BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094052.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 388,050 number of mapped reads = 362,430 (93.4%) number of supplementary alignments = 15,810 (4.07%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 181,990 number of mapped paired reads (second in pair) = 180,440 number of mapped paired reads (both in pair) = 359,946 number of mapped paired reads (singletons) = 2,484 number of mapped bases = 47,833,260 bp number of sequenced bases = 46,598,018 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 346,752 duplication rate = 49.57% >>>>>>> Insert size mean insert size = 418,883.7741 std insert size = 5,712,727.8062 median insert size = 167 >>>>>>> Mapping quality mean mapping quality = 44.3276 >>>>>>> ACTG content number of A's = 12,936,402 bp (27.76%) number of C's = 10,400,790 bp (22.32%) number of T's = 12,356,178 bp (26.52%) number of G's = 10,904,012 bp (23.4%) number of N's = 636 bp (0%) GC percentage = 45.72% >>>>>>> Mismatches and indels general error rate = 0.0448 number of mismatches = 2,039,837 number of insertions = 32,940 mapped reads with insertion percentage = 8.95% number of deletions = 161,538 mapped reads with deletion percentage = 41.53% homopolymer indels = 27.8% >>>>>>> Coverage mean coverageData = 0.0155X std coverageData = 4.4771X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% 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 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 0.01% of reference with a coverageData >= 15X There is a 0.01% 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 1026094 0.00411671592184318 1.9305795613951835 chr2 243199373 2174915 0.008942930128360158 3.209598417771679 chr3 198022430 1649847 0.008331616776947945 2.899660593630925 chr4 191154276 1352336 0.007074578860061702 2.303857793933841 chr5 180915260 261048 0.0014429296898448478 0.44506336887844083 chr6 171115067 1872338 0.010941982099098264 5.517824212962241 chr7 159138663 1081578 0.006796450212730516 1.9946542170677242 chr8 146364022 953061 0.00651157973781289 2.208330080976137 chr9 141213431 768100 0.005439284312835654 2.5047191307770684 chr10 135534747 844206 0.00622870532233332 2.5407017591493943 chr11 135006516 1099032 0.008140584858881923 2.4798512790415046 chr12 133851895 2228107 0.016646062425937264 4.949501285613425 chr13 115169878 1168454 0.010145482658234646 2.8733877787322464 chr14 107349540 340091 0.003168071330347573 1.3494803771178097 chr15 102531392 454064 0.004428536384251957 1.246926502349105 chr16 90354753 388008 0.004294273263078922 1.2943888450773866 chr17 81195210 996019 0.012266967472588592 2.9719626478807584 chr18 78077248 216612 0.0027743293411161213 0.9506851365800965 chr19 59128983 217702 0.0036818153966896405 0.9042757293605337 chr20 63025520 354579 0.005625959135283612 1.6072668916303774 chr21 48129895 93019 0.0019326657579452438 0.6524176209353916 chr22 51304566 125129 0.0024389447130300254 0.49884395198194653 chrMT 16571 3928783 237.08786434131918 998.3071887238722 chrX 155270560 23921339 0.15406229616226025 12.27409918185037 chrY 59373566 318799 0.005369375994697708 1.5632195664947113