BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716249.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 = 3,240,636 number of mapped reads = 3,039,954 (93.81%) number of supplementary alignments = 76,914 (2.37%) number of secondary alignments = 0 number of mapped bases = 232,643,336 bp number of sequenced bases = 232,550,815 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 190,012 duplication rate = 4.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6346 >>>>>>> ACTG content number of A's = 55,720,250 bp (23.96%) number of C's = 48,025,004 bp (20.65%) number of T's = 69,034,334 bp (29.69%) number of G's = 59,762,017 bp (25.7%) number of N's = 9,210 bp (0%) GC percentage = 46.35% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 1,503,807 number of insertions = 18,621 mapped reads with insertion percentage = 0.6% number of deletions = 45,792 mapped reads with deletion percentage = 1.48% homopolymer indels = 38.66% >>>>>>> Coverage mean coverageData = 0.0752X std coverageData = 0.5436X There is a 5.73% of reference with a coverageData >= 1X There is a 1.15% of reference with a coverageData >= 2X There is a 0.32% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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% 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 25250532 0.10130579373762122 1.010984516098341 chr2 243199373 21806270 0.08966417031017593 0.600030015141547 chr3 198022430 14555098 0.07350226941463146 0.34248620326382484 chr4 191154276 10859137 0.05680823483122083 0.46378979170003526 chr5 180915260 13544317 0.07486553096737113 0.3563407958817831 chr6 171115067 14097657 0.08238699985431441 0.3958120598971663 chr7 159138663 14831450 0.09319828205418566 0.767065049217079 chr8 146364022 14544884 0.09937472202014236 0.5872439104521648 chr9 141213431 6937130 0.049125143060931645 0.37526081650508836 chr10 135534747 14011977 0.10338291331299715 0.8016581062894502 chr11 135006516 6812660 0.050461712529490055 0.4206724222485876 chr12 133851895 8080504 0.06036899216107475 0.3090278804204057 chr13 115169878 4282769 0.037186537611857154 0.23626699784926858 chr14 107349540 4423614 0.04120757294348909 0.28014979823453007 chr15 102531392 4816678 0.046977592969770665 0.27105391099534937 chr16 90354753 7143931 0.07906535918481233 0.3860152117526841 chr17 81195210 4373232 0.05386071419730302 0.3351516512507343 chr18 78077248 6932836 0.08879457431696364 0.5872444711881567 chr19 59128983 6119546 0.10349486308600979 0.7421356010820508 chr20 63025520 6251284 0.0991865517333296 0.4262026076925035 chr21 48129895 3913119 0.08130329392989534 0.4445635224272893 chr22 51304566 3754936 0.07318911926864365 0.361693653816709 chrMT 16571 61018 3.6822159193772253 3.376181209958717 chrX 155270560 14514430 0.09347831295256487 0.4174946062499483 chrY 59373566 724327 0.012199486215801827 0.40070019959195013