BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504633.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 350,223,842 number of mapped reads = 304,502,143 (86.95%) number of supplementary alignments = 3,343,341 (0.95%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 152,701,854 number of mapped paired reads (second in pair) = 151,800,289 number of mapped paired reads (both in pair) = 302,253,704 number of mapped paired reads (singletons) = 2,248,439 number of mapped bases = 30,046,663,301 bp number of sequenced bases = 30,039,362,734 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 95,519,427 duplication rate = 25.51% >>>>>>> Insert size mean insert size = 40,550.7097 std insert size = 1,925,289.1263 median insert size = 366 >>>>>>> Mapping quality mean mapping quality = 53.6336 >>>>>>> ACTG content number of A's = 7,553,589,296 bp (25.15%) number of C's = 7,363,742,690 bp (24.51%) number of T's = 7,590,137,043 bp (25.27%) number of G's = 7,520,816,132 bp (25.04%) number of N's = 11,077,573 bp (0.04%) GC percentage = 49.55% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 192,411,219 number of insertions = 2,391,107 mapped reads with insertion percentage = 0.76% number of deletions = 2,930,340 mapped reads with deletion percentage = 0.93% homopolymer indels = 38.8% >>>>>>> Coverage mean coverageData = 9.706X std coverageData = 38.2936X There is a 62.49% of reference with a coverageData >= 1X There is a 51.61% of reference with a coverageData >= 2X There is a 44.25% of reference with a coverageData >= 3X There is a 38.8% of reference with a coverageData >= 4X There is a 34.48% of reference with a coverageData >= 5X There is a 30.98% of reference with a coverageData >= 6X There is a 28.07% of reference with a coverageData >= 7X There is a 25.62% of reference with a coverageData >= 8X There is a 23.52% of reference with a coverageData >= 9X There is a 21.71% of reference with a coverageData >= 10X There is a 20.13% of reference with a coverageData >= 11X There is a 18.74% of reference with a coverageData >= 12X There is a 17.5% of reference with a coverageData >= 13X There is a 16.4% of reference with a coverageData >= 14X There is a 15.42% of reference with a coverageData >= 15X There is a 14.53% of reference with a coverageData >= 16X There is a 13.73% of reference with a coverageData >= 17X There is a 12.99% of reference with a coverageData >= 18X There is a 12.33% of reference with a coverageData >= 19X There is a 11.72% of reference with a coverageData >= 20X There is a 11.15% of reference with a coverageData >= 21X There is a 10.63% of reference with a coverageData >= 22X There is a 10.15% of reference with a coverageData >= 23X There is a 9.71% of reference with a coverageData >= 24X There is a 9.29% of reference with a coverageData >= 25X There is a 8.91% of reference with a coverageData >= 26X There is a 8.55% of reference with a coverageData >= 27X There is a 8.21% of reference with a coverageData >= 28X There is a 7.9% of reference with a coverageData >= 29X There is a 7.6% of reference with a coverageData >= 30X There is a 7.32% of reference with a coverageData >= 31X There is a 7.06% of reference with a coverageData >= 32X There is a 6.81% of reference with a coverageData >= 33X There is a 6.58% of reference with a coverageData >= 34X There is a 6.35% of reference with a coverageData >= 35X There is a 6.14% of reference with a coverageData >= 36X There is a 5.94% of reference with a coverageData >= 37X There is a 5.75% of reference with a coverageData >= 38X There is a 5.57% of reference with a coverageData >= 39X There is a 5.4% of reference with a coverageData >= 40X There is a 5.24% of reference with a coverageData >= 41X There is a 5.08% of reference with a coverageData >= 42X There is a 4.93% of reference with a coverageData >= 43X There is a 4.79% of reference with a coverageData >= 44X There is a 4.65% of reference with a coverageData >= 45X There is a 4.52% of reference with a coverageData >= 46X There is a 4.4% of reference with a coverageData >= 47X There is a 4.28% of reference with a coverageData >= 48X There is a 4.16% of reference with a coverageData >= 49X There is a 4.05% of reference with a coverageData >= 50X There is a 3.95% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2886903936 11.58233397540863 37.51238647079324 chr2 243199373 2437120018 10.021078541185219 29.374040689877074 chr3 198022430 1423821686 7.190204089506426 24.412323526997742 chr4 191154276 930073539 4.8655649167900386 15.114590189443796 chr5 180915260 2023300846 11.183693658567 31.677822525185228 chr6 171115067 864372104 5.0514085004565965 18.51499613046438 chr7 159138663 2067797618 12.99368474649055 33.34091834430963 chr8 146364022 1598957835 10.924527852889968 28.613288989237184 chr9 141213431 1041950074 7.378547965455212 71.3583474404614 chr10 135534747 1219216243 8.995599062135705 28.5944952448959 chr11 135006516 1404584563 10.403827938201145 35.68564777919992 chr12 133851895 1264968457 9.450508392129974 28.09521156874225 chr13 115169878 138710739 1.2044011976812201 5.623915773327889 chr14 107349540 927015198 8.63548365461091 23.34659088688664 chr15 102531392 1094796533 10.677671605199704 30.000273344961872 chr16 90354753 1945638137 21.533323620507268 53.72371042644618 chr17 81195210 1299677480 16.006824540511687 42.0198374944753 chr18 78077248 516051836 6.609503398480438 73.4366141718861 chr19 59128983 1632083594 27.602091414290012 113.44927260180395 chr20 63025520 1026543366 16.287741314946707 49.46560361040538 chr21 48129895 321782128 6.685701849131397 21.712186031074594 chr22 51304566 752327236 14.66394308841829 36.1233799999636 chrMT 16571 2939366 177.3801218997043 68.68936507561777 chrX 155270560 1181346582 7.60831017805307 18.344957592249184 chrY 59373566 44684187 0.7525939573850087 33.84401877044239