BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231733.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 5,457,932 number of mapped reads = 5,149,967 (94.36%) number of supplementary alignments = 50,219 (0.92%) number of secondary alignments = 0 number of mapped bases = 354,623,254 bp number of sequenced bases = 354,499,106 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 720,961 duplication rate = 5.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9359 >>>>>>> ACTG content number of A's = 92,190,736 bp (26.01%) number of C's = 63,927,506 bp (18.03%) number of T's = 99,430,106 bp (28.05%) number of G's = 98,872,881 bp (27.89%) number of N's = 77,877 bp (0.02%) GC percentage = 45.92% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 2,191,289 number of insertions = 24,075 mapped reads with insertion percentage = 0.46% number of deletions = 75,796 mapped reads with deletion percentage = 1.46% homopolymer indels = 47.65% >>>>>>> Coverage mean coverageData = 0.1146X std coverageData = 53.861X There is a 6.66% of reference with a coverageData >= 1X There is a 2.31% of reference with a coverageData >= 2X There is a 0.84% of reference with a coverageData >= 3X There is a 0.32% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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% 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 31653233 0.126993597339924 1.7325838731808996 chr2 243199373 43404328 0.1784722035447024 192.137155327144 chr3 198022430 35468693 0.17911452253161422 0.6220105968475076 chr4 191154276 18964405 0.09920994390938971 0.4919017236405965 chr5 180915260 19370559 0.1070697905748802 0.4786785358598697 chr6 171115067 23673044 0.13834576004928895 0.7323193763382098 chr7 159138663 27178178 0.17078299822086604 1.9615111098238263 chr8 146364022 10037129 0.06857647707986599 0.9106584459502272 chr9 141213431 11809072 0.08362569988119614 0.776816143128513 chr10 135534747 13300772 0.0981355135447296 0.7330969239104097 chr11 135006516 10610913 0.07859556200976255 0.8075920860459923 chr12 133851895 6366930 0.04756697691878027 0.34001062678857624 chr13 115169878 10143914 0.08807783924195874 0.42810354851390653 chr14 107349540 13468061 0.12545988552908563 0.6775610945975109 chr15 102531392 4555801 0.044433230751417085 0.30126502038493697 chr16 90354753 6101199 0.06752493695600054 0.4458845988051997 chr17 81195210 10819039 0.1332472568270961 0.6392591999290926 chr18 78077248 9894661 0.12672912088294916 1.6084505980323844 chr19 59128983 7935029 0.13419863825494852 1.0987642965776605 chr20 63025520 9416599 0.14940930277132183 0.5903846534445215 chr21 48129895 7517742 0.1561969333197174 0.640677846692247 chr22 51304566 4262254 0.08307747891289052 0.41862201839877994 chrMT 16571 16486 0.9948705569971638 1.7860404263520802 chrX 155270560 17826480 0.11480914347188546 0.5834817853855645 chrY 59373566 828733 0.01395794552747598 0.24518949698605164