BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124872.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 = 5,086,044 number of mapped reads = 4,994,593 (98.2%) number of supplementary alignments = 19,674 (0.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,498,780 number of mapped paired reads (second in pair) = 2,495,813 number of mapped paired reads (both in pair) = 4,978,760 number of mapped paired reads (singletons) = 15,833 number of mapped bases = 452,481,298 bp number of sequenced bases = 452,260,766 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 294,829 duplication rate = 3.91% >>>>>>> Insert size mean insert size = 48,185.2901 std insert size = 2,099,326.9651 median insert size = 186 >>>>>>> Mapping quality mean mapping quality = 53.4922 >>>>>>> ACTG content number of A's = 128,420,081 bp (28.4%) number of C's = 88,106,677 bp (19.48%) number of T's = 132,944,674 bp (29.4%) number of G's = 102,783,040 bp (22.73%) number of N's = 6,294 bp (0%) GC percentage = 42.21% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 3,140,586 number of insertions = 54,616 mapped reads with insertion percentage = 1.07% number of deletions = 134,833 mapped reads with deletion percentage = 2.65% homopolymer indels = 47.35% >>>>>>> Coverage mean coverageData = 0.1462X std coverageData = 1.2993X There is a 9.34% of reference with a coverageData >= 1X There is a 2.74% of reference with a coverageData >= 2X There is a 0.88% of reference with a coverageData >= 3X There is a 0.41% of reference with a coverageData >= 4X There is a 0.23% of reference with a coverageData >= 5X There is a 0.15% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% 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 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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 32915452 0.13205765292757285 1.4323744295587921 chr2 243199373 43111615 0.17726861080353196 1.6208615456944961 chr3 198022430 28301771 0.14292204676005643 0.5663125643698746 chr4 191154276 26070297 0.13638354080031148 0.8559655068257579 chr5 180915260 31983324 0.17678621471732126 0.6398873647252444 chr6 171115067 24206634 0.14146407107446593 1.0378441835283907 chr7 159138663 27229886 0.17110792240349537 1.944490893571501 chr8 146364022 28745401 0.19639663222700998 0.75918186179217 chr9 141213431 14121905 0.1000039790832644 1.5124842421702687 chr10 135534747 25916997 0.19122031489091132 3.189245031763707 chr11 135006516 22857862 0.16930932429957676 0.9882790328531608 chr12 133851895 19017117 0.14207581446642947 0.6175766258657096 chr13 115169878 14625792 0.12699320563663358 0.5050333131027613 chr14 107349540 10898335 0.10152195342429972 0.5492974070218153 chr15 102531392 13603359 0.13267506404282506 0.5522190667579545 chr16 90354753 10925172 0.12091419252731508 1.4059107910126798 chr17 81195210 14651599 0.1804490560465328 1.5653109944245 chr18 78077248 9430185 0.12078019194528987 1.7497561929812921 chr19 59128983 8301184 0.1403911174998562 1.0219770982229788 chr20 63025520 10038390 0.15927500479170978 0.7575922077339845 chr21 48129895 4230127 0.08788980320858793 0.5483771762677059 chr22 51304566 5259514 0.10251551489588666 0.5260427898903186 chrMT 16571 460861 27.811296843883895 15.348791019143725 chrX 155270560 24532062 0.15799557881416798 0.8605017492625946 chrY 59373566 1046457 0.01762496461809284 1.1047887344736258