BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081225.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 = 3,081,114 number of mapped reads = 2,678,437 (86.93%) number of supplementary alignments = 33,766 (1.1%) number of secondary alignments = 0 number of mapped bases = 171,950,726 bp number of sequenced bases = 171,888,054 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 150,160 duplication rate = 4.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.023 >>>>>>> ACTG content number of A's = 49,615,084 bp (28.86%) number of C's = 33,369,262 bp (19.41%) number of T's = 52,340,295 bp (30.45%) number of G's = 36,551,878 bp (21.26%) number of N's = 11,535 bp (0.01%) GC percentage = 40.68% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,530,573 number of insertions = 12,590 mapped reads with insertion percentage = 0.47% number of deletions = 38,622 mapped reads with deletion percentage = 1.43% homopolymer indels = 47.68% >>>>>>> Coverage mean coverageData = 0.0555X std coverageData = 0.3872X There is a 4.23% of reference with a coverageData >= 1X There is a 0.92% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.02% 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 17172132 0.06889504199068776 0.5460884437581897 chr2 243199373 13270720 0.054567245944338844 0.44953371164008726 chr3 198022430 12386047 0.06254870723483193 0.315384254478383 chr4 191154276 7816296 0.04088998772907387 0.26396914673449334 chr5 180915260 9435405 0.05215372655684214 0.28914308623027607 chr6 171115067 13120462 0.07667625200999979 0.387156787373273 chr7 159138663 12785984 0.08034492535607139 0.6319584395723963 chr8 146364022 9870594 0.06743866330757159 0.48103041846916805 chr9 141213431 2648786 0.01875732344467999 0.24766058227176369 chr10 135534747 6029608 0.044487543847335324 0.3711159535604506 chr11 135006516 9525331 0.07055460197195222 0.4359859462858876 chr12 133851895 4839909 0.036158688676017625 0.24257752054458942 chr13 115169878 4575758 0.039730510090494324 0.2504732206537395 chr14 107349540 5043105 0.046978356870462604 0.27812739301354583 chr15 102531392 3657051 0.035667622653557655 0.33214912685941306 chr16 90354753 6437811 0.07125038568806669 0.342299005009705 chr17 81195210 2602281 0.03204968618222676 0.2545786834721189 chr18 78077248 4287196 0.0549096709966007 0.4218701475861474 chr19 59128983 4926178 0.08331240873870603 0.47790789865928296 chr20 63025520 5151636 0.0817388892626352 0.3667671673833695 chr21 48129895 3047823 0.06332494596134065 0.3258887851630497 chr22 51304566 1241369 0.024196072528905127 0.1915991408893957 chrMT 16571 61707 3.7237945808943334 3.0172856880620795 chrX 155270560 11603681 0.07473200972547532 0.36564467606247275 chrY 59373566 413856 0.0069703746613434 0.11938026700360137