BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094063.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 = 890,272 number of mapped reads = 848,955 (95.36%) number of supplementary alignments = 26,903 (3.02%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 426,333 number of mapped paired reads (second in pair) = 422,622 number of mapped paired reads (both in pair) = 843,152 number of mapped paired reads (singletons) = 5,803 number of mapped bases = 112,490,946 bp number of sequenced bases = 109,941,326 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 828,903 duplication rate = 50.37% >>>>>>> Insert size mean insert size = 330,098.3795 std insert size = 5,217,357.4389 median insert size = 168 >>>>>>> Mapping quality mean mapping quality = 38.3286 >>>>>>> ACTG content number of A's = 29,019,034 bp (26.4%) number of C's = 25,990,134 bp (23.64%) number of T's = 27,594,454 bp (25.1%) number of G's = 27,336,435 bp (24.86%) number of N's = 1,269 bp (0%) GC percentage = 48.5% >>>>>>> Mismatches and indels general error rate = 0.041 number of mismatches = 4,378,320 number of insertions = 66,049 mapped reads with insertion percentage = 7.68% number of deletions = 351,952 mapped reads with deletion percentage = 39.58% homopolymer indels = 27.58% >>>>>>> Coverage mean coverageData = 0.0363X std coverageData = 10.3541X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% 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% 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 646327 0.0025930808011908626 1.060387278046595 chr2 243199373 4441514 0.018262851360229454 6.697154803539629 chr3 198022430 1699512 0.00858242169839043 2.9723730555903414 chr4 191154276 1676818 0.008772066391023342 3.716346352078802 chr5 180915260 1434806 0.00793081799733201 4.157715621679011 chr6 171115067 2532152 0.014797948797811008 8.381021989790968 chr7 159138663 4369596 0.027457790065761708 10.748983445592376 chr8 146364022 1818646 0.012425498938530125 4.458196621171803 chr9 141213431 1512194 0.010708570631641972 5.49888459272939 chr10 135534747 2227037 0.016431483802452518 6.695426941512315 chr11 135006516 2614747 0.019367561488661776 6.140365509798982 chr12 133851895 2794626 0.020878494099766012 6.206072462977968 chr13 115169878 2492850 0.021644982553511084 6.64891510564549 chr14 107349540 585296 0.005452245067840999 2.2191117995474503 chr15 102531392 2090201 0.020385961403898624 7.121491912838809 chr16 90354753 1186308 0.01312944765617366 4.790405728469151 chr17 81195210 1690686 0.020822484479072104 5.5778923966523095 chr18 78077248 346678 0.004440192359238891 1.8629217144762227 chr19 59128983 665458 0.01125434543665329 2.64614770051087 chr20 63025520 688390 0.010922400957580358 3.660060271064112 chr21 48129895 1522717 0.03163765472582061 11.982260658638417 chr22 51304566 192995 0.003761750952147222 1.0161493269731876 chrMT 16571 2181618 131.65276688190212 615.4425753705127 chrX 155270560 69994232 0.4507888166307895 38.26367189624137 chrY 59373566 1085542 0.018283254201036197 4.911231796092835