BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094016.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 19,042 number of mapped reads = 1,765 (9.27%) number of supplementary alignments = 24 (0.13%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 839 number of mapped paired reads (second in pair) = 926 number of mapped paired reads (both in pair) = 1,614 number of mapped paired reads (singletons) = 151 number of mapped bases = 217,652 bp number of sequenced bases = 216,128 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,057 duplication rate = 20.49% >>>>>>> Insert size mean insert size = 200,315.0467 std insert size = 5,628,158.7681 median insert size = 209 >>>>>>> Mapping quality mean mapping quality = 17.5528 >>>>>>> ACTG content number of A's = 56,193 bp (26%) number of C's = 47,322 bp (21.9%) number of T's = 55,116 bp (25.5%) number of G's = 57,497 bp (26.6%) number of N's = 0 bp (0%) GC percentage = 48.5% >>>>>>> Mismatches and indels general error rate = 0.0214 number of mismatches = 4,360 number of insertions = 81 mapped reads with insertion percentage = 4.36% number of deletions = 257 mapped reads with deletion percentage = 13.94% homopolymer indels = 28.7% >>>>>>> Coverage mean coverageData = 0.0001X std coverageData = 0.0815X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 1599 6.415229753830784E-6 0.004692757269863707 chr2 243199373 16254 6.683405388549255E-5 0.04439344306219478 chr3 198022430 4377 2.2103556652647884E-5 0.012657355584715087 chr4 191154276 2353 1.230942906032612E-5 0.00433183541054719 chr5 180915260 5324 2.94281422142057E-5 0.008235348164910228 chr6 171115067 1821 1.06419617624905E-5 0.004865595030818338 chr7 159138663 1810 1.1373728834205425E-5 0.004557184284877481 chr8 146364022 2680 1.831051076199587E-5 0.008087764663789517 chr9 141213431 1130 8.002071700955981E-6 0.004231065728981957 chr10 135534747 1925 1.4202999914110586E-5 0.004874927873050317 chr11 135006516 2789 2.0658262153805968E-5 0.007568731883044759 chr12 133851895 2837 2.1195067877074136E-5 0.007564357925235037 chr13 115169878 932 8.092393742051199E-6 0.0032493462562282914 chr14 107349540 825 7.68517499003722E-6 0.00350260971723543 chr15 102531392 2008 1.9584245964396932E-5 0.0057125760466104495 chr16 90354753 1648 1.823921758714785E-5 0.004905138486518213 chr17 81195210 2611 3.215706936406717E-5 0.011411227714154554 chr18 78077248 784 1.0041337522552024E-5 0.0038776655088369224 chr19 59128983 456 7.711954051365978E-6 0.0030664495056744855 chr20 63025520 580 9.202621414309632E-6 0.003991237567520128 chr21 48129895 0 0.0 0.0 chr22 51304566 362 7.055902197866755E-6 0.0033448524974423245 chrMT 16571 87849 5.301369863013699 33.466446684591105 chrX 155270560 72573 4.6739703907810987E-4 0.07625972244840713 chrY 59373566 2125 3.5790338077386156E-5 0.017975603525755345