BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174040.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 = 21,385,664 number of mapped reads = 20,704,817 (96.82%) number of supplementary alignments = 2,310,761 (10.81%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,378,982 number of mapped paired reads (second in pair) = 10,325,835 number of mapped paired reads (both in pair) = 20,247,818 number of mapped paired reads (singletons) = 456,999 number of mapped bases = 2,435,120,606 bp number of sequenced bases = 2,433,641,218 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,727,408 duplication rate = 64.9% >>>>>>> Insert size mean insert size = 1,006,910.1971 std insert size = 8,936,946.5314 median insert size = 209 >>>>>>> Mapping quality mean mapping quality = 52.3737 >>>>>>> ACTG content number of A's = 727,289,965 bp (29.88%) number of C's = 480,872,540 bp (19.76%) number of T's = 726,116,357 bp (29.84%) number of G's = 499,332,598 bp (20.52%) number of N's = 29,758 bp (0%) GC percentage = 40.28% >>>>>>> Mismatches and indels general error rate = 0.0112 number of mismatches = 26,615,852 number of insertions = 258,922 mapped reads with insertion percentage = 1.21% number of deletions = 605,081 mapped reads with deletion percentage = 2.85% homopolymer indels = 42.64% >>>>>>> Coverage mean coverageData = 0.7866X std coverageData = 11.1608X There is a 13.71% of reference with a coverageData >= 1X There is a 11.16% of reference with a coverageData >= 2X There is a 9.05% of reference with a coverageData >= 3X There is a 7.67% of reference with a coverageData >= 4X There is a 6.18% of reference with a coverageData >= 5X There is a 5.17% of reference with a coverageData >= 6X There is a 4.09% of reference with a coverageData >= 7X There is a 3.41% of reference with a coverageData >= 8X There is a 2.68% of reference with a coverageData >= 9X There is a 2.26% of reference with a coverageData >= 10X There is a 1.78% of reference with a coverageData >= 11X There is a 1.53% of reference with a coverageData >= 12X There is a 1.21% of reference with a coverageData >= 13X There is a 1.05% of reference with a coverageData >= 14X There is a 0.84% of reference with a coverageData >= 15X There is a 0.74% of reference with a coverageData >= 16X There is a 0.59% of reference with a coverageData >= 17X There is a 0.52% of reference with a coverageData >= 18X There is a 0.42% of reference with a coverageData >= 19X There is a 0.37% of reference with a coverageData >= 20X There is a 0.3% of reference with a coverageData >= 21X There is a 0.27% of reference with a coverageData >= 22X There is a 0.22% of reference with a coverageData >= 23X There is a 0.2% of reference with a coverageData >= 24X There is a 0.17% of reference with a coverageData >= 25X There is a 0.15% of reference with a coverageData >= 26X There is a 0.12% of reference with a coverageData >= 27X There is a 0.11% of reference with a coverageData >= 28X There is a 0.1% of reference with a coverageData >= 29X There is a 0.09% of reference with a coverageData >= 30X There is a 0.07% of reference with a coverageData >= 31X There is a 0.07% of reference with a coverageData >= 32X There is a 0.06% of reference with a coverageData >= 33X There is a 0.05% of reference with a coverageData >= 34X There is a 0.05% of reference with a coverageData >= 35X There is a 0.04% of reference with a coverageData >= 36X There is a 0.04% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.03% of reference with a coverageData >= 39X There is a 0.03% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 237304751 0.9520728576238934 7.103662189493465 chr2 243199373 182577338 0.7507311213339354 34.777517156225095 chr3 198022430 143322123 0.7237671156747243 2.6476048735852835 chr4 191154276 144929519 0.7581808894507805 4.584102392101027 chr5 180915260 116844245 0.645850687222294 2.433263654096019 chr6 171115067 123381872 0.7210462185658963 3.1146600974787777 chr7 159138663 212817516 1.3373086840625272 12.638104096607908 chr8 146364022 216160246 1.4768673547383113 6.385612740934864 chr9 141213431 87896146 0.6224347456015001 5.253066002848685 chr10 135534747 115370499 0.8512245129287769 10.410988476524805 chr11 135006516 96360306 0.7137455943237584 3.081673511507116 chr12 133851895 97032920 0.7249275028941503 2.7447911262392735 chr13 115169878 58037649 0.5039308021147683 2.1682675598279335 chr14 107349540 83871491 0.7812934363761596 2.8388074291904006 chr15 102531392 62041809 0.6051006212809439 2.4307097717324875 chr16 90354753 61175297 0.677056767561525 5.155021598156444 chr17 81195210 65715563 0.8093527068899754 4.0356071379336536 chr18 78077248 41814749 0.5355561328186157 8.061010427539202 chr19 59128983 36098533 0.610504885565172 5.423174828158303 chr20 63025520 98274559 1.5592820019573024 4.122035042209864 chr21 48129895 29032893 0.6032195374621117 2.9656843347190875 chr22 51304566 29893530 0.5826680221795464 2.28390501703665 chrMT 16571 5323482 321.25291171323397 193.778554964645 chrX 155270560 85140599 0.548337038264047 2.445917871846099 chrY 59373566 4702971 0.07920984567442016 3.4103203587831334