BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716832.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 = 1,084,902 number of mapped reads = 886,323 (81.7%) number of supplementary alignments = 938 (0.09%) number of secondary alignments = 0 number of mapped bases = 47,631,022 bp number of sequenced bases = 47,618,257 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,661 duplication rate = 5.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6792 >>>>>>> ACTG content number of A's = 9,754,370 bp (20.48%) number of C's = 8,613,067 bp (18.09%) number of T's = 15,695,411 bp (32.96%) number of G's = 13,554,610 bp (28.47%) number of N's = 799 bp (0%) GC percentage = 46.55% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 300,235 number of insertions = 2,394 mapped reads with insertion percentage = 0.27% number of deletions = 7,503 mapped reads with deletion percentage = 0.84% homopolymer indels = 44.01% >>>>>>> Coverage mean coverageData = 0.0154X std coverageData = 0.1547X There is a 1.36% of reference with a coverageData >= 1X There is a 0.14% 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 4678216 0.018769124751749366 0.1953734650925899 chr2 243199373 4210996 0.01731499529811699 0.19924671239682135 chr3 198022430 3266168 0.01649392950081463 0.14350603239178025 chr4 191154276 3115226 0.016296920294893116 0.14962066959639253 chr5 180915260 2852492 0.015767006055763345 0.13935318349676137 chr6 171115067 2053551 0.012000994628953394 0.13158509245389824 chr7 159138663 2688111 0.016891627397925293 0.16954827245897794 chr8 146364022 3004341 0.020526499333285608 0.16526290627241444 chr9 141213431 2109439 0.014937948784772462 0.14398396823886836 chr10 135534747 2505220 0.018483968542767855 0.18240600139948718 chr11 135006516 1956346 0.01449075243153449 0.14591685112707142 chr12 133851895 2274654 0.016993812452188294 0.1465379091883458 chr13 115169878 787173 0.006834886114926683 0.09245810306901456 chr14 107349540 1539158 0.014337816445231157 0.13392334363213676 chr15 102531392 905858 0.008834933207578026 0.10482194774993286 chr16 90354753 1268073 0.014034380681667073 0.14039789225423846 chr17 81195210 1874981 0.023092261230680974 0.17517602444261002 chr18 78077248 1279167 0.016383351523865185 0.17014322093463072 chr19 59128983 1234535 0.020878678058778723 0.1928588272554053 chr20 63025520 1252658 0.019875409199321164 0.16081405854628827 chr21 48129895 637868 0.0132530519752848 0.13486249897624564 chr22 51304566 529346 0.010317717140419822 0.11557832151021724 chrMT 16571 8842 0.5335827650715105 0.8693571529279054 chrX 155270560 1459122 0.00939728690358301 0.11284037349372598 chrY 59373566 139481 0.0023492104213514815 0.0776671739578774