BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094099.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 = 326,480 number of mapped reads = 304,371 (93.23%) number of supplementary alignments = 19,663 (6.02%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 152,997 number of mapped paired reads (second in pair) = 151,374 number of mapped paired reads (both in pair) = 301,396 number of mapped paired reads (singletons) = 2,975 number of mapped bases = 36,513,613 bp number of sequenced bases = 35,679,184 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 287,532 duplication rate = 50.43% >>>>>>> Insert size mean insert size = 1,565,821.9221 std insert size = 10,980,337.9857 median insert size = 138 >>>>>>> Mapping quality mean mapping quality = 39.7027 >>>>>>> ACTG content number of A's = 10,283,071 bp (28.82%) number of C's = 7,714,076 bp (21.62%) number of T's = 9,608,969 bp (26.93%) number of G's = 8,072,645 bp (22.63%) number of N's = 423 bp (0%) GC percentage = 44.25% >>>>>>> Mismatches and indels general error rate = 0.0396 number of mismatches = 1,373,130 number of insertions = 23,176 mapped reads with insertion percentage = 7.53% number of deletions = 111,057 mapped reads with deletion percentage = 35.43% homopolymer indels = 27.86% >>>>>>> Coverage mean coverageData = 0.0118X std coverageData = 2.769X 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 0.01% 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 969205 0.003888475768331185 1.7192405222256189 chr2 243199373 1609132 0.006616513768725876 2.151141494884817 chr3 198022430 725378 0.003663110285031852 1.246673363442575 chr4 191154276 849846 0.00444586444929958 1.245871726248996 chr5 180915260 797335 0.004407229108257645 2.009613906201295 chr6 171115067 699549 0.004088178862706461 1.479245164891424 chr7 159138663 1151085 0.007233220251448261 2.6881969244798967 chr8 146364022 864287 0.005905050901101911 2.250036922539256 chr9 141213431 725834 0.0051399785053023745 2.8956829657809218 chr10 135534747 510639 0.0037675873626709174 1.0353292406234798 chr11 135006516 1210393 0.008965441342105295 2.5492081647237828 chr12 133851895 1111241 0.008302019183217392 2.1689816355805025 chr13 115169878 732983 0.006364363779216646 1.754357960414767 chr14 107349540 82817 7.71470469272621E-4 0.22481248926797848 chr15 102531392 481542 0.0046965323556711295 1.4397643897024492 chr16 90354753 276911 0.0030647087265016373 1.0693483782866646 chr17 81195210 477539 0.00588136911032067 1.7507190654759148 chr18 78077248 342395 0.004385336429890562 2.215945422444271 chr19 59128983 63168 0.0010683085822734343 0.3057295563064165 chr20 63025520 226355 0.0035914816728207875 1.2158829944558758 chr21 48129895 212529 0.004415737869363729 1.5998719006485758 chr22 51304566 68588 0.001336879060627859 0.40474955761918757 chrMT 16571 53113 3.205177720113451 22.706041996614754 chrX 155270560 21413190 0.13790888626923223 9.261783321637585 chrY 59373566 858559 0.014460290291474154 3.094105222642451