BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084279.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 = 2,781,750 number of mapped reads = 2,526,440 (90.82%) number of supplementary alignments = 19,118 (0.69%) number of secondary alignments = 0 number of mapped bases = 166,972,894 bp number of sequenced bases = 166,915,474 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 84,138 duplication rate = 2.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7483 >>>>>>> ACTG content number of A's = 46,244,092 bp (27.71%) number of C's = 32,529,982 bp (19.49%) number of T's = 50,522,448 bp (30.27%) number of G's = 37,412,930 bp (22.41%) number of N's = 206,022 bp (0.12%) GC percentage = 41.9% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 1,724,264 number of insertions = 12,867 mapped reads with insertion percentage = 0.5% number of deletions = 35,674 mapped reads with deletion percentage = 1.4% homopolymer indels = 45.75% >>>>>>> Coverage mean coverageData = 0.0539X std coverageData = 0.3544X There is a 4.56% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% 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% 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 15755013 0.06320952355821814 0.5449555338575195 chr2 243199373 14706257 0.06046996264254349 0.4230258418161341 chr3 198022430 11113965 0.0561247783900036 0.27544827758381946 chr4 191154276 7441849 0.038931114467980824 0.2315550528468978 chr5 180915260 7890998 0.04361709454470562 0.23870528149338596 chr6 171115067 7646710 0.04468753181156163 0.26711997879065885 chr7 159138663 9672456 0.06078005066562611 0.52620473422076 chr8 146364022 9239458 0.06312656535224209 0.37821467944614046 chr9 141213431 5666754 0.040129001610335495 0.2719886821394097 chr10 135534747 12356266 0.09116677659050781 0.5146020508312267 chr11 135006516 9417373 0.06975495167951745 0.3555096215186678 chr12 133851895 8334042 0.06226316033852192 0.2847217210718701 chr13 115169878 3993450 0.034674431104285794 0.21217241971752976 chr14 107349540 4791349 0.04463315818586647 0.24929388266189162 chr15 102531392 3823835 0.03729428544186741 0.22900835600139527 chr16 90354753 3966868 0.04390325764046967 0.26823921071999873 chr17 81195210 5031461 0.06196746088839477 0.30641447575061714 chr18 78077248 4407653 0.05645246359092984 0.4299417767827728 chr19 59128983 3607693 0.06101395317419885 0.4270751150263772 chr20 63025520 3913742 0.06209773437807415 0.28771559593056456 chr21 48129895 1833502 0.03809486806484826 0.22919793627370458 chr22 51304566 1502256 0.02928113649767547 0.19386521105747878 chrMT 16571 39008 2.353991913583972 2.1813756148014853 chrX 155270560 10436136 0.06721258685484229 0.3233908599058552 chrY 59373566 384800 0.006480998631613267 0.11558264776716803