BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514737.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 50,558,673 number of mapped reads = 47,757,138 (94.46%) number of supplementary alignments = 1,915,629 (3.79%) number of secondary alignments = 0 number of mapped bases = 4,424,437,278 bp number of sequenced bases = 4,420,510,056 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,185,096 duplication rate = 39.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6246 >>>>>>> ACTG content number of A's = 1,142,726,839 bp (25.85%) number of C's = 1,041,489,635 bp (23.56%) number of T's = 1,155,514,845 bp (26.14%) number of G's = 1,046,475,068 bp (23.67%) number of N's = 34,303,669 bp (0.78%) GC percentage = 47.23% >>>>>>> Mismatches and indels general error rate = 0.0112 number of mismatches = 44,882,278 number of insertions = 2,356,250 mapped reads with insertion percentage = 4.61% number of deletions = 1,565,707 mapped reads with deletion percentage = 3.12% homopolymer indels = 37.38% >>>>>>> Coverage mean coverageData = 1.4292X std coverageData = 75.2075X There is a 5.7% of reference with a coverageData >= 1X There is a 3.46% of reference with a coverageData >= 2X There is a 2.68% of reference with a coverageData >= 3X There is a 2.32% of reference with a coverageData >= 4X There is a 2.08% of reference with a coverageData >= 5X There is a 1.91% of reference with a coverageData >= 6X There is a 1.78% of reference with a coverageData >= 7X There is a 1.67% of reference with a coverageData >= 8X There is a 1.57% of reference with a coverageData >= 9X There is a 1.49% of reference with a coverageData >= 10X There is a 1.41% of reference with a coverageData >= 11X There is a 1.35% of reference with a coverageData >= 12X There is a 1.29% of reference with a coverageData >= 13X There is a 1.24% of reference with a coverageData >= 14X There is a 1.19% of reference with a coverageData >= 15X There is a 1.14% of reference with a coverageData >= 16X There is a 1.1% of reference with a coverageData >= 17X There is a 1.06% of reference with a coverageData >= 18X There is a 1.03% of reference with a coverageData >= 19X There is a 0.99% of reference with a coverageData >= 20X There is a 0.96% of reference with a coverageData >= 21X There is a 0.93% of reference with a coverageData >= 22X There is a 0.9% of reference with a coverageData >= 23X There is a 0.88% of reference with a coverageData >= 24X There is a 0.85% of reference with a coverageData >= 25X There is a 0.83% of reference with a coverageData >= 26X There is a 0.81% of reference with a coverageData >= 27X There is a 0.78% of reference with a coverageData >= 28X There is a 0.76% of reference with a coverageData >= 29X There is a 0.74% of reference with a coverageData >= 30X There is a 0.73% of reference with a coverageData >= 31X There is a 0.71% of reference with a coverageData >= 32X There is a 0.69% of reference with a coverageData >= 33X There is a 0.68% of reference with a coverageData >= 34X There is a 0.66% of reference with a coverageData >= 35X There is a 0.64% of reference with a coverageData >= 36X There is a 0.63% of reference with a coverageData >= 37X There is a 0.62% of reference with a coverageData >= 38X There is a 0.6% of reference with a coverageData >= 39X There is a 0.59% of reference with a coverageData >= 40X There is a 0.58% of reference with a coverageData >= 41X There is a 0.57% of reference with a coverageData >= 42X There is a 0.56% of reference with a coverageData >= 43X There is a 0.54% of reference with a coverageData >= 44X There is a 0.53% of reference with a coverageData >= 45X There is a 0.52% of reference with a coverageData >= 46X There is a 0.51% of reference with a coverageData >= 47X There is a 0.5% of reference with a coverageData >= 48X There is a 0.49% of reference with a coverageData >= 49X There is a 0.49% of reference with a coverageData >= 50X There is a 0.48% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 214097485 0.8589647004329831 137.2372196691003 chr2 243199373 553716076 2.2767989455301763 75.74544692174506 chr3 198022430 521029017 2.6311616163886082 81.85278522913845 chr4 191154276 210334693 1.100339984024213 36.557123025302 chr5 180915260 210309249 1.1624737957428246 41.1518052838421 chr6 171115067 82432143 0.4817351531060675 14.769296318978958 chr7 159138663 121733675 0.7649534858791669 43.26251646797703 chr8 146364022 92009576 0.6286351983412973 18.01357359905832 chr9 141213431 207638714 1.4703892719666305 181.9338542822639 chr10 135534747 223130398 1.646296635651668 56.53631715522616 chr11 135006516 312671177 2.3159710083919207 32.58272914743378 chr12 133851895 184064708 1.3751371095642688 28.4989440837432 chr13 115169878 37240206 0.3233502253080445 41.293057201357705 chr14 107349540 101151168 0.9422599109413976 34.316118894250835 chr15 102531392 214230840 2.0894170636052616 52.402222398163765 chr16 90354753 290596447 3.216172225051625 131.19487631938412 chr17 81195210 225681411 2.779491684300096 44.99062571848741 chr18 78077248 57411939 0.7353222669938366 22.756961412713324 chr19 59128983 291503457 4.929958917101619 128.1620092332142 chr20 63025520 101895123 1.6167280016095067 25.36728680690704 chr21 48129895 12685746 0.26357310773273035 13.281450555365572 chr22 51304566 88375313 1.7225623349001724 67.67688996848094 chrMT 16571 7165169 432.3920704845815 355.8834093332381 chrX 155270560 46265160 0.2979647912650022 16.305566541063705 chrY 59373566 17068388 0.28747453033223574 45.067519311402386