BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094048.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 = 384,602 number of mapped reads = 363,502 (94.51%) number of supplementary alignments = 13,375 (3.48%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 182,550 number of mapped paired reads (second in pair) = 180,952 number of mapped paired reads (both in pair) = 360,926 number of mapped paired reads (singletons) = 2,576 number of mapped bases = 48,091,576 bp number of sequenced bases = 46,821,529 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 342,699 duplication rate = 50.77% >>>>>>> Insert size mean insert size = 498,980.9462 std insert size = 6,213,542.7648 median insert size = 169 >>>>>>> Mapping quality mean mapping quality = 45.3447 >>>>>>> ACTG content number of A's = 12,898,256 bp (27.55%) number of C's = 10,411,009 bp (22.24%) number of T's = 12,509,037 bp (26.72%) number of G's = 11,002,606 bp (23.5%) number of N's = 621 bp (0%) GC percentage = 45.73% >>>>>>> Mismatches and indels general error rate = 0.0454 number of mismatches = 2,075,982 number of insertions = 31,371 mapped reads with insertion percentage = 8.49% number of deletions = 166,653 mapped reads with deletion percentage = 42.2% homopolymer indels = 29.58% >>>>>>> Coverage mean coverageData = 0.0155X std coverageData = 3.8135X 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 0.01% 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% 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 1040586 0.0041748582042650155 1.3943846442610113 chr2 243199373 1932801 0.007947393022267372 2.3556453338439822 chr3 198022430 1269260 0.0064096779339592996 2.3601922452790216 chr4 191154276 931228 0.004871604337012058 2.014246424045076 chr5 180915260 645721 0.00356919034911704 1.4459183526723802 chr6 171115067 1172451 0.006851827957382619 3.3401461348706785 chr7 159138663 1375067 0.008640684633626713 2.584470811493148 chr8 146364022 961505 0.006569271511273447 2.605306817010853 chr9 141213431 977828 0.006924468820533084 2.8265598132328225 chr10 135534747 1113536 0.008215871019407297 2.427276951193584 chr11 135006516 1318595 0.009766898954714156 2.434677831968841 chr12 133851895 1414051 0.010564295709074571 2.7493671725045594 chr13 115169878 1204647 0.010459740176159603 2.7482995648065907 chr14 107349540 254687 0.0023725020153789202 1.0141254564421425 chr15 102531392 514386 0.005016863518248148 1.7163897851716279 chr16 90354753 255211 0.002824544271622324 0.915091185536881 chr17 81195210 1090535 0.013431026288373416 3.3149853996307344 chr18 78077248 264473 0.003387324819645283 1.1083433520971848 chr19 59128983 363677 0.0061505708630233 1.3214832762376287 chr20 63025520 296851 0.004710012705964187 0.9831272630318827 chr21 48129895 73163 0.0015201155124065823 0.3205238201148269 chr22 51304566 219466 0.004277708927505595 0.8680656929160013 chrMT 16571 3202069 193.23329913704666 804.789434384115 chrX 155270560 25924203 0.1669614832328807 11.13301249023197 chrY 59373566 275579 0.004641442624483764 1.1054058902995434