BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094074.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 = 372,454 number of mapped reads = 359,368 (96.49%) number of supplementary alignments = 13,519 (3.63%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 180,555 number of mapped paired reads (second in pair) = 178,813 number of mapped paired reads (both in pair) = 356,918 number of mapped paired reads (singletons) = 2,450 number of mapped bases = 47,928,209 bp number of sequenced bases = 46,861,799 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 341,239 duplication rate = 49.88% >>>>>>> Insert size mean insert size = 438,983.8018 std insert size = 5,978,868.7882 median insert size = 168 >>>>>>> Mapping quality mean mapping quality = 38.7607 >>>>>>> ACTG content number of A's = 12,715,955 bp (27.14%) number of C's = 10,816,153 bp (23.08%) number of T's = 12,001,519 bp (25.61%) number of G's = 11,327,658 bp (24.17%) number of N's = 514 bp (0%) GC percentage = 47.25% >>>>>>> Mismatches and indels general error rate = 0.041 number of mismatches = 1,852,443 number of insertions = 30,196 mapped reads with insertion percentage = 8.25% number of deletions = 144,893 mapped reads with deletion percentage = 38.42% homopolymer indels = 27.74% >>>>>>> Coverage mean coverageData = 0.0155X std coverageData = 4.1481X There is a 0.01% 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% 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 440304 0.0017665111454225825 0.6866588155887043 chr2 243199373 1661188 0.006830560373196357 2.6326036906052206 chr3 198022430 1061669 0.005361357296746637 2.068440767634576 chr4 191154276 559871 0.0029288960295086467 1.1222260455191542 chr5 180915260 438065 0.0024213822537689743 0.8959722479562403 chr6 171115067 1007889 0.005890124216823058 3.1274666467170102 chr7 159138663 1685481 0.01059127284486486 3.7635819497152245 chr8 146364022 898454 0.006138489416476953 1.801936715710457 chr9 141213431 531006 0.0037603080403874616 1.4076879734073002 chr10 135534747 723503 0.005338136647718832 1.932965201821432 chr11 135006516 1805838 0.01337593216611856 3.467075857177615 chr12 133851895 1316609 0.009836311992445083 3.2685250951197284 chr13 115169878 1494954 0.012980425315723612 3.8868443124104823 chr14 107349540 251753 0.0023451707385052606 1.0257112251912583 chr15 102531392 648690 0.006326745276217453 2.4051286150052738 chr16 90354753 344081 0.003808111787987512 1.2394925417386877 chr17 81195210 942471 0.0116074704406824 3.6670124507079853 chr18 78077248 98164 0.0012572676741885165 0.4138880510902947 chr19 59128983 282020 0.004769572985890862 1.0274038111184778 chr20 63025520 211339 0.0033532289777220402 0.7803285785051587 chr21 48129895 550192 0.011431398302447989 4.145925792980717 chr22 51304566 104123 0.0020295074711283983 0.4881717601739806 chrMT 16571 1540852 92.98485305654457 432.37571478630036 chrX 155270560 28634524 0.18441695579638537 14.727855563258334 chrY 59373566 695169 0.011708392249843979 2.699204317581351