BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472466.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 = 12,905,066 number of mapped reads = 12,608,380 (97.7%) number of supplementary alignments = 48,346 (0.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,338,650 number of mapped paired reads (second in pair) = 6,269,730 number of mapped paired reads (both in pair) = 12,508,616 number of mapped paired reads (singletons) = 99,764 number of mapped bases = 1,233,315,482 bp number of sequenced bases = 1,233,169,560 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,399,119 duplication rate = 44.85% >>>>>>> Insert size mean insert size = 20,918.7413 std insert size = 1,431,819.4151 median insert size = 204 >>>>>>> Mapping quality mean mapping quality = 55.1036 >>>>>>> ACTG content number of A's = 331,694,184 bp (26.9%) number of C's = 285,276,132 bp (23.13%) number of T's = 332,999,704 bp (27%) number of G's = 283,046,806 bp (22.95%) number of N's = 152,734 bp (0.01%) GC percentage = 46.09% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 6,415,390 number of insertions = 72,129 mapped reads with insertion percentage = 0.57% number of deletions = 59,923 mapped reads with deletion percentage = 0.47% homopolymer indels = 46% >>>>>>> Coverage mean coverageData = 0.3984X std coverageData = 13.3576X There is a 4.11% of reference with a coverageData >= 1X There is a 1.84% of reference with a coverageData >= 2X There is a 0.76% of reference with a coverageData >= 3X There is a 0.57% of reference with a coverageData >= 4X There is a 0.42% of reference with a coverageData >= 5X There is a 0.38% of reference with a coverageData >= 6X There is a 0.35% of reference with a coverageData >= 7X There is a 0.33% of reference with a coverageData >= 8X There is a 0.31% of reference with a coverageData >= 9X There is a 0.3% of reference with a coverageData >= 10X There is a 0.29% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.26% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.23% of reference with a coverageData >= 18X There is a 0.23% of reference with a coverageData >= 19X There is a 0.22% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.21% of reference with a coverageData >= 22X There is a 0.21% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.19% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.18% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.17% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.15% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 143452560 0.5755354166198847 16.074446739382637 chr2 243199373 118308917 0.4864688405261637 21.192346669477413 chr3 198022430 105933058 0.5349548432467979 12.463585077569608 chr4 191154276 37302426 0.19514303723972148 6.880037668424947 chr5 180915260 59527109 0.3290331009114433 11.137601801286479 chr6 171115067 99738783 0.5828755161577911 14.858572540236862 chr7 159138663 60952826 0.38301707989088735 13.271113805842498 chr8 146364022 62983847 0.43032328668858255 12.52847604079767 chr9 141213431 52172196 0.3694563302551582 11.38474593250253 chr10 135534747 30878010 0.2278235705859251 9.296401256358767 chr11 135006516 61821291 0.4579133869360794 16.930229944827705 chr12 133851895 54086921 0.4040803531395652 11.791545190700571 chr13 115169878 30111904 0.26145642005455627 12.805892108949955 chr14 107349540 29483757 0.27465191746513307 9.614070189530858 chr15 102531392 26117090 0.2547228657541292 7.589967484444895 chr16 90354753 69641270 0.7707538086015243 23.913174286271047 chr17 81195210 59897375 0.7376959182690703 15.975705178943617 chr18 78077248 16277500 0.20847942796344462 6.413150109405457 chr19 59128983 24443912 0.4133998381132312 10.669538918939462 chr20 63025520 21992694 0.3489490289013085 8.832887661792284 chr21 48129895 7626494 0.15845648530918258 6.49273652438517 chr22 51304566 12163049 0.2370753706405001 6.234313401279535 chrMT 16571 914 0.05515659887755718 0.24089062772998523 chrX 155270560 46234614 0.2977680636947532 9.465469742321044 chrY 59373566 2166965 0.036497134094994395 2.562073892101877