BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438257.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP178894/SRP178894.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 = 727,335,368 number of mapped reads = 723,916,776 (99.53%) number of supplementary alignments = 29,899,648 (4.11%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 362,147,785 number of mapped paired reads (second in pair) = 361,768,991 number of mapped paired reads (both in pair) = 722,534,870 number of mapped paired reads (singletons) = 1,381,906 number of mapped bases = 88,125,850,214 bp number of sequenced bases = 88,101,953,758 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 342,327,008 duplication rate = 42.24% >>>>>>> Insert size mean insert size = 209,005.2373 std insert size = 4,445,886.2568 median insert size = 163 >>>>>>> Mapping quality mean mapping quality = 53.0456 >>>>>>> ACTG content number of A's = 26,739,393,393 bp (30.35%) number of C's = 17,512,043,602 bp (19.88%) number of T's = 26,107,296,540 bp (29.63%) number of G's = 17,743,019,390 bp (20.14%) number of N's = 200,833 bp (0%) GC percentage = 40.02% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 246,989,590 number of insertions = 13,763,454 mapped reads with insertion percentage = 1.86% number of deletions = 9,331,143 mapped reads with deletion percentage = 1.26% homopolymer indels = 49.07% >>>>>>> Coverage mean coverageData = 28.4672X std coverageData = 194.9445X There is a 77.71% of reference with a coverageData >= 1X There is a 71.92% of reference with a coverageData >= 2X There is a 65.15% of reference with a coverageData >= 3X There is a 60.42% of reference with a coverageData >= 4X There is a 56.14% of reference with a coverageData >= 5X There is a 52.71% of reference with a coverageData >= 6X There is a 49.74% of reference with a coverageData >= 7X There is a 47.23% of reference with a coverageData >= 8X There is a 45.03% of reference with a coverageData >= 9X There is a 43.1% of reference with a coverageData >= 10X There is a 41.39% of reference with a coverageData >= 11X There is a 39.84% of reference with a coverageData >= 12X There is a 38.44% of reference with a coverageData >= 13X There is a 37.15% of reference with a coverageData >= 14X There is a 35.96% of reference with a coverageData >= 15X There is a 34.86% of reference with a coverageData >= 16X There is a 33.83% of reference with a coverageData >= 17X There is a 32.86% of reference with a coverageData >= 18X There is a 31.95% of reference with a coverageData >= 19X There is a 31.09% of reference with a coverageData >= 20X There is a 30.27% of reference with a coverageData >= 21X There is a 29.49% of reference with a coverageData >= 22X There is a 28.75% of reference with a coverageData >= 23X There is a 28.04% of reference with a coverageData >= 24X There is a 27.36% of reference with a coverageData >= 25X There is a 26.71% of reference with a coverageData >= 26X There is a 26.08% of reference with a coverageData >= 27X There is a 25.48% of reference with a coverageData >= 28X There is a 24.9% of reference with a coverageData >= 29X There is a 24.34% of reference with a coverageData >= 30X There is a 23.8% of reference with a coverageData >= 31X There is a 23.28% of reference with a coverageData >= 32X There is a 22.77% of reference with a coverageData >= 33X There is a 22.28% of reference with a coverageData >= 34X There is a 21.81% of reference with a coverageData >= 35X There is a 21.36% of reference with a coverageData >= 36X There is a 20.91% of reference with a coverageData >= 37X There is a 20.48% of reference with a coverageData >= 38X There is a 20.07% of reference with a coverageData >= 39X There is a 19.66% of reference with a coverageData >= 40X There is a 19.27% of reference with a coverageData >= 41X There is a 18.89% of reference with a coverageData >= 42X There is a 18.51% of reference with a coverageData >= 43X There is a 18.15% of reference with a coverageData >= 44X There is a 17.8% of reference with a coverageData >= 45X There is a 17.46% of reference with a coverageData >= 46X There is a 17.13% of reference with a coverageData >= 47X There is a 16.81% of reference with a coverageData >= 48X There is a 16.49% of reference with a coverageData >= 49X There is a 16.18% of reference with a coverageData >= 50X There is a 15.89% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 6520979198 26.16233882121401 65.813672196112 chr2 243199373 7321108115 30.103318214558062 661.6067722596814 chr3 198022430 6737519015 34.02401947597552 66.65581765836932 chr4 191154276 6787915745 35.510143361898955 66.55053330346122 chr5 180915260 6791367041 37.5389397279146 67.10107460588767 chr6 171115067 6846399875 40.010502844848844 75.2302222078891 chr7 159138663 4160101644 26.14136354783878 61.25388816378102 chr8 146364022 5094258701 34.805402525765516 69.28818278663019 chr9 141213431 3743301867 26.50811498943043 57.92820932576722 chr10 135534747 3606681194 26.61074944862663 55.65626521488921 chr11 135006516 3818163531 28.28132777680153 57.37091134876472 chr12 133851895 4318554729 32.26368015932834 71.01560171148036 chr13 115169878 2619436607 22.744112023805393 53.770462885413245 chr14 107349540 2952902340 27.507359044109553 61.756871015481586 chr15 102531392 2792554284 27.236090620909547 59.7871286956393 chr16 90354753 1388063286 15.362371540100387 37.55412754243706 chr17 81195210 1700815498 20.94723935069569 52.44879748788946 chr18 78077248 2013360559 25.786776693256403 51.9882556948056 chr19 59128983 928228411 15.69836590965889 39.91996606046658 chr20 63025520 1135456432 18.01582013127381 41.95624007654521 chr21 48129895 751927203 15.622872291743 43.85697784729573 chr22 51304566 554617020 10.810285774564393 29.06542163272458 chrMT 16571 345736 20.863918894454166 16.009622625618906 chrX 155270560 5493238221 35.378491717940605 83.89577515812759 chrY 59373566 48553962 0.8177706894007343 7.295882481643131