BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617649.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,496,656 (95.3%) number of supplementary alignments = 143,449 (0.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,262,514 number of mapped paired reads (second in pair) = 15,234,142 number of mapped paired reads (both in pair) = 29,917,156 number of mapped paired reads (singletons) = 579,500 number of mapped bases = 2,963,837,514 bp number of sequenced bases = 2,962,028,489 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,055,245 duplication rate = 10.78% >>>>>>> Insert size mean insert size = 32,421.2512 std insert size = 1,646,001.6366 median insert size = 224 >>>>>>> Mapping quality mean mapping quality = 52.6949 >>>>>>> ACTG content number of A's = 881,526,432 bp (29.76%) number of C's = 590,969,855 bp (19.95%) number of T's = 880,215,675 bp (29.72%) number of G's = 607,412,015 bp (20.51%) number of N's = 1,904,512 bp (0.06%) GC percentage = 40.46% >>>>>>> Mismatches and indels general error rate = 0.0146 number of mismatches = 42,233,051 number of insertions = 462,847 mapped reads with insertion percentage = 1.49% number of deletions = 1,090,086 mapped reads with deletion percentage = 3.5% homopolymer indels = 47.7% >>>>>>> Coverage mean coverageData = 0.9574X std coverageData = 10.7836X There is a 33.44% of reference with a coverageData >= 1X There is a 19.42% of reference with a coverageData >= 2X There is a 11.9% of reference with a coverageData >= 3X There is a 7.62% of reference with a coverageData >= 4X There is a 5.03% of reference with a coverageData >= 5X There is a 3.41% of reference with a coverageData >= 6X There is a 2.37% of reference with a coverageData >= 7X There is a 1.69% of reference with a coverageData >= 8X There is a 1.22% of reference with a coverageData >= 9X There is a 0.91% of reference with a coverageData >= 10X There is a 0.68% of reference with a coverageData >= 11X There is a 0.52% of reference with a coverageData >= 12X There is a 0.41% of reference with a coverageData >= 13X There is a 0.32% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.21% of reference with a coverageData >= 16X There is a 0.17% of reference with a coverageData >= 17X There is a 0.14% of reference with a coverageData >= 18X There is a 0.12% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.08% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 181657728 0.728815548266979 10.425134869969147 chr2 243199373 306089348 1.258594313892413 12.319833460531456 chr3 198022430 248240632 1.2535985544667845 2.5000982301958814 chr4 191154276 165336677 0.8649384175952203 8.561154934128135 chr5 180915260 195822716 1.0824002132268997 2.3436470377779663 chr6 171115067 143645067 0.8394647503483723 5.890264735902688 chr7 159138663 232093138 1.4584333789457562 13.500939169193426 chr8 146364022 131650246 0.8994713605232849 4.134502050151524 chr9 141213431 121754725 0.8622035746727236 21.036688699027604 chr10 135534747 125820729 0.9283282094443279 21.825622178675403 chr11 135006516 162899423 1.206604153832101 12.041113832827905 chr12 133851895 126621046 0.9459787326880953 2.1597981481682478 chr13 115169878 127420878 1.1063733001436364 2.3112016362521315 chr14 107349540 84891240 0.7907927691166632 2.4656053949318624 chr15 102531392 63327659 0.6176416584688521 1.5852040366970825 chr16 90354753 82373923 0.9116722725145405 17.035341329971754 chr17 81195210 73244146 0.9020747159838616 12.982277852096434 chr18 78077248 54731156 0.7009872581574597 18.626872656782737 chr19 59128983 31486761 0.5325097676718031 6.0792057534273924 chr20 63025520 80132229 1.2714251147789022 3.114897443072797 chr21 48129895 43170930 0.8969670513513482 4.42765979801215 chr22 51304566 19121796 0.372711387910386 1.2813039315862778 chrMT 16571 3192525 192.65735320741052 133.22592954038342 chrX 155270560 147185628 0.9479300390234955 4.380396731475504 chrY 59373566 11927168 0.20088347060036785 17.707282617836725