BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618631.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 22,755,702 number of mapped reads = 21,751,332 (95.59%) number of supplementary alignments = 61,388 (0.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 11,048,802 number of mapped paired reads (second in pair) = 10,702,530 number of mapped paired reads (both in pair) = 21,216,516 number of mapped paired reads (singletons) = 534,816 number of mapped bases = 2,047,802,376 bp number of sequenced bases = 2,046,398,966 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,784,835 duplication rate = 15.45% >>>>>>> Insert size mean insert size = 67,275.0725 std insert size = 2,602,160.3353 median insert size = 227 >>>>>>> Mapping quality mean mapping quality = 53.6706 >>>>>>> ACTG content number of A's = 553,713,507 bp (27.06%) number of C's = 450,824,901 bp (22.03%) number of T's = 559,491,909 bp (27.34%) number of G's = 482,316,736 bp (23.57%) number of N's = 51,913 bp (0%) GC percentage = 45.6% >>>>>>> Mismatches and indels general error rate = 0.013 number of mismatches = 26,057,065 number of insertions = 368,457 mapped reads with insertion percentage = 1.67% number of deletions = 1,038,799 mapped reads with deletion percentage = 4.66% homopolymer indels = 53.11% >>>>>>> Coverage mean coverageData = 0.6615X std coverageData = 2.5959X There is a 20.02% of reference with a coverageData >= 1X There is a 11.63% of reference with a coverageData >= 2X There is a 7.64% of reference with a coverageData >= 3X There is a 5.38% of reference with a coverageData >= 4X There is a 3.95% of reference with a coverageData >= 5X There is a 2.99% of reference with a coverageData >= 6X There is a 2.33% of reference with a coverageData >= 7X There is a 1.84% of reference with a coverageData >= 8X There is a 1.48% of reference with a coverageData >= 9X There is a 1.21% of reference with a coverageData >= 10X There is a 1% of reference with a coverageData >= 11X There is a 0.83% of reference with a coverageData >= 12X There is a 0.69% of reference with a coverageData >= 13X There is a 0.59% of reference with a coverageData >= 14X There is a 0.5% of reference with a coverageData >= 15X There is a 0.43% of reference with a coverageData >= 16X There is a 0.37% of reference with a coverageData >= 17X There is a 0.32% of reference with a coverageData >= 18X There is a 0.28% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.21% of reference with a coverageData >= 21X There is a 0.19% of reference with a coverageData >= 22X There is a 0.16% of reference with a coverageData >= 23X There is a 0.14% of reference with a coverageData >= 24X There is a 0.13% of reference with a coverageData >= 25X There is a 0.11% of reference with a coverageData >= 26X There is a 0.1% of reference with a coverageData >= 27X There is a 0.09% of reference with a coverageData >= 28X There is a 0.08% of reference with a coverageData >= 29X There is a 0.07% of reference with a coverageData >= 30X There is a 0.07% of reference with a coverageData >= 31X There is a 0.06% of reference with a coverageData >= 32X There is a 0.05% of reference with a coverageData >= 33X There is a 0.05% of reference with a coverageData >= 34X There is a 0.05% of reference with a coverageData >= 35X There is a 0.04% of reference with a coverageData >= 36X There is a 0.04% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.03% of reference with a coverageData >= 39X There is a 0.03% of reference with a coverageData >= 40X There is a 0.03% 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 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 175127972 0.7026179966869571 2.8751370745497415 chr2 243199373 171745342 0.706191549268509 2.941263600838368 chr3 198022430 129349652 0.6532070735623232 2.2313534035668763 chr4 191154276 99602173 0.5210564737772332 2.045136390327286 chr5 180915260 115477064 0.6382936630110694 2.186037560995589 chr6 171115067 111061913 0.6490481226881091 2.2352220347722946 chr7 159138663 102880643 0.646484273906461 2.271119030876381 chr8 146364022 100189194 0.6845206399151835 2.4117573603293403 chr9 141213431 87778228 0.621599711715807 2.8080025203286563 chr10 135534747 101309759 0.7474818173379554 2.6060197830370067 chr11 135006516 105315050 0.7800738299179575 2.8273978871075225 chr12 133851895 91808286 0.6858945553217607 2.4450308865585617 chr13 115169878 54084748 0.469608450918043 1.8483821450395546 chr14 107349540 64810507 0.6037334393794328 2.2563274050517794 chr15 102531392 66167436 0.6453383174589106 2.5389159478893992 chr16 90354753 73755441 0.8162873401911684 4.385655148712502 chr17 81195210 71267988 0.8777363590783249 3.0871941325732393 chr18 78077248 52205322 0.6686368095350902 2.7442801006684374 chr19 59128983 42585517 0.7202139262229489 2.831522425704191 chr20 63025520 58696969 0.9313206618525322 3.0471515407842023 chr21 48129895 26878285 0.5584530155322384 3.065955345494969 chr22 51304566 37307479 0.7271765830744967 2.812383470511573 chrMT 16571 5028 0.30342164021483314 1.3102050440437487 chrX 155270560 105828700 0.6815760824202605 2.264359109613771 chrY 59373566 2563680 0.04317881125752157 1.5595908634365716