BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514734.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 62,771,213 number of mapped reads = 62,255,685 (99.18%) number of supplementary alignments = 4,291,290 (6.84%) number of secondary alignments = 0 number of mapped bases = 5,927,210,464 bp number of sequenced bases = 5,922,078,684 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,855,984 duplication rate = 52.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6793 >>>>>>> ACTG content number of A's = 1,704,266,652 bp (28.78%) number of C's = 1,246,447,741 bp (21.05%) number of T's = 1,698,549,540 bp (28.68%) number of G's = 1,264,563,796 bp (21.35%) number of N's = 8,250,955 bp (0.14%) GC percentage = 42.4% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 44,896,908 number of insertions = 3,125,179 mapped reads with insertion percentage = 4.8% number of deletions = 2,230,663 mapped reads with deletion percentage = 3.36% homopolymer indels = 41.1% >>>>>>> Coverage mean coverageData = 1.9147X std coverageData = 166.8923X There is a 3.18% of reference with a coverageData >= 1X There is a 1.36% of reference with a coverageData >= 2X There is a 0.83% of reference with a coverageData >= 3X There is a 0.64% of reference with a coverageData >= 4X There is a 0.54% of reference with a coverageData >= 5X There is a 0.48% of reference with a coverageData >= 6X There is a 0.44% of reference with a coverageData >= 7X There is a 0.42% of reference with a coverageData >= 8X There is a 0.39% of reference with a coverageData >= 9X There is a 0.38% of reference with a coverageData >= 10X There is a 0.36% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.34% of reference with a coverageData >= 13X There is a 0.33% of reference with a coverageData >= 14X There is a 0.32% of reference with a coverageData >= 15X There is a 0.31% of reference with a coverageData >= 16X There is a 0.3% of reference with a coverageData >= 17X There is a 0.3% of reference with a coverageData >= 18X There is a 0.29% of reference with a coverageData >= 19X There is a 0.29% of reference with a coverageData >= 20X There is a 0.28% of reference with a coverageData >= 21X There is a 0.28% of reference with a coverageData >= 22X There is a 0.27% of reference with a coverageData >= 23X There is a 0.27% of reference with a coverageData >= 24X There is a 0.26% of reference with a coverageData >= 25X There is a 0.26% of reference with a coverageData >= 26X There is a 0.26% of reference with a coverageData >= 27X There is a 0.25% of reference with a coverageData >= 28X There is a 0.25% of reference with a coverageData >= 29X There is a 0.25% of reference with a coverageData >= 30X There is a 0.24% of reference with a coverageData >= 31X There is a 0.24% of reference with a coverageData >= 32X There is a 0.24% of reference with a coverageData >= 33X There is a 0.23% of reference with a coverageData >= 34X There is a 0.23% of reference with a coverageData >= 35X There is a 0.23% of reference with a coverageData >= 36X There is a 0.23% of reference with a coverageData >= 37X There is a 0.22% of reference with a coverageData >= 38X There is a 0.22% of reference with a coverageData >= 39X There is a 0.22% of reference with a coverageData >= 40X There is a 0.22% of reference with a coverageData >= 41X There is a 0.22% of reference with a coverageData >= 42X There is a 0.21% of reference with a coverageData >= 43X There is a 0.21% of reference with a coverageData >= 44X There is a 0.21% of reference with a coverageData >= 45X There is a 0.21% of reference with a coverageData >= 46X There is a 0.21% of reference with a coverageData >= 47X There is a 0.21% of reference with a coverageData >= 48X There is a 0.2% of reference with a coverageData >= 49X There is a 0.2% of reference with a coverageData >= 50X There is a 0.2% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 360727148 1.4472467372508573 73.8211172596144 chr2 243199373 414105560 1.7027410675108936 92.03041011550579 chr3 198022430 608653962 3.073661715998536 192.29338217080635 chr4 191154276 339585665 1.776500490106745 78.02302812826133 chr5 180915260 330109405 1.8246631323416278 131.92434527075946 chr6 171115067 321304243 1.8777086590510466 82.6303993568318 chr7 159138663 303920945 1.9097869698704204 172.45750782220352 chr8 146364022 359122517 2.4536256389565465 229.72844505058617 chr9 141213431 314495557 2.2270938024301667 432.62243556825956 chr10 135534747 320385325 2.3638611654323594 225.0075661024586 chr11 135006516 215253511 1.594393495792455 89.09916540475942 chr12 133851895 240241272 1.794829068352002 82.16785214577014 chr13 115169878 101673516 0.8828134384235433 42.35376197309613 chr14 107349540 367536848 3.423739384444498 319.2936248049113 chr15 102531392 181379736 1.7690166149309667 101.38211257100536 chr16 90354753 190014735 2.102985495406091 122.6931432636717 chr17 81195210 142793504 1.758644432350135 119.64041965982604 chr18 78077248 112035112 1.434926497409335 68.4139801087159 chr19 59128983 104643240 1.769745304092242 189.01881724133455 chr20 63025520 86923240 1.3791752928020269 71.8654284933097 chr21 48129895 121649844 2.5275318801339584 155.46593438986253 chr22 51304566 112492151 2.192634296916185 217.27422257892823 chrMT 16571 48659 2.9363949067648303 3.2291787945289605 chrX 155270560 224433790 1.4454368555120816 84.65840070878859 chrY 59373566 53680979 0.904122534934149 28.825657174606928