BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094123.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 = 522,048 number of mapped reads = 484,946 (92.89%) number of supplementary alignments = 1,941 (0.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 243,105 number of mapped paired reads (second in pair) = 241,841 number of mapped paired reads (both in pair) = 482,220 number of mapped paired reads (singletons) = 2,726 number of mapped bases = 71,782,985 bp number of sequenced bases = 71,706,790 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 482,569 duplication rate = 39.65% >>>>>>> Insert size mean insert size = 10,110.2417 std insert size = 989,995.4137 median insert size = 237 >>>>>>> Mapping quality mean mapping quality = 21.0994 >>>>>>> ACTG content number of A's = 19,935,259 bp (27.8%) number of C's = 15,280,120 bp (21.31%) number of T's = 20,602,532 bp (28.73%) number of G's = 15,887,892 bp (22.16%) number of N's = 987 bp (0%) GC percentage = 43.47% >>>>>>> Mismatches and indels general error rate = 0.0163 number of mismatches = 1,140,663 number of insertions = 20,635 mapped reads with insertion percentage = 4.2% number of deletions = 48,954 mapped reads with deletion percentage = 9.88% homopolymer indels = 65.24% >>>>>>> Coverage mean coverageData = 0.0232X std coverageData = 42.4103X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% 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 45097 1.8093034159381293E-4 0.21781063828149738 chr2 243199373 228894 9.411784133177021E-4 0.8295961846713654 chr3 198022430 11424 5.7690434361400375E-5 0.014039976464057032 chr4 191154276 11327 5.92558023656243E-5 0.017060631872069687 chr5 180915260 34028 1.880880584644988E-4 0.11448201137773183 chr6 171115067 37483 2.1905142929348238E-4 0.16079909496110995 chr7 159138663 20730 1.302637562061207E-4 0.03193920193661154 chr8 146364022 21686 1.4816482700919493E-4 0.0698907005908073 chr9 141213431 11022 7.8052065741537E-5 0.023352792401771755 chr10 135534747 12595 9.292819943803784E-5 0.023006250791585005 chr11 135006516 19174 1.4202277466370585E-4 0.027662972008905076 chr12 133851895 13336 9.96325080044627E-5 0.026902112686530633 chr13 115169878 15035 1.3054628745894824E-4 0.04603609518550647 chr14 107349540 10465 9.748528032816908E-5 0.0431082559430605 chr15 102531392 8143 7.941957912753199E-5 0.01916751395471503 chr16 90354753 6505 7.199399903179415E-5 0.017795193194835243 chr17 81195210 14293 1.7603255167392265E-4 0.04108364294790114 chr18 78077248 3395 4.3482577664622606E-5 0.012525223095532466 chr19 59128983 6350 1.0739234260125867E-4 0.09521944887044002 chr20 63025520 1769 2.8067995313644377E-5 0.006342008748836915 chr21 48129895 14527 3.018290399345355E-4 0.13722613614547158 chr22 51304566 1476 2.8769369182462238E-5 0.006812366750222234 chrMT 16571 70268990 4240.479753786736 17832.271410577916 chrX 155270560 963121 0.006202856484835245 2.381707426321129 chrY 59373566 2120 3.570612551720407E-5 0.010078490546407798