BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549145.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 12,015,465 number of mapped reads = 10,534,129 (87.67%) number of secondary alignments = 0 number of mapped bases = 418,109,510 bp number of sequenced bases = 418,069,670 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 517,644 duplication rate = 3.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.139 >>>>>>> ACTG content number of A's = 119,400,746 bp (28.56%) number of C's = 88,760,514 bp (21.23%) number of T's = 121,095,885 bp (28.97%) number of G's = 88,727,921 bp (21.22%) number of N's = 84,604 bp (0.02%) GC percentage = 42.45% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 1,280,909 number of insertions = 10,522 mapped reads with insertion percentage = 0.1% number of deletions = 31,780 mapped reads with deletion percentage = 0.3% homopolymer indels = 46.15% >>>>>>> Coverage mean coverageData = 0.1351X std coverageData = 0.7759X There is a 9.87% of reference with a coverageData >= 1X There is a 2.46% of reference with a coverageData >= 2X There is a 0.67% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% 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% 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 34735183 0.13935846121723403 1.484963981224814 chr2 243199373 35014626 0.14397498467234945 0.7410958233774674 chr3 198022430 28577612 0.14431502532314142 0.4895425029768719 chr4 191154276 26846528 0.14044429746368844 0.5121703652906339 chr5 180915260 25491527 0.14090313332330284 0.4947793118509294 chr6 171115067 24125715 0.14099117876043024 0.5663214815781195 chr7 159138663 23486792 0.14758696320076536 1.148118668287922 chr8 146364022 21419870 0.14634655229684793 0.6955047246159254 chr9 141213431 18095612 0.12814370327139774 0.7083527547221857 chr10 135534747 20347963 0.15013096973575343 0.7298111169075843 chr11 135006516 19490621 0.14436800220813045 0.6555966103595555 chr12 133851895 19614435 0.14653834374179014 0.5256764627422804 chr13 115169878 13180054 0.11444011428057604 0.4275685578687722 chr14 107349540 13275845 0.12366932359467958 0.5973568904521809 chr15 102531392 12760680 0.1244563226060561 0.4518289209938404 chr16 90354753 12567923 0.1390953168783495 0.5401557296635805 chr17 81195210 11929579 0.1469246646446262 0.5405377099827723 chr18 78077248 11174013 0.14311484185508178 1.3834461105831144 chr19 59128983 9001787 0.1522398415004026 1.2592047648508498 chr20 63025520 9211759 0.146159190753206 0.5271277354652302 chr21 48129895 5510022 0.11448231914904447 0.5284554450382719 chr22 51304566 5294615 0.10319968402032677 0.4534700627567921 chrMT 16571 59242 3.5750407338120813 4.848664045583001 chrX 155270560 13663782 0.08799982430668118 0.4936299376709511 chrY 59373566 3233725 0.05446405223496261 0.42439326135624544