BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926943.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 11,855,356 number of mapped reads = 11,723,466 (98.89%) number of supplementary alignments = 40,836 (0.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,881,119 number of mapped paired reads (second in pair) = 5,842,347 number of mapped paired reads (both in pair) = 11,648,958 number of mapped paired reads (singletons) = 74,508 number of mapped bases = 1,129,780,640 bp number of sequenced bases = 1,128,943,249 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 503,221 duplication rate = 3.49% >>>>>>> Insert size mean insert size = 41,005.7523 std insert size = 2,006,025.2281 median insert size = 199 >>>>>>> Mapping quality mean mapping quality = 53.4119 >>>>>>> ACTG content number of A's = 322,721,214 bp (28.59%) number of C's = 230,789,719 bp (20.44%) number of T's = 324,680,040 bp (28.76%) number of G's = 250,499,288 bp (22.19%) number of N's = 252,988 bp (0.02%) GC percentage = 42.63% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 10,058,054 number of insertions = 172,530 mapped reads with insertion percentage = 1.45% number of deletions = 596,855 mapped reads with deletion percentage = 4.96% homopolymer indels = 53.73% >>>>>>> Coverage mean coverageData = 0.365X std coverageData = 1.6081X There is a 17.07% of reference with a coverageData >= 1X There is a 8.25% of reference with a coverageData >= 2X There is a 4.26% of reference with a coverageData >= 3X There is a 2.42% of reference with a coverageData >= 4X There is a 1.43% of reference with a coverageData >= 5X There is a 0.88% of reference with a coverageData >= 6X There is a 0.56% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.24% of reference with a coverageData >= 9X There is a 0.16% of reference with a coverageData >= 10X There is a 0.11% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% 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% 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 103161419 0.41388630682689453 1.801740506188243 chr2 243199373 148453722 0.6104198385412778 3.0722917032256793 chr3 198022430 18402749 0.09293264909434755 0.5084883372386965 chr4 191154276 13460598 0.07041745694456765 0.5751331246701862 chr5 180915260 39289825 0.2171725314934738 0.7845781820214114 chr6 171115067 97558016 0.5701310685867306 1.5832252165476195 chr7 159138663 85078775 0.5346203957991026 1.4272381273000823 chr8 146364022 61749984 0.42189318902428086 1.219116711048413 chr9 141213431 77051159 0.5456361937696989 2.123072818063446 chr10 135534747 85125807 0.6280736776673217 2.4071579957994973 chr11 135006516 13056797 0.09671234683220771 0.5935139691934913 chr12 133851895 63501234 0.47441415752836374 1.2190344854234645 chr13 115169878 32514586 0.2823184895620016 0.8843115595511897 chr14 107349540 42330797 0.39432676656090004 1.1351225741312136 chr15 102531392 25507897 0.24878133908491168 0.8682891449214629 chr16 90354753 56315441 0.6232703773757203 2.9134617930316686 chr17 81195210 26034358 0.32063908696091803 1.1059732043336623 chr18 78077248 52805709 0.6763264632482948 2.195700013669748 chr19 59128983 11522000 0.19486213723648857 1.1359741681361264 chr20 63025520 9316395 0.14781940712270203 0.7479089763268616 chr21 48129895 19198953 0.39889870941958216 1.3218600766922064 chr22 51304566 15054752 0.29343883349485894 1.0287855401097326 chrMT 16571 8098 0.4886850521996259 1.1012446705053869 chrX 155270560 32134741 0.2069596515913899 0.7846105469952654 chrY 59373566 1146828 0.019315464393700053 0.6183062258034483