BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777278.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 12,666,134 number of mapped reads = 12,486,345 (98.58%) number of supplementary alignments = 74,497 (0.59%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,260,068 number of mapped paired reads (second in pair) = 6,226,277 number of mapped paired reads (both in pair) = 12,441,654 number of mapped paired reads (singletons) = 44,691 number of mapped bases = 1,190,336,990 bp number of sequenced bases = 1,189,526,783 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,085,491 duplication rate = 8.88% >>>>>>> Insert size mean insert size = 78,033.8082 std insert size = 2,821,530.8478 median insert size = 150 >>>>>>> Mapping quality mean mapping quality = 53.9349 >>>>>>> ACTG content number of A's = 331,394,337 bp (27.86%) number of C's = 262,209,293 bp (22.04%) number of T's = 324,568,518 bp (27.29%) number of G's = 271,332,065 bp (22.81%) number of N's = 22,570 bp (0%) GC percentage = 44.85% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 8,733,141 number of insertions = 195,780 mapped reads with insertion percentage = 1.55% number of deletions = 590,861 mapped reads with deletion percentage = 4.62% homopolymer indels = 54.16% >>>>>>> Coverage mean coverageData = 0.3845X std coverageData = 1.4327X There is a 17.56% of reference with a coverageData >= 1X There is a 9.57% of reference with a coverageData >= 2X There is a 4.45% of reference with a coverageData >= 3X There is a 2.52% of reference with a coverageData >= 4X There is a 1.46% of reference with a coverageData >= 5X There is a 0.9% of reference with a coverageData >= 6X There is a 0.57% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.25% of reference with a coverageData >= 9X There is a 0.17% of reference with a coverageData >= 10X There is a 0.12% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 109744556 0.44029802437282595 1.3427930832399089 chr2 243199373 110796991 0.4555809072747897 1.5991017444774969 chr3 198022430 71845307 0.36281398526419456 1.0594220796393123 chr4 191154276 53958136 0.28227532822755164 0.9462746574838362 chr5 180915260 70686019 0.39071341466717624 1.086668449675036 chr6 171115067 52305932 0.30567695128798916 3.3187195762879345 chr7 159138663 76079319 0.4780693614348136 1.2923626460190256 chr8 146364022 56842319 0.3883626469351874 1.2317136433945173 chr9 141213431 46802720 0.33143249667235974 1.295246669966926 chr10 135534747 58469381 0.4313977212057658 1.2002567569912717 chr11 135006516 76366397 0.5656497127886776 1.4568315059184476 chr12 133851895 54705981 0.40870531567745083 1.1244646801287521 chr13 115169878 40575763 0.3523122860302066 1.074868859171354 chr14 107349540 23894975 0.2225903809182601 0.7756723919437034 chr15 102531392 50810696 0.49556233470428257 1.3651459151618628 chr16 90354753 41676797 0.461257383991742 1.548444317411446 chr17 81195210 39441651 0.48576327347389087 1.3714469193986978 chr18 78077248 23693889 0.3034672661618401 1.2692064588645953 chr19 59128983 22304665 0.3772205079191029 1.192687290502736 chr20 63025520 44942565 0.7130851915224182 1.676158395130997 chr21 48129895 10401965 0.21612274450214364 1.06876901109229 chr22 51304566 16831968 0.32807933703210745 1.072499581128766 chrMT 16571 188632 11.383259911894273 10.773258189425022 chrX 155270560 35540830 0.22889612815204632 0.7667857168775413 chrY 59373566 1429536 0.024076977286491434 0.6312814498817872