BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514754.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 59,616,975 number of mapped reads = 56,439,751 (94.67%) number of supplementary alignments = 7,583,800 (12.72%) number of secondary alignments = 0 number of mapped bases = 5,408,545,702 bp number of sequenced bases = 5,405,682,598 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 42,274,438 duplication rate = 44.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8058 >>>>>>> ACTG content number of A's = 1,697,381,904 bp (31.4%) number of C's = 1,007,719,902 bp (18.64%) number of T's = 1,664,562,296 bp (30.79%) number of G's = 1,035,646,833 bp (19.16%) number of N's = 371,663 bp (0.01%) GC percentage = 37.8% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 25,309,925 number of insertions = 3,463,207 mapped reads with insertion percentage = 5.91% number of deletions = 1,086,684 mapped reads with deletion percentage = 1.83% homopolymer indels = 58.22% >>>>>>> Coverage mean coverageData = 1.7471X std coverageData = 39.665X There is a 5.55% of reference with a coverageData >= 1X There is a 3.74% of reference with a coverageData >= 2X There is a 3.07% of reference with a coverageData >= 3X There is a 2.7% of reference with a coverageData >= 4X There is a 2.44% of reference with a coverageData >= 5X There is a 2.25% of reference with a coverageData >= 6X There is a 2.1% of reference with a coverageData >= 7X There is a 1.98% of reference with a coverageData >= 8X There is a 1.87% of reference with a coverageData >= 9X There is a 1.78% of reference with a coverageData >= 10X There is a 1.7% of reference with a coverageData >= 11X There is a 1.63% of reference with a coverageData >= 12X There is a 1.56% of reference with a coverageData >= 13X There is a 1.51% of reference with a coverageData >= 14X There is a 1.45% of reference with a coverageData >= 15X There is a 1.4% of reference with a coverageData >= 16X There is a 1.36% of reference with a coverageData >= 17X There is a 1.32% of reference with a coverageData >= 18X There is a 1.28% of reference with a coverageData >= 19X There is a 1.24% of reference with a coverageData >= 20X There is a 1.21% of reference with a coverageData >= 21X There is a 1.18% of reference with a coverageData >= 22X There is a 1.15% of reference with a coverageData >= 23X There is a 1.12% of reference with a coverageData >= 24X There is a 1.09% of reference with a coverageData >= 25X There is a 1.07% of reference with a coverageData >= 26X There is a 1.04% of reference with a coverageData >= 27X There is a 1.02% of reference with a coverageData >= 28X There is a 1% of reference with a coverageData >= 29X There is a 0.98% of reference with a coverageData >= 30X There is a 0.96% of reference with a coverageData >= 31X There is a 0.94% of reference with a coverageData >= 32X There is a 0.92% of reference with a coverageData >= 33X There is a 0.9% of reference with a coverageData >= 34X There is a 0.88% of reference with a coverageData >= 35X There is a 0.87% of reference with a coverageData >= 36X There is a 0.85% of reference with a coverageData >= 37X There is a 0.84% of reference with a coverageData >= 38X There is a 0.82% of reference with a coverageData >= 39X There is a 0.81% of reference with a coverageData >= 40X There is a 0.79% of reference with a coverageData >= 41X There is a 0.78% of reference with a coverageData >= 42X There is a 0.77% of reference with a coverageData >= 43X There is a 0.75% of reference with a coverageData >= 44X There is a 0.74% of reference with a coverageData >= 45X There is a 0.73% of reference with a coverageData >= 46X There is a 0.72% of reference with a coverageData >= 47X There is a 0.71% of reference with a coverageData >= 48X There is a 0.7% of reference with a coverageData >= 49X There is a 0.69% of reference with a coverageData >= 50X There is a 0.68% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 415225341 1.6658949106489889 29.1250005540276 chr2 243199373 467702008 1.9231217672588325 38.74772018317933 chr3 198022430 501898157 2.534552055542395 35.89897851070754 chr4 191154276 396147978 2.072399248866397 42.42933903518855 chr5 180915260 349755754 1.933257338269862 27.758652655791202 chr6 171115067 421072881 2.4607586484479476 31.866420556803636 chr7 159138663 305895585 1.9221952681605727 52.74883042740792 chr8 146364022 214165126 1.4632361359952244 41.183332695636224 chr9 141213431 229118943 1.6225010707373861 36.572903968985045 chr10 135534747 222693162 1.643070628965722 26.008993792947468 chr11 135006516 198867052 1.47301817639676 23.750045776935547 chr12 133851895 150913976 1.1274698501653637 18.181886771853843 chr13 115169878 215400145 1.8702819586211596 42.89933200995482 chr14 107349540 143301803 1.3349084029610188 23.721356764451944 chr15 102531392 141159357 1.3767428125817311 29.801469542735838 chr16 90354753 162919753 1.8031121506137038 29.524848250029102 chr17 81195210 120362512 1.4823843918871569 33.83126690993759 chr18 78077248 215928810 2.7655791607818965 33.195516335671705 chr19 59128983 55834921 0.944290230731687 16.60450652072019 chr20 63025520 102294387 1.6230629592584083 28.205343617048563 chr21 48129895 41539516 0.8630709873769723 25.68794471236553 chr22 51304566 30764242 0.5996394550925546 21.530446585878042 chrMT 16571 113579616 6854.119606541549 6350.167619407015 chrX 155270560 173939214 1.120233056414558 24.587708756542362 chrY 59373566 18065463 0.30426777802094623 9.747626472382827