BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365374.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP102259/SRP102259.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 = 518,060,238 number of mapped reads = 450,078,614 (86.88%) number of supplementary alignments = 2,099,527 (0.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 224,389,397 number of mapped paired reads (second in pair) = 225,689,217 number of mapped paired reads (both in pair) = 446,343,208 number of mapped paired reads (singletons) = 3,735,406 number of mapped bases = 43,279,706,966 bp number of sequenced bases = 43,267,123,853 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 231,160,140 duplication rate = 29.02% >>>>>>> Insert size mean insert size = 63,144.6778 std insert size = 2,431,888.6461 median insert size = 141 >>>>>>> Mapping quality mean mapping quality = 53.4189 >>>>>>> ACTG content number of A's = 12,620,184,892 bp (29.17%) number of C's = 8,608,435,324 bp (19.9%) number of T's = 12,210,543,886 bp (28.22%) number of G's = 9,070,577,753 bp (20.96%) number of N's = 757,381,998 bp (1.75%) GC percentage = 40.86% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 209,787,779 number of insertions = 11,102,803 mapped reads with insertion percentage = 2.42% number of deletions = 6,147,904 mapped reads with deletion percentage = 1.34% homopolymer indels = 48.88% >>>>>>> Coverage mean coverageData = 13.9806X std coverageData = 177.1795X There is a 83.82% of reference with a coverageData >= 1X There is a 80.57% of reference with a coverageData >= 2X There is a 76.4% of reference with a coverageData >= 3X There is a 72.68% of reference with a coverageData >= 4X There is a 68.58% of reference with a coverageData >= 5X There is a 64.75% of reference with a coverageData >= 6X There is a 60.81% of reference with a coverageData >= 7X There is a 57.12% of reference with a coverageData >= 8X There is a 53.45% of reference with a coverageData >= 9X There is a 50.01% of reference with a coverageData >= 10X There is a 46.65% of reference with a coverageData >= 11X There is a 43.52% of reference with a coverageData >= 12X There is a 40.51% of reference with a coverageData >= 13X There is a 37.71% of reference with a coverageData >= 14X There is a 35.04% of reference with a coverageData >= 15X There is a 32.56% of reference with a coverageData >= 16X There is a 30.22% of reference with a coverageData >= 17X There is a 28.05% of reference with a coverageData >= 18X There is a 26.01% of reference with a coverageData >= 19X There is a 24.12% of reference with a coverageData >= 20X There is a 22.34% of reference with a coverageData >= 21X There is a 20.71% of reference with a coverageData >= 22X There is a 19.18% of reference with a coverageData >= 23X There is a 17.77% of reference with a coverageData >= 24X There is a 16.45% of reference with a coverageData >= 25X There is a 15.24% of reference with a coverageData >= 26X There is a 14.1% of reference with a coverageData >= 27X There is a 13.06% of reference with a coverageData >= 28X There is a 12.09% of reference with a coverageData >= 29X There is a 11.2% of reference with a coverageData >= 30X There is a 10.37% of reference with a coverageData >= 31X There is a 9.61% of reference with a coverageData >= 32X There is a 8.91% of reference with a coverageData >= 33X There is a 8.26% of reference with a coverageData >= 34X There is a 7.65% of reference with a coverageData >= 35X There is a 7.1% of reference with a coverageData >= 36X There is a 6.59% of reference with a coverageData >= 37X There is a 6.11% of reference with a coverageData >= 38X There is a 5.68% of reference with a coverageData >= 39X There is a 5.28% of reference with a coverageData >= 40X There is a 4.91% of reference with a coverageData >= 41X There is a 4.56% of reference with a coverageData >= 42X There is a 4.25% of reference with a coverageData >= 43X There is a 3.96% of reference with a coverageData >= 44X There is a 3.69% of reference with a coverageData >= 45X There is a 3.44% of reference with a coverageData >= 46X There is a 3.21% of reference with a coverageData >= 47X There is a 3% of reference with a coverageData >= 48X There is a 2.8% of reference with a coverageData >= 49X There is a 2.62% of reference with a coverageData >= 50X There is a 2.45% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3631572160 14.569962335219216 502.79810611393816 chr2 243199373 3773176230 15.51474489204378 110.29502386269483 chr3 198022430 2893644832 14.612712468986468 28.936874855129133 chr4 191154276 2863874671 14.982006842473144 63.706789941451824 chr5 180915260 2651591057 14.656536198217884 20.223733130242447 chr6 171115067 2550244307 14.903680615103285 72.98226383664975 chr7 159138663 2393204944 15.038488440738 122.63721217170362 chr8 146364022 2221692261 15.179223901075908 73.39390444515716 chr9 141213431 1863927758 13.199365986653211 156.4700421988504 chr10 135534747 2267865182 16.73272155073267 294.8671873194683 chr11 135006516 2023680475 14.989502247432265 100.6962085027947 chr12 133851895 1946812788 14.544529145440936 33.34657917858255 chr13 115169878 1406235481 12.210097860831285 14.703252476462005 chr14 107349540 1332418856 12.411966143497215 21.231237507836333 chr15 102531392 1225071448 11.948257251788798 19.94250282837322 chr16 90354753 1253947734 13.878049492316137 47.92358140400833 chr17 81195210 1188458025 14.637046015399184 78.37392655907695 chr18 78077248 1224466608 15.682758285742858 201.63963774361847 chr19 59128983 875396906 14.804869990745486 247.8343373644666 chr20 63025520 909732083 14.434344738448806 31.072049706079863 chr21 48129895 612863047 12.733521380007167 49.94992728704201 chr22 51304566 533936397 10.407190599760654 42.82632205040333 chrMT 16571 25578844 1543.5908514875384 282.5561642095547 chrX 155270560 1194557859 7.693395702314721 44.27414453636063 chrY 59373566 415757013 7.002392495677285 135.05290920468474