BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819051.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 926,268 number of mapped reads = 824,180 (88.98%) number of supplementary alignments = 3,526 (0.38%) number of secondary alignments = 0 number of mapped bases = 46,733,963 bp number of sequenced bases = 46,721,849 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,506 duplication rate = 1.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8873 >>>>>>> ACTG content number of A's = 11,732,811 bp (25.11%) number of C's = 8,901,105 bp (19.05%) number of T's = 14,790,712 bp (31.66%) number of G's = 11,296,196 bp (24.18%) number of N's = 1,025 bp (0%) GC percentage = 43.23% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 228,621 number of insertions = 3,323 mapped reads with insertion percentage = 0.4% number of deletions = 7,159 mapped reads with deletion percentage = 0.86% homopolymer indels = 40.71% >>>>>>> Coverage mean coverageData = 0.0151X std coverageData = 0.1485X There is a 1.42% of reference with a coverageData >= 1X There is a 0.07% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% 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 5240157 0.021023646717413795 0.21129368170661908 chr2 243199373 3930022 0.01615967159586386 0.1665079000239142 chr3 198022430 3146916 0.015891714893105795 0.13246835771812943 chr4 191154276 2994973 0.015667831568674927 0.13692638869292828 chr5 180915260 2364636 0.013070406553875003 0.12073021945910015 chr6 171115067 2537779 0.014830833102499384 0.1332134834974013 chr7 159138663 2046135 0.01285756057910327 0.13283506705721462 chr8 146364022 2961522 0.020233947930181913 0.16323348720373518 chr9 141213431 1727227 0.012231322387457607 0.1450614983650772 chr10 135534747 2215761 0.01634828742477381 0.16058756011594022 chr11 135006516 1483805 0.010990617667668722 0.1317021154672963 chr12 133851895 2122817 0.015859446741489914 0.13293765309558694 chr13 115169878 1436876 0.012476144152900813 0.11637337560819903 chr14 107349540 1274511 0.011872533408154334 0.12012502421862935 chr15 102531392 1348729 0.013154303025555335 0.1212779840320993 chr16 90354753 1398584 0.015478809399213343 0.13739490629044432 chr17 81195210 1039293 0.012799929946606456 0.12051550975673715 chr18 78077248 1152112 0.014756052877273542 0.22640755862048936 chr19 59128983 909370 0.015379429069497103 0.16412711743185265 chr20 63025520 1492154 0.023675393713530647 0.1643595752489056 chr21 48129895 606141 0.012593856687200335 0.125438771726705 chr22 51304566 564049 0.01099412867073079 0.11027310081413251 chrMT 16571 1805 0.10892523082493513 0.34882925813108606 chrX 155270560 2603215 0.01676567019530296 0.14504848202082518 chrY 59373566 135374 0.002280038224417917 0.06541743387890686