BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004045.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 = 2,711,427 number of mapped reads = 2,465,052 (90.91%) number of supplementary alignments = 18,781 (0.69%) number of secondary alignments = 0 number of mapped bases = 162,761,276 bp number of sequenced bases = 162,682,447 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 108,086 duplication rate = 3.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8411 >>>>>>> ACTG content number of A's = 44,814,110 bp (27.55%) number of C's = 30,543,088 bp (18.77%) number of T's = 50,646,908 bp (31.13%) number of G's = 36,660,166 bp (22.53%) number of N's = 18,175 bp (0.01%) GC percentage = 41.31% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 1,202,820 number of insertions = 11,230 mapped reads with insertion percentage = 0.45% number of deletions = 44,967 mapped reads with deletion percentage = 1.8% homopolymer indels = 45.15% >>>>>>> Coverage mean coverageData = 0.0526X std coverageData = 0.4174X There is a 4.29% of reference with a coverageData >= 1X There is a 0.69% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 13677067 0.05487274994592691 0.7566712258468187 chr2 243199373 10456450 0.04299538222904876 0.46044423709198806 chr3 198022430 8714366 0.0440069642615738 0.24497544077181352 chr4 191154276 7718361 0.04037765286506068 0.26233874765346943 chr5 180915260 15212856 0.08408829636593397 0.3472896642649062 chr6 171115067 12110049 0.07077137748483597 0.37859779612634176 chr7 159138663 9544639 0.05997687061126057 0.5151636592335053 chr8 146364022 11024382 0.0753216661400573 0.5190914154379525 chr9 141213431 7271090 0.051490073915136304 0.38763980077057236 chr10 135534747 8141294 0.06006794700402547 0.4237601480662597 chr11 135006516 5465511 0.04048331267210836 0.3161316628634514 chr12 133851895 8845257 0.06608241893026617 0.3084777800790922 chr13 115169878 4468686 0.03880082255535601 0.23042656258088148 chr14 107349540 2977231 0.02773398935850121 0.2291543505939735 chr15 102531392 4886985 0.047663304912509134 0.26801012518694267 chr16 90354753 4256132 0.04710468302647012 0.28641378876098195 chr17 81195210 3309137 0.04075532288173157 0.253838663667479 chr18 78077248 4343201 0.055626973430211064 0.632588893685129 chr19 59128983 2435252 0.04118542001644101 0.5395612592661564 chr20 63025520 3099628 0.04918052242964437 0.26856912222037127 chr21 48129895 1314161 0.02730446430435803 0.22066272513563737 chr22 51304566 1653936 0.032237598501466715 0.20872853053191118 chrMT 16571 341472 20.60660189487659 12.464416968269747 chrX 155270560 11108833 0.0715450050544031 0.3523665703779223 chrY 59373566 385300 0.006489419887631476 0.1390777558795018