BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524596.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,174,310 number of mapped reads = 1,092,019 (92.99%) number of supplementary alignments = 2,294 (0.2%) number of secondary alignments = 0 number of mapped bases = 63,508,360 bp number of sequenced bases = 63,488,229 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 40,916 duplication rate = 2.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4326 >>>>>>> ACTG content number of A's = 16,284,161 bp (25.65%) number of C's = 11,625,026 bp (18.31%) number of T's = 20,605,519 bp (32.46%) number of G's = 14,973,149 bp (23.58%) number of N's = 374 bp (0%) GC percentage = 41.89% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 298,572 number of insertions = 4,745 mapped reads with insertion percentage = 0.43% number of deletions = 11,882 mapped reads with deletion percentage = 1.08% homopolymer indels = 41.45% >>>>>>> Coverage mean coverageData = 0.0205X std coverageData = 0.2018X There is a 1.85% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 6429384 0.025794856495061653 0.3281534913510171 chr2 243199373 5804597 0.023867647882463906 0.2328414542565296 chr3 198022430 4257432 0.02149974626611743 0.15974315468316092 chr4 191154276 2934694 0.015352489420639484 0.15333491484009132 chr5 180915260 4098322 0.02265326871818331 0.16336604569768584 chr6 171115067 4259365 0.02489181738741919 0.17993648222230912 chr7 159138663 3866097 0.02429388890869342 0.26400786247186664 chr8 146364022 4910893 0.03355259668936947 0.255285715023526 chr9 141213431 2418152 0.017124093529035492 0.17972091680450958 chr10 135534747 2791416 0.020595574653634763 0.20728328685329855 chr11 135006516 3281204 0.02430404173973351 0.20126614470878457 chr12 133851895 2112015 0.015778745605357324 0.14022768398361543 chr13 115169878 1416946 0.012303095432644288 0.12112143136348708 chr14 107349540 1215696 0.011324650296591863 0.12002339248416881 chr15 102531392 1629312 0.015890860040210904 0.14051223836022012 chr16 90354753 1748645 0.019353104755872666 0.15844345284568126 chr17 81195210 1442846 0.017770087668964707 0.14911361360385375 chr18 78077248 1712645 0.02193526339452948 0.2805100166521487 chr19 59128983 1266265 0.02141530152818627 0.23919614586029586 chr20 63025520 1208345 0.019172313056679262 0.1524140788312915 chr21 48129895 566555 0.011771374111661785 0.13033635711127148 chr22 51304566 979310 0.019088164589483127 0.14914522453185694 chrMT 16571 15816 0.9544384768571601 1.1779026211603347 chrX 155270560 2984469 0.019221087371617648 0.16348855228287867 chrY 59373566 157939 0.002660089508519667 0.08266367668058333