BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081056.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 = 2,179,337 number of mapped reads = 1,998,976 (91.72%) number of supplementary alignments = 20,493 (0.94%) number of secondary alignments = 0 number of mapped bases = 134,105,249 bp number of sequenced bases = 134,056,655 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 82,231 duplication rate = 3.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6362 >>>>>>> ACTG content number of A's = 37,140,441 bp (27.71%) number of C's = 25,236,487 bp (18.83%) number of T's = 41,883,102 bp (31.24%) number of G's = 29,795,175 bp (22.23%) number of N's = 1,450 bp (0%) GC percentage = 41.05% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,189,218 number of insertions = 10,280 mapped reads with insertion percentage = 0.51% number of deletions = 29,636 mapped reads with deletion percentage = 1.47% homopolymer indels = 46.99% >>>>>>> Coverage mean coverageData = 0.0433X std coverageData = 0.3306X There is a 3.71% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% 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 11405847 0.045760555998775224 0.4516513664094217 chr2 243199373 8718743 0.035850186998631774 0.35828513226787545 chr3 198022430 11169294 0.05640418613184375 0.2675298983838317 chr4 191154276 8723874 0.04563787001029472 0.25909953217250953 chr5 180915260 7230649 0.03996704866134565 0.22718414466019196 chr6 171115067 11105456 0.06490051516036283 0.4217327661960334 chr7 159138663 6287248 0.03950798556099469 0.29632635598159796 chr8 146364022 9394087 0.06418303399724831 0.4104301950099519 chr9 141213431 6585892 0.04663785840597556 0.3815376887195904 chr10 135534747 6501682 0.04797059162990875 0.3417189269180832 chr11 135006516 6021934 0.04460476559516579 0.31209565547790546 chr12 133851895 6848906 0.05116779258149464 0.2646767638849178 chr13 115169878 3843504 0.03337247609136132 0.20525578339002856 chr14 107349540 3860945 0.03596610660837485 0.27088455951540885 chr15 102531392 3645509 0.03555505225170453 0.21499740032673853 chr16 90354753 3122786 0.034561391585011585 0.2613316023514946 chr17 81195210 2896529 0.03567364380238686 0.22164806523254565 chr18 78077248 3138636 0.04019911152606198 0.650187021953936 chr19 59128983 2644357 0.044721841402210485 0.38868492495579243 chr20 63025520 2134729 0.03387086691232377 0.22101948848728487 chr21 48129895 2510219 0.052155089887480535 0.296803056449985 chr22 51304566 1209238 0.02356979298879558 0.17057790979503587 chrMT 16571 241989 14.603162150745279 7.369345165225728 chrX 155270560 4504891 0.029013169012850858 0.21959871949472182 chrY 59373566 358305 0.006034756275208398 0.1439396887087653