BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472415.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 18,140,012 number of mapped reads = 17,981,689 (99.13%) number of supplementary alignments = 71,937 (0.4%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,016,804 number of mapped paired reads (second in pair) = 8,964,885 number of mapped paired reads (both in pair) = 17,887,816 number of mapped paired reads (singletons) = 93,873 number of mapped bases = 1,763,604,061 bp number of sequenced bases = 1,763,405,936 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,579,857 duplication rate = 47.35% >>>>>>> Insert size mean insert size = 17,909.3945 std insert size = 1,291,779.7422 median insert size = 216 >>>>>>> Mapping quality mean mapping quality = 55.1167 >>>>>>> ACTG content number of A's = 474,022,625 bp (26.88%) number of C's = 409,156,020 bp (23.2%) number of T's = 475,066,328 bp (26.94%) number of G's = 404,948,991 bp (22.96%) number of N's = 211,972 bp (0.01%) GC percentage = 46.17% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 9,431,877 number of insertions = 100,070 mapped reads with insertion percentage = 0.55% number of deletions = 86,359 mapped reads with deletion percentage = 0.48% homopolymer indels = 46.64% >>>>>>> Coverage mean coverageData = 0.5697X std coverageData = 19.9493X There is a 4.77% of reference with a coverageData >= 1X There is a 2.09% of reference with a coverageData >= 2X There is a 0.89% of reference with a coverageData >= 3X There is a 0.65% of reference with a coverageData >= 4X There is a 0.49% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.41% of reference with a coverageData >= 7X There is a 0.39% of reference with a coverageData >= 8X There is a 0.37% of reference with a coverageData >= 9X There is a 0.35% of reference with a coverageData >= 10X There is a 0.34% of reference with a coverageData >= 11X There is a 0.33% of reference with a coverageData >= 12X There is a 0.32% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.3% of reference with a coverageData >= 15X There is a 0.3% of reference with a coverageData >= 16X There is a 0.29% of reference with a coverageData >= 17X There is a 0.28% of reference with a coverageData >= 18X There is a 0.28% of reference with a coverageData >= 19X There is a 0.27% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.26% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.24% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.23% of reference with a coverageData >= 29X There is a 0.23% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.21% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.19% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 292650731 1.174122374603833 41.14162277984912 chr2 243199373 95578229 0.3930035995610893 14.760164278031073 chr3 198022430 167499113 0.8458592948283686 18.545503437039233 chr4 191154276 63658178 0.33301990063774456 22.343480887044215 chr5 180915260 82605718 0.4565989513543523 12.386716038324666 chr6 171115067 109428399 0.6395018329975583 15.676207859716495 chr7 159138663 122336393 0.7687408621750202 22.231740643938192 chr8 146364022 98557929 0.6733753804606435 20.566958469965964 chr9 141213431 74901618 0.5304142634987744 18.99735857306382 chr10 135534747 57416356 0.42362831134365864 14.924864029159572 chr11 135006516 73155429 0.5418659126052849 18.01757471197667 chr12 133851895 82440999 0.6159120795413467 16.052434115174197 chr13 115169878 23524480 0.20425896431009505 8.052039102680183 chr14 107349540 55579439 0.5177426843189081 19.728363585719404 chr15 102531392 31230184 0.30459143673773587 9.087695333172542 chr16 90354753 87715052 0.9707851450825171 28.388906378326322 chr17 81195210 82668418 1.0181440259837988 22.087250333333248 chr18 78077248 24438587 0.31300523040976036 9.189898788135286 chr19 59128983 34341797 0.5807946502310043 14.33994738114778 chr20 63025520 25299758 0.40142085301319214 11.743905727779076 chr21 48129895 6064220 0.12599695054393947 4.677615274746345 chr22 51304566 22138767 0.4315165047882873 13.015518079099124 chrMT 16571 6708 0.4048035725061855 0.8475770021968028 chrX 155270560 48087532 0.30970154290678154 10.024905296867281 chrY 59373566 2280027 0.03840138219085577 3.109232047447939