BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094111.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 = 423,716 number of mapped reads = 404,799 (95.54%) number of supplementary alignments = 32,341 (7.63%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 203,485 number of mapped paired reads (second in pair) = 201,314 number of mapped paired reads (both in pair) = 401,396 number of mapped paired reads (singletons) = 3,403 number of mapped bases = 49,097,560 bp number of sequenced bases = 48,023,534 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 393,111 duplication rate = 54.4% >>>>>>> Insert size mean insert size = 1,820,800.9933 std insert size = 11,762,390.2777 median insert size = 141 >>>>>>> Mapping quality mean mapping quality = 40.0739 >>>>>>> ACTG content number of A's = 13,858,791 bp (28.86%) number of C's = 10,293,640 bp (21.43%) number of T's = 12,973,339 bp (27.01%) number of G's = 10,897,195 bp (22.69%) number of N's = 569 bp (0%) GC percentage = 44.13% >>>>>>> Mismatches and indels general error rate = 0.0376 number of mismatches = 1,756,417 number of insertions = 30,978 mapped reads with insertion percentage = 7.53% number of deletions = 137,002 mapped reads with deletion percentage = 32.83% homopolymer indels = 27.44% >>>>>>> Coverage mean coverageData = 0.0159X std coverageData = 3.4496X 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 0.01% 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 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% 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 1480401 0.0059394074689186034 2.347733441943324 chr2 243199373 2177550 0.008953764860240819 3.292398836275814 chr3 198022430 994198 0.005020633268665575 1.9332277699431617 chr4 191154276 1845964 0.009656932811693943 2.541445817600321 chr5 180915260 1031420 0.005701122171783629 2.396991000578224 chr6 171115067 1409837 0.008239116664110004 3.0372324162677558 chr7 159138663 1278720 0.008035256649102299 3.1441248499366314 chr8 146364022 1257818 0.008593764934937357 2.977003283512154 chr9 141213431 790962 0.005601181094452694 2.54259550081782 chr10 135534747 859467 0.00634130375437968 2.154566471455416 chr11 135006516 1680107 0.012444636375921293 3.425680848705649 chr12 133851895 1813154 0.013545971837006865 3.745218348480099 chr13 115169878 1123929 0.009758879834881825 2.4341389382512912 chr14 107349540 288106 0.0026838121523389854 1.0189607725110224 chr15 102531392 561929 0.005480555652653189 1.4064838318239699 chr16 90354753 198066 0.0021920927612961326 0.7109892559339175 chr17 81195210 516262 0.006358281479905034 1.7315450524506206 chr18 78077248 248691 0.0031851916706900326 1.03285864904821 chr19 59128983 88121 0.0014903182082465379 0.5395910295791294 chr20 63025520 316702 0.005024980357163257 1.784784234545924 chr21 48129895 79715 0.0016562471204227642 0.33763571717080126 chr22 51304566 110806 0.0021597687815934356 0.7566458549970964 chrMT 16571 285169 17.20891919618611 117.42508696393007 chrX 155270560 27727431 0.1785749404136882 10.746226379572986 chrY 59373566 933035 0.015714653217898347 3.099992282431066