BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173854.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 1,909,322 number of mapped reads = 1,858,987 (97.36%) number of supplementary alignments = 177,049 (9.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 931,894 number of mapped paired reads (second in pair) = 927,093 number of mapped paired reads (both in pair) = 1,828,702 number of mapped paired reads (singletons) = 30,285 number of mapped bases = 218,360,340 bp number of sequenced bases = 218,227,070 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,347,194 duplication rate = 60.9% >>>>>>> Insert size mean insert size = 907,353.0866 std insert size = 8,915,742.3468 median insert size = 186 >>>>>>> Mapping quality mean mapping quality = 53.1535 >>>>>>> ACTG content number of A's = 66,317,439 bp (30.39%) number of C's = 42,248,983 bp (19.36%) number of T's = 65,985,121 bp (30.24%) number of G's = 43,672,937 bp (20.01%) number of N's = 2,590 bp (0%) GC percentage = 39.37% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 2,217,053 number of insertions = 24,003 mapped reads with insertion percentage = 1.24% number of deletions = 55,169 mapped reads with deletion percentage = 2.89% homopolymer indels = 41.76% >>>>>>> Coverage mean coverageData = 0.0705X std coverageData = 1.1686X There is a 1.75% of reference with a coverageData >= 1X There is a 1.28% of reference with a coverageData >= 2X There is a 0.91% of reference with a coverageData >= 3X There is a 0.72% of reference with a coverageData >= 4X There is a 0.51% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.29% of reference with a coverageData >= 7X There is a 0.24% of reference with a coverageData >= 8X There is a 0.17% of reference with a coverageData >= 9X There is a 0.14% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 18309629 0.07345870965753783 0.873532905456257 chr2 243199373 19279040 0.07927257279565438 3.1400601356691533 chr3 198022430 15582516 0.07869066145688647 0.7705529914049579 chr4 191154276 15523967 0.08121171717864162 0.9101964477689499 chr5 180915260 13693353 0.07568931996117961 0.7556993721317241 chr6 171115067 12740466 0.07445554750593646 0.7756693343389108 chr7 159138663 12097756 0.07602021892065286 0.8466274819463169 chr8 146364022 11418400 0.07801370749431852 0.972431686978475 chr9 141213431 9134201 0.06468365604685293 0.772719880147863 chr10 135534747 10394856 0.07669513707802177 1.051446259362888 chr11 135006516 9832955 0.07283318828848231 0.7456322359130027 chr12 133851895 10298650 0.07694063651470903 0.7592727778276446 chr13 115169878 7347858 0.06380017177755454 0.7016149684947331 chr14 107349540 6774017 0.06310243155210539 0.6901531891328363 chr15 102531392 6589228 0.06426546905751558 0.6889784989700485 chr16 90354753 6310955 0.06984640863331229 0.7543085207821694 chr17 81195210 5655976 0.06965898604117164 0.7304697128912117 chr18 78077248 6132337 0.07854192043244147 1.0240772634422348 chr19 59128983 3493208 0.05907776225408781 0.7036976963445799 chr20 63025520 4506391 0.07150105227215896 0.7290193460117577 chr21 48129895 3002676 0.06238692189126945 0.7504908175796958 chr22 51304566 2542091 0.049549020646622366 0.6022245627819655 chrMT 16571 372984 22.50823728199867 20.02245200869201 chrX 155270560 5603120 0.036086171132505736 0.5186224792618134 chrY 59373566 1723710 0.029031606422292373 0.5743006093096178