BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124966.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 3,871,382 number of mapped reads = 3,730,796 (96.37%) number of supplementary alignments = 13,739 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,896,152 number of mapped paired reads (second in pair) = 1,834,644 number of mapped paired reads (both in pair) = 3,647,660 number of mapped paired reads (singletons) = 83,136 number of mapped bases = 227,987,016 bp number of sequenced bases = 227,874,508 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 210,437 duplication rate = 3.28% >>>>>>> Insert size mean insert size = 87,675.1976 std insert size = 2,841,140.1316 median insert size = 171 >>>>>>> Mapping quality mean mapping quality = 51.5049 >>>>>>> ACTG content number of A's = 63,198,048 bp (27.73%) number of C's = 40,097,434 bp (17.6%) number of T's = 68,688,447 bp (30.14%) number of G's = 55,890,578 bp (24.53%) number of N's = 1 bp (0%) GC percentage = 42.12% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 1,636,053 number of insertions = 29,012 mapped reads with insertion percentage = 0.77% number of deletions = 68,876 mapped reads with deletion percentage = 1.82% homopolymer indels = 47.1% >>>>>>> Coverage mean coverageData = 0.0736X std coverageData = 0.8157X There is a 5.97% of reference with a coverageData >= 1X There is a 0.83% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% 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 18839269 0.07558363916774354 0.4705768984790498 chr2 243199373 19925015 0.0819287268474989 0.9242803707669088 chr3 198022430 16255522 0.08208929665189948 0.3558592054891302 chr4 191154276 13662063 0.07147139622448205 0.8614854091909323 chr5 180915260 12944766 0.07155154297100201 0.312877427305315 chr6 171115067 13040194 0.07620716415346405 0.37059211922241747 chr7 159138663 14234241 0.08944552336725363 0.521667080925359 chr8 146364022 13312509 0.09095479078868166 0.37681060194263377 chr9 141213431 9457550 0.0669734453233418 0.4871275133101172 chr10 135534747 12849018 0.094802390415795 2.7297084898593234 chr11 135006516 9046113 0.06700501033594557 0.34532030941053354 chr12 133851895 10688248 0.07985130132076203 0.32561095556659647 chr13 115169878 6049323 0.05252521844296822 0.25783067298424617 chr14 107349540 7220435 0.06726097755053259 0.32537339711080104 chr15 102531392 5899644 0.0575398800788738 0.27914706491668034 chr16 90354753 8086078 0.08949255829408333 1.3557515028524456 chr17 81195210 5065970 0.06239247364468914 0.4468316830528822 chr18 78077248 4541058 0.058161091948322766 0.6359253726788702 chr19 59128983 3684683 0.06231602190756435 0.42654208906179014 chr20 63025520 4696757 0.07452151128622184 0.4144574659820922 chr21 48129895 2630916 0.05466282442544285 0.48047904093693367 chr22 51304566 2153189 0.04196875966166442 0.2658341097329682 chrMT 16571 100364 6.056604912196005 4.243235218956383 chrX 155270560 9414174 0.060630772504459314 0.33111730816205565 chrY 59373566 4189917 0.07056872750408827 1.6175917023697548