BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777253.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 = 12,193,444 number of mapped reads = 11,525,424 (94.52%) number of supplementary alignments = 1,659,455 (13.61%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,800,532 number of mapped paired reads (second in pair) = 5,724,892 number of mapped paired reads (both in pair) = 11,242,756 number of mapped paired reads (singletons) = 282,668 number of mapped bases = 996,604,469 bp number of sequenced bases = 993,186,595 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,486,972 duplication rate = 6.5% >>>>>>> Insert size mean insert size = 1,031,151.1727 std insert size = 4,817,912.165 median insert size = 162 >>>>>>> Mapping quality mean mapping quality = 52.45 >>>>>>> ACTG content number of A's = 292,731,731 bp (29.47%) number of C's = 205,135,977 bp (20.65%) number of T's = 286,579,594 bp (28.85%) number of G's = 208,721,970 bp (21.02%) number of N's = 17,323 bp (0%) GC percentage = 41.67% >>>>>>> Mismatches and indels general error rate = 0.0146 number of mismatches = 12,004,355 number of insertions = 870,762 mapped reads with insertion percentage = 6.88% number of deletions = 984,066 mapped reads with deletion percentage = 7.37% homopolymer indels = 23.29% >>>>>>> Coverage mean coverageData = 0.3219X std coverageData = 141.047X There is a 14.14% of reference with a coverageData >= 1X There is a 5.26% of reference with a coverageData >= 2X There is a 1.21% of reference with a coverageData >= 3X There is a 0.39% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% 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 56667497 0.22735147769200542 3.8749361351386873 chr2 243199373 65704753 0.2701682664288777 1.8273009417627664 chr3 198022430 44675195 0.225606740610142 0.8660943016127192 chr4 191154276 73993698 0.38708889776548866 96.24348219547241 chr5 180915260 45099914 0.24928750620594414 0.8056332250042463 chr6 171115067 31521082 0.18420985686783503 3.3191868415933046 chr7 159138663 45603751 0.2865661313241019 2.7709997693763957 chr8 146364022 34190442 0.23359867768596848 1.3168243163457447 chr9 141213431 306133618 2.167878903813335 650.7542518503877 chr10 135534747 34353508 0.25346642658358304 4.284814269091278 chr11 135006516 40191170 0.2976980014801656 1.9827151175511177 chr12 133851895 30624011 0.22879026852776346 0.7930983219637335 chr13 115169878 28635369 0.24863592370914903 0.7139784754292308 chr14 107349540 13553803 0.1262586034369593 1.1205807205128444 chr15 102531392 24532459 0.23926778444595778 0.678558169878469 chr16 90354753 21143886 0.23400967074748133 2.5205131483608616 chr17 81195210 15948850 0.19642599606553146 1.1131474148233154 chr18 78077248 14837255 0.19003301704486306 2.145786381858466 chr19 59128983 11953382 0.2021577472421604 2.2171520418783994 chr20 63025520 18117836 0.2874682509561206 0.9442562262646472 chr21 48129895 6369169 0.13233290868388556 2.917681366488063 chr22 51304566 4992503 0.09731108533302864 0.641725730222279 chrMT 16571 3273336 197.53400518978938 39.6234338767637 chrX 155270560 22955737 0.1478434611171622 0.6933649562547699 chrY 59373566 1532245 0.02580685485523979 1.286523908864677