0.3457686732071817 0.8741087473558917 chr20 63025520 25590789 0.4060385221732403 0.9439117411290882 chr21 48129895 14518770 0.30165804434021726 0.7690983697041739 chr22 51304566 15904799 0.3100074757478701 0.8139599102093569 chrMT 16571 4905 0.2959990344577877 0.6043671021104797 chrX 155270560 35814437 0.2306582587194894 0.6657476155865698 chrY 59373566 6023672 0.10145376816342815 0.4154981518295355