BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094033.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 = 352,050 number of mapped reads = 319,644 (90.8%) number of supplementary alignments = 19,997 (5.68%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 160,834 number of mapped paired reads (second in pair) = 158,810 number of mapped paired reads (both in pair) = 314,560 number of mapped paired reads (singletons) = 5,084 number of mapped bases = 40,101,367 bp number of sequenced bases = 39,365,278 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 288,024 duplication rate = 44.5% >>>>>>> Insert size mean insert size = 677,628.467 std insert size = 7,602,530.4348 median insert size = 162 >>>>>>> Mapping quality mean mapping quality = 47.1051 >>>>>>> ACTG content number of A's = 11,147,962 bp (28.32%) number of C's = 8,602,529 bp (21.85%) number of T's = 10,560,035 bp (26.83%) number of G's = 9,054,189 bp (23%) number of N's = 563 bp (0%) GC percentage = 44.85% >>>>>>> Mismatches and indels general error rate = 0.0352 number of mismatches = 1,339,721 number of insertions = 23,487 mapped reads with insertion percentage = 7.2% number of deletions = 105,136 mapped reads with deletion percentage = 31.72% homopolymer indels = 30.8% >>>>>>> Coverage mean coverageData = 0.013X std coverageData = 3.2971X There is a 0.04% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.02% 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 604047 0.0024234523371558622 0.53044240712659 chr2 243199373 2049964 0.008429150020876082 2.3979096148140084 chr3 198022430 529459 0.0026737324655595834 0.6596841744588114 chr4 191154276 1296271 0.006781281732876328 1.8007612425852675 chr5 180915260 675442 0.0037334716817144114 1.0540936461663666 chr6 171115067 907876 0.005305646170830766 2.0304424311769234 chr7 159138663 871140 0.005474093998137963 1.2429413308233586 chr8 146364022 824384 0.00563242242687209 1.5332703526981988 chr9 141213431 1112587 0.007878761900488064 2.18639885618305 chr10 135534747 820567 0.0060542924833880424 1.3284205886550369 chr11 135006516 1456165 0.010785886808604112 2.0614909540580926 chr12 133851895 1451045 0.01084067580813854 2.4266525672497035 chr13 115169878 1566997 0.013605962142288628 3.2076919799261296 chr14 107349540 315143 0.0029356716386488473 0.4043761911128839 chr15 102531392 510927 0.004983127508890155 1.0141055910163503 chr16 90354753 220960 0.002445471794937008 0.3184638375000579 chr17 81195210 662712 0.008161959307698077 1.9662688012219656 chr18 78077248 406864 0.005211044323693376 1.3694926463692525 chr19 59128983 396941 0.006713137616454523 2.1234447718375975 chr20 63025520 496340 0.007875222608238695 2.779207622154799 chr21 48129895 228582 0.004749272775267845 1.041919292755939 chr22 51304566 347772 0.006778577953471042 0.5817350439991501 chrMT 16571 3979257 240.13378794279163 1000.7973997229038 chrX 155270560 17640947 0.11361424213321572 6.8286611795111805 chrY 59373566 728978 0.012277820739283202 2.29415890326474