BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174000.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 = 3,223,726 number of mapped reads = 3,141,923 (97.46%) number of supplementary alignments = 299,111 (9.28%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,572,344 number of mapped paired reads (second in pair) = 1,569,579 number of mapped paired reads (both in pair) = 3,088,390 number of mapped paired reads (singletons) = 53,533 number of mapped bases = 371,969,164 bp number of sequenced bases = 371,758,949 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,405,628 duplication rate = 64.39% >>>>>>> Insert size mean insert size = 672,054.2724 std insert size = 7,493,371.0115 median insert size = 199 >>>>>>> Mapping quality mean mapping quality = 52.8388 >>>>>>> ACTG content number of A's = 112,174,793 bp (30.17%) number of C's = 72,677,133 bp (19.55%) number of T's = 111,915,316 bp (30.1%) number of G's = 74,987,414 bp (20.17%) number of N's = 4,293 bp (0%) GC percentage = 39.72% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 3,765,921 number of insertions = 39,218 mapped reads with insertion percentage = 1.21% number of deletions = 86,136 mapped reads with deletion percentage = 2.67% homopolymer indels = 43.66% >>>>>>> Coverage mean coverageData = 0.1202X std coverageData = 1.8889X There is a 2.58% of reference with a coverageData >= 1X There is a 2.02% of reference with a coverageData >= 2X There is a 1.54% of reference with a coverageData >= 3X There is a 1.26% of reference with a coverageData >= 4X There is a 0.95% of reference with a coverageData >= 5X There is a 0.77% of reference with a coverageData >= 6X There is a 0.56% of reference with a coverageData >= 7X There is a 0.46% of reference with a coverageData >= 8X There is a 0.33% of reference with a coverageData >= 9X There is a 0.28% of reference with a coverageData >= 10X There is a 0.2% of reference with a coverageData >= 11X There is a 0.17% of reference with a coverageData >= 12X There is a 0.13% of reference with a coverageData >= 13X There is a 0.11% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% 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 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% 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 28220472 0.11322127057007413 1.6748291514696036 chr2 243199373 28937402 0.11898633472217052 5.275526808302459 chr3 198022430 31568862 0.15942063734901143 1.1533164568213026 chr4 191154276 18959954 0.09918665905229344 1.0355587691543013 chr5 180915260 24471280 0.13526376934704126 1.0507054712339645 chr6 171115067 21444973 0.12532486692127467 1.1191418790848606 chr7 159138663 21174381 0.13305617001444833 1.2811205771626915 chr8 146364022 22496714 0.15370385216662055 1.3499531336863075 chr9 141213431 16016067 0.11341744823125217 1.1448011967324532 chr10 135534747 19942035 0.14713595916477418 2.0215901518965333 chr11 135006516 13425192 0.09944106697783386 0.9102180028333762 chr12 133851895 15614161 0.1166525210569488 0.979706117893469 chr13 115169878 8901728 0.07729215446420808 0.8006080585708378 chr14 107349540 11143756 0.103808139280336 0.920664503118546 chr15 102531392 10382904 0.10126561043860596 0.893615771308888 chr16 90354753 12186036 0.1348687876995248 1.2434812889710392 chr17 81195210 15196367 0.187158417349989 1.30477247045628 chr18 78077248 7489856 0.09592879093279517 1.5854886089937055 chr19 59128983 5810083 0.09826116914610218 1.1619132267309602 chr20 63025520 16349141 0.2594050949520131 1.5287416200986297 chr21 48129895 4778120 0.09927551265175209 0.9436823732442868 chr22 51304566 2782988 0.054244450679107194 0.6317327706096552 chrMT 16571 646957 39.04151831512884 34.46655738626509 chrX 155270560 13307271 0.08570376122814267 0.8318047509701848 chrY 59373566 722464 0.012168108615877981 0.5820116181904039