BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240216.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 = 1,797,095 number of mapped reads = 1,364,321 (75.92%) number of supplementary alignments = 10,246 (0.57%) number of secondary alignments = 0 number of mapped bases = 88,273,079 bp number of sequenced bases = 88,233,892 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 130,370 duplication rate = 7.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7048 >>>>>>> ACTG content number of A's = 24,436,816 bp (27.7%) number of C's = 15,962,401 bp (18.09%) number of T's = 28,469,609 bp (32.27%) number of G's = 19,357,310 bp (21.94%) number of N's = 7,756 bp (0.01%) GC percentage = 40.03% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 721,876 number of insertions = 6,395 mapped reads with insertion percentage = 0.47% number of deletions = 22,670 mapped reads with deletion percentage = 1.65% homopolymer indels = 47.91% >>>>>>> Coverage mean coverageData = 0.0285X std coverageData = 0.3243X There is a 1.82% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 6521598 0.026164821470996455 0.4420130480949812 chr2 243199373 7281359 0.029939875708478902 0.33709328413378997 chr3 198022430 6017266 0.030386790021716226 0.25532887311836344 chr4 191154276 6000232 0.03138947307671004 0.26658923384366395 chr5 180915260 6116421 0.03380820943462702 0.274339446248711 chr6 171115067 5442812 0.03180790619682836 0.2897573305889268 chr7 159138663 4666292 0.02932217672332713 0.3457259859156246 chr8 146364022 4496006 0.0307179724809694 0.6072518487681596 chr9 141213431 3547470 0.025121335661053373 0.28573385254211586 chr10 135534747 4459528 0.032903208208298056 0.3094914358258429 chr11 135006516 3827190 0.02834818728304936 0.29230648789044283 chr12 133851895 4106947 0.03068277068471836 0.2596468609625811 chr13 115169878 2802930 0.02433735320966477 0.23349197820628953 chr14 107349540 2701018 0.025160964825745875 0.23998568421694963 chr15 102531392 2342883 0.022850396881376585 0.22587975239563762 chr16 90354753 2343190 0.025933223457541853 0.24432715606729538 chr17 81195210 2517068 0.031000203090798092 0.26749144449852746 chr18 78077248 2351993 0.030123922912856763 0.4700418001230218 chr19 59128983 1593490 0.026949389608138533 0.3159212142418107 chr20 63025520 1833627 0.02909340533802815 0.2529849888613953 chr21 48129895 1176441 0.024443041066264534 0.23377183015314715 chr22 51304566 891910 0.01738461251187662 0.186891359828563 chrMT 16571 197738 11.932774123468711 9.92355308924172 chrX 155270560 4780962 0.030791168654251005 0.2721065164288419 chrY 59373566 256708 0.004323607579844539 0.10351125066452593