BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472455.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 = 12,547,244 number of mapped reads = 12,436,500 (99.12%) number of supplementary alignments = 38,437 (0.31%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,238,602 number of mapped paired reads (second in pair) = 6,197,898 number of mapped paired reads (both in pair) = 12,378,564 number of mapped paired reads (singletons) = 57,936 number of mapped bases = 1,214,437,910 bp number of sequenced bases = 1,214,295,413 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,555,100 duplication rate = 44.29% >>>>>>> Insert size mean insert size = 17,388.4549 std insert size = 1,287,274.1448 median insert size = 203 >>>>>>> Mapping quality mean mapping quality = 55.1298 >>>>>>> ACTG content number of A's = 335,028,860 bp (27.59%) number of C's = 272,243,016 bp (22.42%) number of T's = 337,239,659 bp (27.77%) number of G's = 269,619,670 bp (22.2%) number of N's = 164,208 bp (0.01%) GC percentage = 44.62% >>>>>>> Mismatches and indels general error rate = 0.0046 number of mismatches = 5,433,590 number of insertions = 77,886 mapped reads with insertion percentage = 0.62% number of deletions = 60,362 mapped reads with deletion percentage = 0.48% homopolymer indels = 46.54% >>>>>>> Coverage mean coverageData = 0.3923X std coverageData = 9.647X There is a 3.71% of reference with a coverageData >= 1X There is a 1.63% of reference with a coverageData >= 2X There is a 0.71% of reference with a coverageData >= 3X There is a 0.59% of reference with a coverageData >= 4X There is a 0.48% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.42% of reference with a coverageData >= 7X There is a 0.4% of reference with a coverageData >= 8X There is a 0.39% of reference with a coverageData >= 9X There is a 0.37% of reference with a coverageData >= 10X There is a 0.36% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.34% of reference with a coverageData >= 13X There is a 0.33% of reference with a coverageData >= 14X There is a 0.33% of reference with a coverageData >= 15X There is a 0.32% of reference with a coverageData >= 16X There is a 0.31% of reference with a coverageData >= 17X There is a 0.3% of reference with a coverageData >= 18X There is a 0.3% of reference with a coverageData >= 19X There is a 0.29% of reference with a coverageData >= 20X There is a 0.29% of reference with a coverageData >= 21X There is a 0.28% of reference with a coverageData >= 22X There is a 0.27% of reference with a coverageData >= 23X There is a 0.27% of reference with a coverageData >= 24X There is a 0.26% of reference with a coverageData >= 25X There is a 0.26% of reference with a coverageData >= 26X There is a 0.25% of reference with a coverageData >= 27X There is a 0.25% of reference with a coverageData >= 28X There is a 0.25% of reference with a coverageData >= 29X There is a 0.24% of reference with a coverageData >= 30X There is a 0.24% of reference with a coverageData >= 31X There is a 0.23% of reference with a coverageData >= 32X There is a 0.23% of reference with a coverageData >= 33X There is a 0.23% of reference with a coverageData >= 34X There is a 0.22% of reference with a coverageData >= 35X There is a 0.22% of reference with a coverageData >= 36X There is a 0.22% of reference with a coverageData >= 37X There is a 0.21% of reference with a coverageData >= 38X There is a 0.21% of reference with a coverageData >= 39X There is a 0.21% of reference with a coverageData >= 40X There is a 0.2% of reference with a coverageData >= 41X There is a 0.2% of reference with a coverageData >= 42X There is a 0.2% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.19% of reference with a coverageData >= 46X There is a 0.19% 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 0.18% of reference with a coverageData >= 50X There is a 0.18% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 128558916 0.5157817279821341 11.418009235465394 chr2 243199373 106909840 0.4395975149162905 11.418618052250547 chr3 198022430 91060430 0.4598490686130859 8.236807026566254 chr4 191154276 32301821 0.1689829894257767 5.275415240565043 chr5 180915260 52874394 0.29226055336625556 7.176564944963715 chr6 171115067 98313548 0.5745464132623692 10.817550098388852 chr7 159138663 81812475 0.5140955281244257 12.907244991843664 chr8 146364022 91999254 0.628564675545743 14.081968171451818 chr9 141213431 45738342 0.3238951258113685 6.425628633252255 chr10 135534747 27455561 0.20257211975317296 5.969350717542079 chr11 135006516 40789265 0.3021281209863974 7.633969503832215 chr12 133851895 52333365 0.390979634617799 7.530281472024048 chr13 115169878 43251213 0.3755427525936947 11.348355807066426 chr14 107349540 26720454 0.24891074521604845 6.39753295279697 chr15 102531392 24966271 0.2434988008355529 6.1624222982535946 chr16 90354753 68579747 0.7590054172357706 17.424714675173185 chr17 81195210 45869015 0.5649226721625574 10.006567787966507 chr18 78077248 10784388 0.1381245916864283 3.5819536421880045 chr19 59128983 21535247 0.3642079722561776 6.297470689821429 chr20 63025520 37765753 0.5992136677333245 13.934778059060282 chr21 48129895 10112765 0.21011400502743668 11.617028277466186 chr22 51304566 12924094 0.2519092355249628 6.100661422279101 chrMT 16571 95112 5.739665681008992 3.6587653684554615 chrX 155270560 60966897 0.39264943077425624 8.560774861988074 chrY 59373566 719743 0.012122280140626891 0.516981562806161