BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083646.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,618,404 number of mapped reads = 1,240,782 (76.67%) number of supplementary alignments = 6,242 (0.39%) number of secondary alignments = 0 number of mapped bases = 75,158,599 bp number of sequenced bases = 75,135,216 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 28,781 duplication rate = 1.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3664 >>>>>>> ACTG content number of A's = 21,943,233 bp (29.2%) number of C's = 14,336,715 bp (19.08%) number of T's = 21,674,498 bp (28.85%) number of G's = 17,170,312 bp (22.85%) number of N's = 10,458 bp (0.01%) GC percentage = 41.93% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 632,841 number of insertions = 4,957 mapped reads with insertion percentage = 0.4% number of deletions = 14,875 mapped reads with deletion percentage = 1.19% homopolymer indels = 45.51% >>>>>>> Coverage mean coverageData = 0.0243X std coverageData = 0.2126X There is a 2.24% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% 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 6931682 0.02781008918730036 0.4130970068875037 chr2 243199373 7794685 0.03205059661070755 0.21240204392893075 chr3 198022430 6018309 0.030392057101814172 0.18675710670747828 chr4 191154276 3521298 0.01842123583989301 0.14460254488962962 chr5 180915260 3910872 0.021617148271516732 0.15647192876145583 chr6 171115067 5827509 0.034056083442377406 0.2240488388038562 chr7 159138663 4127290 0.025935180817750116 0.2254443017753468 chr8 146364022 5011916 0.034242814125454955 0.24595107705659272 chr9 141213431 3349560 0.023719840076685057 0.17801125771831133 chr10 135534747 3853928 0.02843498132622773 0.2210112998271956 chr11 135006516 2432412 0.0180169970462759 0.15797219295399603 chr12 133851895 2670163 0.01994863800770247 0.15031996606447665 chr13 115169878 2311685 0.020071958398705608 0.14955678752414187 chr14 107349540 1758854 0.01638436457203263 0.13597908304847162 chr15 102531392 1773435 0.017296507590572847 0.13942377062191838 chr16 90354753 2345407 0.025957760074890583 0.1752252480462305 chr17 81195210 1679711 0.020687316406965386 0.15428820874367186 chr18 78077248 1998417 0.02559538215281358 0.2342721737686751 chr19 59128983 1780351 0.0301096164633848 0.2946782552640007 chr20 63025520 1513700 0.024017255232483603 0.16542999333216116 chr21 48129895 1036771 0.02154110246864241 0.15776870076076246 chr22 51304566 628369 0.012247818254616948 0.1169492054119059 chrMT 16571 8087 0.4880212419286706 0.8533240783972316 chrX 155270560 2731079 0.017589161783148073 0.1468518377543843 chrY 59373566 143109 0.0024103150550196027 0.05795844187983701