BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472417.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 = 19,744,316 number of mapped reads = 19,591,061 (99.22%) number of supplementary alignments = 72,554 (0.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,827,003 number of mapped paired reads (second in pair) = 9,764,058 number of mapped paired reads (both in pair) = 19,494,914 number of mapped paired reads (singletons) = 96,147 number of mapped bases = 1,920,827,799 bp number of sequenced bases = 1,920,538,417 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,245,317 duplication rate = 47.23% >>>>>>> Insert size mean insert size = 16,809.472 std insert size = 1,263,696.6392 median insert size = 213 >>>>>>> Mapping quality mean mapping quality = 54.8339 >>>>>>> ACTG content number of A's = 519,793,335 bp (27.06%) number of C's = 441,943,618 bp (23.01%) number of T's = 520,347,367 bp (27.09%) number of G's = 438,213,036 bp (22.82%) number of N's = 241,061 bp (0.01%) GC percentage = 45.83% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 10,246,882 number of insertions = 110,500 mapped reads with insertion percentage = 0.56% number of deletions = 100,476 mapped reads with deletion percentage = 0.51% homopolymer indels = 45.35% >>>>>>> Coverage mean coverageData = 0.6205X std coverageData = 18.2571X There is a 5.6% of reference with a coverageData >= 1X There is a 2.43% of reference with a coverageData >= 2X There is a 0.99% of reference with a coverageData >= 3X There is a 0.73% of reference with a coverageData >= 4X There is a 0.54% of reference with a coverageData >= 5X There is a 0.49% of reference with a coverageData >= 6X There is a 0.45% of reference with a coverageData >= 7X There is a 0.42% of reference with a coverageData >= 8X There is a 0.41% of reference with a coverageData >= 9X There is a 0.39% of reference with a coverageData >= 10X There is a 0.38% of reference with a coverageData >= 11X There is a 0.37% of reference with a coverageData >= 12X There is a 0.36% of reference with a coverageData >= 13X There is a 0.35% of reference with a coverageData >= 14X There is a 0.34% of reference with a coverageData >= 15X There is a 0.33% of reference with a coverageData >= 16X There is a 0.33% of reference with a coverageData >= 17X There is a 0.32% of reference with a coverageData >= 18X There is a 0.31% of reference with a coverageData >= 19X There is a 0.31% of reference with a coverageData >= 20X There is a 0.3% of reference with a coverageData >= 21X There is a 0.29% of reference with a coverageData >= 22X There is a 0.29% of reference with a coverageData >= 23X There is a 0.28% of reference with a coverageData >= 24X There is a 0.28% of reference with a coverageData >= 25X There is a 0.28% of reference with a coverageData >= 26X There is a 0.27% of reference with a coverageData >= 27X There is a 0.27% of reference with a coverageData >= 28X There is a 0.26% of reference with a coverageData >= 29X There is a 0.26% of reference with a coverageData >= 30X There is a 0.26% of reference with a coverageData >= 31X There is a 0.25% of reference with a coverageData >= 32X There is a 0.25% of reference with a coverageData >= 33X There is a 0.24% of reference with a coverageData >= 34X There is a 0.24% of reference with a coverageData >= 35X There is a 0.24% of reference with a coverageData >= 36X There is a 0.23% of reference with a coverageData >= 37X There is a 0.23% of reference with a coverageData >= 38X There is a 0.23% of reference with a coverageData >= 39X There is a 0.23% of reference with a coverageData >= 40X There is a 0.22% of reference with a coverageData >= 41X There is a 0.22% of reference with a coverageData >= 42X There is a 0.22% of reference with a coverageData >= 43X There is a 0.22% of reference with a coverageData >= 44X There is a 0.21% of reference with a coverageData >= 45X There is a 0.21% of reference with a coverageData >= 46X There is a 0.21% of reference with a coverageData >= 47X There is a 0.21% of reference with a coverageData >= 48X There is a 0.2% of reference with a coverageData >= 49X There is a 0.2% of reference with a coverageData >= 50X There is a 0.2% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 146608331 0.588196452276843 16.52535483948629 chr2 243199373 144760969 0.5952357821251455 16.38176995708231 chr3 198022430 135539568 0.6844657345130044 15.125604190609062 chr4 191154276 44304945 0.23177585104086293 6.983911404062463 chr5 180915260 100117373 0.5533937435681213 24.234212857044188 chr6 171115067 181146663 1.058624855051484 26.659484895080045 chr7 159138663 156257726 0.9818966871677186 27.133334168993255 chr8 146364022 92071763 0.6290600773460571 16.839409690359012 chr9 141213431 66149352 0.4684352722794477 11.33908481908519 chr10 135534747 48524475 0.3580223970167591 11.269440174930565 chr11 135006516 59758845 0.44263674651081286 13.032266909181393 chr12 133851895 99183841 0.7409969130433305 17.33445383012383 chr13 115169878 69843043 0.6064349829388549 21.148260458956177 chr14 107349540 32885508 0.3063404649894168 10.545822120713005 chr15 102531392 53696320 0.5237061445532701 15.76308929969955 chr16 90354753 94359412 1.0443215090190108 27.632160983098963 chr17 81195210 96689164 1.190823498085663 27.931544293895794 chr18 78077248 23498118 0.30095986477392234 9.53262575716016 chr19 59128983 53886836 0.9113438666787149 19.003567145894788 chr20 63025520 54914332 0.8713031165788081 18.63406225384342 chr21 48129895 15763282 0.32751540388775 14.983325032663567 chr22 51304566 11038229 0.21515100624767003 7.480045817512422 chrMT 16571 23920 1.443485607386398 1.7577249389789893 chrX 155270560 139025914 0.8953784542285415 21.699985717073293 chrY 59373566 779870 0.013134969861840536 2.055758348083735