BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236088.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 = 3,403,578 number of mapped reads = 2,930,416 (86.1%) number of supplementary alignments = 24,555 (0.72%) number of secondary alignments = 0 number of mapped bases = 193,674,626 bp number of sequenced bases = 193,573,303 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 285,426 duplication rate = 7.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1758 >>>>>>> ACTG content number of A's = 53,843,600 bp (27.82%) number of C's = 34,261,777 bp (17.7%) number of T's = 62,949,435 bp (32.52%) number of G's = 42,443,058 bp (21.93%) number of N's = 75,433 bp (0.04%) GC percentage = 39.63% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,598,806 number of insertions = 13,408 mapped reads with insertion percentage = 0.45% number of deletions = 58,431 mapped reads with deletion percentage = 1.97% homopolymer indels = 46.49% >>>>>>> Coverage mean coverageData = 0.0626X std coverageData = 0.7672X There is a 4.12% of reference with a coverageData >= 1X There is a 1.3% of reference with a coverageData >= 2X There is a 0.44% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 14356500 0.05759865288359703 1.5269090830515202 chr2 243199373 11107302 0.0456715897865411 0.49777875711032993 chr3 198022430 11935502 0.06027348518044143 0.3465643912718335 chr4 191154276 8095362 0.04234988706190386 0.2934612363431566 chr5 180915260 6262329 0.0346147085657672 0.2655856425636219 chr6 171115067 17402603 0.10170117281373008 0.626630837374109 chr7 159138663 22753915 0.1429816901251709 1.6562007025295222 chr8 146364022 8315721 0.05681533539711009 1.2993193107436196 chr9 141213431 7613603 0.05391557266248987 0.44001731767477503 chr10 135534747 12826291 0.0946347064786272 0.6295474028189331 chr11 135006516 8672326 0.06423635137729204 0.5325817730296237 chr12 133851895 12822103 0.09579321234114765 0.43646154583275804 chr13 115169878 10712358 0.0930135395298413 0.4314583740637983 chr14 107349540 4233796 0.03943934925105408 0.2862406501267362 chr15 102531392 11422757 0.11140741169299642 0.47412439716848936 chr16 90354753 5328281 0.05897067750270979 0.35585257906760176 chr17 81195210 4390917 0.05407852261235607 0.5290405424264195 chr18 78077248 3144230 0.040270758518537945 0.7614765553611292 chr19 59128983 1900182 0.032136219897440144 0.9305637816065964 chr20 63025520 1889630 0.029981981901934327 0.24791795518497647 chr21 48129895 1091728 0.022682949962803782 0.2297449826505487 chr22 51304566 1872083 0.036489598216267925 0.2584446795014921 chrMT 16571 512792 30.945145133063786 18.384026286671148 chrX 155270560 4568058 0.029419987923016443 0.279463542105609 chrY 59373566 444257 0.007482403869762513 0.18177266146595203