BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230371.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 = 5,144,818 number of mapped reads = 4,882,623 (94.9%) number of supplementary alignments = 37,287 (0.72%) number of secondary alignments = 0 number of mapped bases = 349,371,138 bp number of sequenced bases = 349,194,759 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 222,387 duplication rate = 3.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0899 >>>>>>> ACTG content number of A's = 103,291,342 bp (29.58%) number of C's = 70,568,055 bp (20.21%) number of T's = 102,407,358 bp (29.33%) number of G's = 72,725,495 bp (20.83%) number of N's = 202,509 bp (0.06%) GC percentage = 41.04% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 3,123,817 number of insertions = 31,824 mapped reads with insertion percentage = 0.65% number of deletions = 101,501 mapped reads with deletion percentage = 2.05% homopolymer indels = 45.8% >>>>>>> Coverage mean coverageData = 0.1129X std coverageData = 0.9043X There is a 6.71% of reference with a coverageData >= 1X There is a 2.47% of reference with a coverageData >= 2X There is a 1.02% of reference with a coverageData >= 3X There is a 0.44% of reference with a coverageData >= 4X There is a 0.2% of reference with a coverageData >= 5X There is a 0.1% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% 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 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 15547779 0.06237809533882766 1.1603044316719937 chr2 243199373 14105985 0.05800173259492737 0.8497317085466276 chr3 198022430 24582249 0.12413870994311099 0.5370651531633872 chr4 191154276 34500248 0.18048378891613182 0.7997063081341265 chr5 180915260 14001733 0.07739387490032626 0.4336052573186635 chr6 171115067 28992285 0.16943151475959742 0.9037467811307783 chr7 159138663 16380602 0.10293288690002379 1.4854253376501092 chr8 146364022 22434945 0.15328182905495724 0.8934600934888178 chr9 141213431 21615947 0.15307288298943747 1.0386047095422006 chr10 135534747 13677630 0.10091604037155136 1.0342226113273343 chr11 135006516 22553474 0.16705470719650303 1.1755272199472426 chr12 133851895 20294479 0.15161891432317787 0.6231595797847491 chr13 115169878 12339215 0.10713925563071275 0.4958159360986108 chr14 107349540 8689067 0.08094181866079725 0.5472040721820454 chr15 102531392 9864890 0.09621336263531856 0.4692721896866894 chr16 90354753 8803242 0.09742976111063023 0.7187580374421163 chr17 81195210 13762105 0.1694940502032078 0.8147685012417715 chr18 78077248 7630279 0.0977273046304091 1.9806892330039558 chr19 59128983 6981422 0.11807106508156923 0.8620516252745508 chr20 63025520 6989185 0.11089452336133046 0.5594212136701652 chr21 48129895 5227442 0.10861112412566036 0.6869029140109332 chr22 51304566 3971347 0.07740728183920316 0.4258474160545222 chrMT 16571 3390 0.20457425623076458 0.5692889179922587 chrX 155270560 15427460 0.09935856481743867 0.5862459489190435 chrY 59373566 994738 0.016753886738081387 0.568865442016066