BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472551.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 = 18,919,372 number of mapped reads = 18,665,651 (98.66%) number of supplementary alignments = 62,254 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,379,066 number of mapped paired reads (second in pair) = 9,286,585 number of mapped paired reads (both in pair) = 18,520,232 number of mapped paired reads (singletons) = 145,419 number of mapped bases = 1,837,093,031 bp number of sequenced bases = 1,836,879,439 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,885,756 duplication rate = 46.97% >>>>>>> Insert size mean insert size = 24,668.1015 std insert size = 1,573,879.8978 median insert size = 230 >>>>>>> Mapping quality mean mapping quality = 55.2005 >>>>>>> ACTG content number of A's = 505,644,358 bp (27.53%) number of C's = 415,091,560 bp (22.6%) number of T's = 503,279,084 bp (27.4%) number of G's = 412,577,283 bp (22.46%) number of N's = 287,154 bp (0.02%) GC percentage = 45.06% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 10,875,672 number of insertions = 99,516 mapped reads with insertion percentage = 0.53% number of deletions = 90,412 mapped reads with deletion percentage = 0.48% homopolymer indels = 46.61% >>>>>>> Coverage mean coverageData = 0.5934X std coverageData = 19.3345X There is a 5.63% of reference with a coverageData >= 1X There is a 2.49% of reference with a coverageData >= 2X There is a 1.06% of reference with a coverageData >= 3X There is a 0.74% of reference with a coverageData >= 4X There is a 0.52% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.41% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.36% 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 0.29% 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 0.27% 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 0.22% 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 0.18% 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 208438522 0.8362607931075124 24.460766186897065 chr2 243199373 143250931 0.5890267282884812 23.235661507594337 chr3 198022430 207102966 1.0458560982207925 25.47533386926167 chr4 191154276 63742141 0.33345914270837446 10.547665438176136 chr5 180915260 85943784 0.4750499432717837 14.989379911280162 chr6 171115067 122799257 0.7176414044240768 23.186460263601496 chr7 159138663 56119149 0.3526430846035196 9.359219975999427 chr8 146364022 90963573 0.6214886128231705 19.5839806770305 chr9 141213431 107875443 0.763917725361407 19.154007129703352 chr10 135534747 43519914 0.32109783626187016 12.7372959342498 chr11 135006516 65099164 0.4821927557926167 14.953657183689687 chr12 133851895 118550783 0.8856862504636188 27.989125063938047 chr13 115169878 46368984 0.40261381539363966 18.885917248926088 chr14 107349540 40651828 0.3786865598119936 12.796611546798962 chr15 102531392 53331099 0.5201441037687268 17.17867759257435 chr16 90354753 64584542 0.714788540233185 23.547264617660808 chr17 81195210 63878932 0.7867327641618268 20.60413743714668 chr18 78077248 31365700 0.40172650552437505 13.659900142055815 chr19 59128983 46915525 0.7934438006484907 22.049320957506897 chr20 63025520 40437321 0.6416023382274355 17.713564474294696 chr21 48129895 6157821 0.12794170857842097 3.905880955367261 chr22 51304566 26615090 0.518766497313319 16.18164707825388 chrMT 16571 3526 0.21278136503530265 0.7051019719160707 chrX 155270560 98723914 0.6358186252435748 20.025633926815598 chrY 59373566 4653122 0.0783702632919168 6.211791851587482