BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038418.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 14,203,802 number of mapped reads = 13,928,118 (98.06%) number of supplementary alignments = 186,349 (1.31%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,019,526 number of mapped paired reads (second in pair) = 6,908,592 number of mapped paired reads (both in pair) = 13,804,276 number of mapped paired reads (singletons) = 123,842 number of mapped bases = 2,015,525,049 bp number of sequenced bases = 2,014,231,252 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,043,935 duplication rate = 9.6% >>>>>>> Insert size mean insert size = 65,866.2171 std insert size = 2,454,012.6353 median insert size = 248 >>>>>>> Mapping quality mean mapping quality = 53.798 >>>>>>> ACTG content number of A's = 596,836,214 bp (29.63%) number of C's = 406,818,763 bp (20.2%) number of T's = 593,845,200 bp (29.48%) number of G's = 416,687,842 bp (20.69%) number of N's = 43,233 bp (0%) GC percentage = 40.88% >>>>>>> Mismatches and indels general error rate = 0.0134 number of mismatches = 26,234,226 number of insertions = 331,525 mapped reads with insertion percentage = 2.27% number of deletions = 682,917 mapped reads with deletion percentage = 4.73% homopolymer indels = 48.24% >>>>>>> Coverage mean coverageData = 0.6511X std coverageData = 9.8165X There is a 26.68% of reference with a coverageData >= 1X There is a 14.73% of reference with a coverageData >= 2X There is a 7.72% of reference with a coverageData >= 3X There is a 4.56% of reference with a coverageData >= 4X There is a 2.62% of reference with a coverageData >= 5X There is a 1.59% of reference with a coverageData >= 6X There is a 0.97% of reference with a coverageData >= 7X There is a 0.61% of reference with a coverageData >= 8X There is a 0.39% of reference with a coverageData >= 9X There is a 0.26% of reference with a coverageData >= 10X There is a 0.17% of reference with a coverageData >= 11X There is a 0.12% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 131383811 0.5271152804871045 14.817373180573183 chr2 243199373 225654320 0.9278573263426958 10.274217079210107 chr3 198022430 133602565 0.6746839991813048 1.4791242952685646 chr4 191154276 101472533 0.5308410312516367 6.031764452589607 chr5 180915260 117825342 0.6512736515427168 1.5280848870607 chr6 171115067 149923505 0.8761560722177668 17.50582581339598 chr7 159138663 145455853 0.9140195742375943 9.792070828656744 chr8 146364022 83523413 0.5706553554534051 2.5644928380938157 chr9 141213431 83025752 0.587945150911318 15.443230387041368 chr10 135534747 83289605 0.6145258455383401 18.23505268205097 chr11 135006516 102170257 0.7567801912612869 9.689253149183973 chr12 133851895 62774923 0.4689879287850202 1.2142853486896823 chr13 115169878 117803805 1.0228699295834975 1.9645523340921165 chr14 107349540 37947047 0.35349054127292956 1.1865295184128912 chr15 102531392 35490849 0.34614617345680826 0.9747569321823257 chr16 90354753 77539097 0.8581629015133272 13.39222058301085 chr17 81195210 46691638 0.575054094939837 9.271419832154805 chr18 78077248 33319043 0.4267445876166127 12.668903634712109 chr19 59128983 24971342 0.4223198291775118 8.734456420869561 chr20 63025520 63114238 1.0014076520114392 2.632261244481632 chr21 48129895 17185294 0.35706070000776025 2.882825086094703 chr22 51304566 12131327 0.23645706310038758 0.8220615549275878 chrMT 16571 4625961 279.1600386216885 211.09577306503013 chrX 155270560 101821389 0.6557675131718466 2.6945994867348433 chrY 59373566 22782140 0.3837084671653375 8.955590650681378