BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094102.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 = 450,616 number of mapped reads = 436,673 (96.91%) number of supplementary alignments = 31,538 (7%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 219,401 number of mapped paired reads (second in pair) = 217,272 number of mapped paired reads (both in pair) = 433,124 number of mapped paired reads (singletons) = 3,549 number of mapped bases = 54,323,130 bp number of sequenced bases = 53,340,113 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 425,543 duplication rate = 53.29% >>>>>>> Insert size mean insert size = 1,693,681.0833 std insert size = 11,607,936.1746 median insert size = 147 >>>>>>> Mapping quality mean mapping quality = 39.8164 >>>>>>> ACTG content number of A's = 15,325,701 bp (28.73%) number of C's = 11,541,383 bp (21.64%) number of T's = 14,295,299 bp (26.8%) number of G's = 12,177,150 bp (22.83%) number of N's = 580 bp (0%) GC percentage = 44.47% >>>>>>> Mismatches and indels general error rate = 0.0338 number of mismatches = 1,728,908 number of insertions = 35,018 mapped reads with insertion percentage = 7.91% number of deletions = 132,369 mapped reads with deletion percentage = 29.32% homopolymer indels = 26.13% >>>>>>> Coverage mean coverageData = 0.0175X std coverageData = 4.2081X 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% 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 1695030 0.0068005046214107525 2.6850501015126627 chr2 243199373 2697869 0.011093239948443452 4.369199490317607 chr3 198022430 1326385 0.0066981553554312 2.50317084006746 chr4 191154276 2321471 0.01214448898856963 3.8963865941655444 chr5 180915260 945272 0.005224943434843473 2.3207118892769873 chr6 171115067 1356682 0.0079284777418227 2.6710093759807623 chr7 159138663 1414401 0.008887852727529828 2.9899141628508548 chr8 146364022 962814 0.0065782149659702575 1.8727350894506112 chr9 141213431 871429 0.006171006495833955 3.5193636475128067 chr10 135534747 998851 0.007369704242706116 2.5892129109909083 chr11 135006516 2457606 0.018203610261300275 4.936684118221156 chr12 133851895 1913716 0.014297264898640397 5.033111442779196 chr13 115169878 1119003 0.009716108234481241 2.6898667843229203 chr14 107349540 297856 0.002774636947675789 1.0372175610032077 chr15 102531392 476833 0.004650604958138089 1.2115188148792175 chr16 90354753 286253 0.0031681011844501418 1.096611934165384 chr17 81195210 361448 0.004451592649369341 1.1450918044989917 chr18 78077248 243469 0.0031183091904058912 1.1859021814852935 chr19 59128983 142930 0.0024172578784248666 0.8361550280278867 chr20 63025520 335686 0.005326191676006798 1.697439810133061 chr21 48129895 500526 0.01039948248380762 4.7326570241545305 chr22 51304566 47387 9.236409874318009E-4 0.25357876705462407 chrMT 16571 388777 23.461287791925653 144.30395084816035 chrX 155270560 30533079 0.196644354216279 13.241585848312642 chrY 59373566 628357 0.010583110335666886 2.7617213480853566