BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819084.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 = 820,411 number of mapped reads = 751,488 (91.6%) number of supplementary alignments = 3,319 (0.4%) number of secondary alignments = 0 number of mapped bases = 43,702,362 bp number of sequenced bases = 43,688,622 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,045 duplication rate = 1.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6752 >>>>>>> ACTG content number of A's = 11,177,917 bp (25.59%) number of C's = 8,574,239 bp (19.63%) number of T's = 13,615,733 bp (31.17%) number of G's = 10,320,001 bp (23.62%) number of N's = 732 bp (0%) GC percentage = 43.25% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 218,219 number of insertions = 2,975 mapped reads with insertion percentage = 0.39% number of deletions = 8,320 mapped reads with deletion percentage = 1.1% homopolymer indels = 43.41% >>>>>>> Coverage mean coverageData = 0.0141X std coverageData = 0.1543X There is a 1.33% of reference with a coverageData >= 1X There is a 0.06% 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 4477680 0.017964569083260176 0.251158377640084 chr2 243199373 3432177 0.01411260628537887 0.1630993224453513 chr3 198022430 2400141 0.012120551192104855 0.11581054821420744 chr4 191154276 2428152 0.01270257747203102 0.12426209691281997 chr5 180915260 2369581 0.013097739792652096 0.11977977052913859 chr6 171115067 1876891 0.010968589925514858 0.12655597004541777 chr7 159138663 2154434 0.01353809287690195 0.18214658603014539 chr8 146364022 4082675 0.027893979300459507 0.18692563636965553 chr9 141213431 1835203 0.012995952205141166 0.13995095791548828 chr10 135534747 2289074 0.016889204065139104 0.16511849221101516 chr11 135006516 1486435 0.011010098208889414 0.14128766128939266 chr12 133851895 2030996 0.015173457200587262 0.1287910379698574 chr13 115169878 948064 0.008231874657364836 0.09456741744196191 chr14 107349540 1051228 0.00979257107203254 0.10435933300202872 chr15 102531392 1124166 0.010964115263352711 0.11192935341960648 chr16 90354753 1363629 0.015091945412102448 0.13343620824243577 chr17 81195210 1580961 0.0194711116579414 0.14887573299162807 chr18 78077248 1009981 0.012935663408628336 0.22129857294197747 chr19 59128983 832668 0.01408223104395352 0.18774236595178254 chr20 63025520 1207889 0.01916507789225698 0.145468357561216 chr21 48129895 575653 0.011960404235247137 0.11851104856562968 chr22 51304566 352945 0.006879407185707408 0.08666110277907303 chrMT 16571 3186 0.1922635930239575 0.4331789098438178 chrX 155270560 2648983 0.017060433091759315 0.1441123144441085 chrY 59373566 139570 0.002350709404922723 0.07536290311331234