BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094044.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 = 438,438 number of mapped reads = 418,101 (95.36%) number of supplementary alignments = 14,352 (3.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 210,034 number of mapped paired reads (second in pair) = 208,067 number of mapped paired reads (both in pair) = 415,118 number of mapped paired reads (singletons) = 2,983 number of mapped bases = 56,180,149 bp number of sequenced bases = 54,860,332 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 398,751 duplication rate = 49.46% >>>>>>> Insert size mean insert size = 374,641.921 std insert size = 5,568,858.3108 median insert size = 173 >>>>>>> Mapping quality mean mapping quality = 38.1237 >>>>>>> ACTG content number of A's = 15,287,512 bp (27.87%) number of C's = 12,121,373 bp (22.09%) number of T's = 14,660,670 bp (26.72%) number of G's = 12,790,363 bp (23.31%) number of N's = 414 bp (0%) GC percentage = 45.41% >>>>>>> Mismatches and indels general error rate = 0.0434 number of mismatches = 2,299,031 number of insertions = 41,497 mapped reads with insertion percentage = 9.59% number of deletions = 182,727 mapped reads with deletion percentage = 40.48% homopolymer indels = 29.99% >>>>>>> Coverage mean coverageData = 0.0181X std coverageData = 5.2103X 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% 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 762169 0.0030578419301109786 1.083965986304306 chr2 243199373 2713501 0.01115751642994573 3.804781662599895 chr3 198022430 1289880 0.006513807552003073 2.7213063031364033 chr4 191154276 1563836 0.008181015003818173 3.2422849673957197 chr5 180915260 301072 0.001664160336723392 0.6130062169638808 chr6 171115067 1013954 0.00592556820259434 2.7324682519750096 chr7 159138663 1730561 0.01087454781494551 3.700551882493308 chr8 146364022 1084606 0.0074103320281810785 3.646802329332924 chr9 141213431 772697 0.005471837873551844 1.9000784622009568 chr10 135534747 737264 0.005439667807104845 1.6489333165083895 chr11 135006516 1149645 0.00851547787515678 2.4154680611358366 chr12 133851895 1485580 0.011098684856124003 3.837602674684408 chr13 115169878 1079409 0.009372320425658522 2.641743144143259 chr14 107349540 311543 0.002902136329601412 1.3655472081586166 chr15 102531392 469527 0.004579348732532569 1.7539641803239412 chr16 90354753 444614 0.004920759398235531 1.9080379975920025 chr17 81195210 1317084 0.01622120319659251 4.485674665587067 chr18 78077248 84278 0.0010794181680173973 0.24946108953381824 chr19 59128983 417134 0.007054645265926526 2.740123727277978 chr20 63025520 329126 0.005222106854493228 1.1151532244195745 chr21 48129895 184005 0.003823091656443464 1.0648533181225839 chr22 51304566 95573 0.001862855637449501 0.42174088395817083 chrMT 16571 4755557 286.980689155754 1192.159482197121 chrX 155270560 31605669 0.20355223166580966 15.735006690875073 chrY 59373566 481865 0.008115817062428084 2.6163496700421147