BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617403.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,271,929 (94.6%) number of supplementary alignments = 494,936 (1.55%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,251,542 number of mapped paired reads (second in pair) = 15,020,387 number of mapped paired reads (both in pair) = 29,752,770 number of mapped paired reads (singletons) = 519,159 number of mapped bases = 2,981,750,833 bp number of sequenced bases = 2,981,092,327 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,430,179 duplication rate = 4.25% >>>>>>> Insert size mean insert size = 55,819.5693 std insert size = 2,259,558.0953 median insert size = 209 >>>>>>> Mapping quality mean mapping quality = 53.9244 >>>>>>> ACTG content number of A's = 889,403,570 bp (29.83%) number of C's = 599,664,474 bp (20.12%) number of T's = 881,287,355 bp (29.56%) number of G's = 609,995,610 bp (20.46%) number of N's = 741,318 bp (0.02%) GC percentage = 40.58% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 25,422,073 number of insertions = 244,705 mapped reads with insertion percentage = 0.8% number of deletions = 292,508 mapped reads with deletion percentage = 0.95% homopolymer indels = 45.07% >>>>>>> Coverage mean coverageData = 0.9632X std coverageData = 2.9583X There is a 29.68% of reference with a coverageData >= 1X There is a 17.09% of reference with a coverageData >= 2X There is a 10.97% of reference with a coverageData >= 3X There is a 7.6% of reference with a coverageData >= 4X There is a 5.53% of reference with a coverageData >= 5X There is a 4.17% of reference with a coverageData >= 6X There is a 3.23% of reference with a coverageData >= 7X There is a 2.56% of reference with a coverageData >= 8X There is a 2.06% of reference with a coverageData >= 9X There is a 1.69% of reference with a coverageData >= 10X There is a 1.4% of reference with a coverageData >= 11X There is a 1.17% of reference with a coverageData >= 12X There is a 0.99% of reference with a coverageData >= 13X There is a 0.85% of reference with a coverageData >= 14X There is a 0.73% of reference with a coverageData >= 15X There is a 0.63% of reference with a coverageData >= 16X There is a 0.55% of reference with a coverageData >= 17X There is a 0.48% of reference with a coverageData >= 18X There is a 0.43% of reference with a coverageData >= 19X There is a 0.38% of reference with a coverageData >= 20X There is a 0.33% of reference with a coverageData >= 21X There is a 0.3% of reference with a coverageData >= 22X There is a 0.27% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.19% of reference with a coverageData >= 26X There is a 0.18% of reference with a coverageData >= 27X There is a 0.16% of reference with a coverageData >= 28X There is a 0.14% of reference with a coverageData >= 29X There is a 0.13% of reference with a coverageData >= 30X There is a 0.12% of reference with a coverageData >= 31X There is a 0.11% of reference with a coverageData >= 32X There is a 0.1% of reference with a coverageData >= 33X There is a 0.09% of reference with a coverageData >= 34X There is a 0.09% of reference with a coverageData >= 35X There is a 0.08% of reference with a coverageData >= 36X There is a 0.07% of reference with a coverageData >= 37X There is a 0.07% of reference with a coverageData >= 38X There is a 0.06% of reference with a coverageData >= 39X There is a 0.06% of reference with a coverageData >= 40X There is a 0.05% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.05% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 191948012 0.770100436379655 2.7656755654280234 chr2 243199373 297433739 1.22300372460253 3.1220105041365374 chr3 198022430 251807947 1.2716132561346711 3.4598715231226063 chr4 191154276 142759723 0.7468298695028931 2.293239181466395 chr5 180915260 190880606 1.055082948779445 2.8940741271526718 chr6 171115067 136308190 0.796587889013888 2.6164842005650772 chr7 159138663 222811450 1.400108847213326 3.2624172083459406 chr8 146364022 131874194 0.9010014359949742 3.2943554756417837 chr9 141213431 119125215 0.843582753824599 2.6435804213813934 chr10 135534747 95779850 0.7066811435446883 2.4338826171149317 chr11 135006516 221356584 1.6395992620089537 3.8731970334625028 chr12 133851895 142058960 1.0613145222934648 2.813814315760006 chr13 115169878 128831329 1.1186200006220377 2.784927079679323 chr14 107349540 86664520 0.8073115171243398 2.928107036891768 chr15 102531392 68353105 0.6666553888198455 2.391142773542194 chr16 90354753 75512433 0.8357328252560217 3.3650417037827514 chr17 81195210 92146992 1.1348821192777259 3.7841142116534665 chr18 78077248 42704770 0.5469553691236658 2.025756314601709 chr19 59128983 42920986 0.7258874383143035 2.3816602470537545 chr20 63025520 102044890 1.6191042929911565 4.800406255844108 chr21 48129895 40900359 0.8497911537101837 2.57743165633496 chr22 51304566 24203666 0.47176436498848856 2.109751354692171 chrMT 16571 181808 10.971456158348923 5.026030585097945 chrX 155270560 130719471 0.8418818802482583 2.5832399384973996 chrY 59373566 2422034 0.04079313679761125 0.6153261781215422