BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081734.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 = 2,676,105 number of mapped reads = 2,436,148 (91.03%) number of supplementary alignments = 15,417 (0.58%) number of secondary alignments = 0 number of mapped bases = 163,312,676 bp number of sequenced bases = 163,251,284 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 95,536 duplication rate = 2.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.157 >>>>>>> ACTG content number of A's = 44,514,531 bp (27.27%) number of C's = 31,816,223 bp (19.49%) number of T's = 49,349,494 bp (30.23%) number of G's = 37,569,196 bp (23.01%) number of N's = 1,840 bp (0%) GC percentage = 42.5% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,362,932 number of insertions = 12,504 mapped reads with insertion percentage = 0.51% number of deletions = 34,279 mapped reads with deletion percentage = 1.39% homopolymer indels = 45.7% >>>>>>> Coverage mean coverageData = 0.0528X std coverageData = 0.4436X There is a 4.46% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.1% 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 0.01% 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 13489186 0.05411896646789097 0.7536601631322702 chr2 243199373 14600933 0.0600368858681227 0.5962826963247035 chr3 198022430 11270688 0.05691621903639906 0.27820309861588943 chr4 191154276 10847990 0.056749920676637124 0.3227609335004561 chr5 180915260 9880775 0.05461548683068526 0.2684264018799227 chr6 171115067 7896427 0.046146883137999764 0.3033792343173352 chr7 159138663 9146085 0.05747242579259322 0.6072820690672317 chr8 146364022 7947884 0.054302169969065214 0.453616642948661 chr9 141213431 6568393 0.046513939598280846 0.4185890382032643 chr10 135534747 7630731 0.05630092038316934 0.5550420645797647 chr11 135006516 7731850 0.057270198721371346 0.40299457118878856 chr12 133851895 7642612 0.057097525589757246 0.274686733158457 chr13 115169878 5183404 0.04500659451944544 0.24126253064563025 chr14 107349540 4929530 0.045920364446834144 0.25932242380115417 chr15 102531392 4587046 0.044737966690240584 0.24913018513336366 chr16 90354753 4995406 0.055286587967320326 0.32260040192952044 chr17 81195210 4422782 0.05447097187137025 0.28863944081531173 chr18 78077248 4260684 0.05457010984813399 0.7286440531801378 chr19 59128983 3574315 0.060449458432254785 0.6068427178070585 chr20 63025520 3417516 0.05422432056094103 0.28033930452511485 chr21 48129895 2073664 0.043084739744393794 0.2831917546678127 chr22 51304566 1993679 0.038859679662819877 0.22499502089092688 chrMT 16571 2101 0.12678776175245912 0.3788681306740024 chrX 155270560 8730635 0.056228527803338896 0.31343865863704173 chrY 59373566 488360 0.008225209178104613 0.23554466829813053