BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081133.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 = 1,924,848 number of mapped reads = 1,703,893 (88.52%) number of supplementary alignments = 11,062 (0.57%) number of secondary alignments = 0 number of mapped bases = 112,875,141 bp number of sequenced bases = 112,834,980 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,486 duplication rate = 2.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3057 >>>>>>> ACTG content number of A's = 31,215,868 bp (27.67%) number of C's = 20,958,147 bp (18.57%) number of T's = 35,136,642 bp (31.14%) number of G's = 25,491,153 bp (22.59%) number of N's = 33,170 bp (0.03%) GC percentage = 41.17% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 946,693 number of insertions = 8,971 mapped reads with insertion percentage = 0.52% number of deletions = 24,830 mapped reads with deletion percentage = 1.44% homopolymer indels = 47.19% >>>>>>> Coverage mean coverageData = 0.0365X std coverageData = 0.3249X There is a 3.22% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.04% 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% 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 9381610 0.03763926429695836 0.5096385441163347 chr2 243199373 9468978 0.03893504281361778 0.42369857638574154 chr3 198022430 7571863 0.038237400682336845 0.2146483367679676 chr4 191154276 7355255 0.038478108645605184 0.22542173156216574 chr5 180915260 6746211 0.03728934198253923 0.2132183008901351 chr6 171115067 6548179 0.03826769386707484 0.2794054952562618 chr7 159138663 6049555 0.03801436361194011 0.48523075208399924 chr8 146364022 5766428 0.03939785147472922 0.38044326194372363 chr9 141213431 4665962 0.03304191369728847 0.31212944895703565 chr10 135534747 5305682 0.039146286228726276 0.2716845419849989 chr11 135006516 5335314 0.039518936997085384 0.30170289451556176 chr12 133851895 5214713 0.03895882833784311 0.22096599111502038 chr13 115169878 3911350 0.033961571097609396 0.2026232138478152 chr14 107349540 3677562 0.03425782728086212 0.22599551890626735 chr15 102531392 3188462 0.03109742233871164 0.20116878124724297 chr16 90354753 2873669 0.031804292575510665 0.21892313718386575 chr17 81195210 2731037 0.03363544475098962 0.2259615729711451 chr18 78077248 3177046 0.040691060217696196 0.6017055059250028 chr19 59128983 2140012 0.03619226801178028 0.3743172721101426 chr20 63025520 2069275 0.03283233521913028 0.2078628209268639 chr21 48129895 1434994 0.02981502452893363 0.2049735322211285 chr22 51304566 1134979 0.02212237795754865 0.16269475665873703 chrMT 16571 2747 0.16577152857401484 0.4821117034333043 chrX 155270560 6852169 0.04413050999494045 0.2601690894427249 chrY 59373566 272089 0.004582662257476669 0.10380384262614072