BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068104.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 5,533,327 number of mapped reads = 5,271,730 (95.27%) number of supplementary alignments = 31,965 (0.58%) number of secondary alignments = 0 number of mapped bases = 341,832,553 bp number of sequenced bases = 341,677,419 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 914,231 duplication rate = 14.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6998 >>>>>>> ACTG content number of A's = 91,447,348 bp (26.76%) number of C's = 60,236,213 bp (17.63%) number of T's = 112,832,479 bp (33.02%) number of G's = 77,122,132 bp (22.57%) number of N's = 39,247 bp (0.01%) GC percentage = 40.2% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 1,885,536 number of insertions = 22,333 mapped reads with insertion percentage = 0.42% number of deletions = 88,444 mapped reads with deletion percentage = 1.66% homopolymer indels = 45.38% >>>>>>> Coverage mean coverageData = 0.1104X std coverageData = 1.0537X There is a 7.11% of reference with a coverageData >= 1X There is a 2.32% of reference with a coverageData >= 2X There is a 0.83% of reference with a coverageData >= 3X There is a 0.31% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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% 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 23474593 0.09418068009547707 2.11245881116004 chr2 243199373 39403776 0.16202252297747494 1.4550532813804842 chr3 198022430 21921761 0.11070342384951039 0.47631268489375367 chr4 191154276 22696137 0.11873203924561959 0.5576498079374277 chr5 180915260 18599996 0.1028105423500483 0.4675150700309682 chr6 171115067 12216686 0.07139456632419167 0.5435789873271855 chr7 159138663 19502907 0.12255291474957283 1.5602422540231258 chr8 146364022 17615292 0.12035260960511183 1.2506338767199596 chr9 141213431 11124906 0.07878079245875699 0.8917558379116688 chr10 135534747 18041007 0.13310982902413948 0.959400861834839 chr11 135006516 22845525 0.16921794352503697 0.8541042963933361 chr12 133851895 23238623 0.17361444901471138 0.648620397506727 chr13 115169878 9968842 0.08655771954538322 0.4605960089426082 chr14 107349540 8149537 0.07591590052458538 0.4957757746267545 chr15 102531392 10360270 0.10104485853464273 0.49211575185132983 chr16 90354753 6716054 0.07432983630645308 0.49740834969990394 chr17 81195210 10032362 0.12355854489445868 0.563852642064871 chr18 78077248 7828998 0.10027246349666423 1.6884048395789972 chr19 59128983 3624619 0.061300208731816005 1.4480635140933042 chr20 63025520 4918705 0.07804306890288251 0.47929381560955403 chr21 48129895 8972641 0.18642552617245478 0.6677187967631424 chr22 51304566 1939444 0.03780256127690467 0.26504834553827367 chrMT 16571 451705 27.258765312896024 16.113420085135715 chrX 155270560 17290953 0.11136015095198987 0.6010353509142923 chrY 59373566 897214 0.015111337594241854 0.5885535979854468