BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975300.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 2,254,124 number of mapped reads = 2,222,281 (98.59%) number of supplementary alignments = 34,009 (1.51%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,113,045 number of mapped paired reads (second in pair) = 1,109,236 number of mapped paired reads (both in pair) = 2,213,972 number of mapped paired reads (singletons) = 8,309 number of mapped bases = 295,259,486 bp number of sequenced bases = 295,028,006 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 379,581 duplication rate = 15.73% >>>>>>> Insert size mean insert size = 88,385.6871 std insert size = 2,806,098.0803 median insert size = 167 >>>>>>> Mapping quality mean mapping quality = 53.2791 >>>>>>> ACTG content number of A's = 86,965,993 bp (29.48%) number of C's = 58,315,329 bp (19.77%) number of T's = 87,329,280 bp (29.6%) number of G's = 62,400,135 bp (21.15%) number of N's = 17,269 bp (0.01%) GC percentage = 40.92% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 2,924,703 number of insertions = 61,373 mapped reads with insertion percentage = 2.56% number of deletions = 99,817 mapped reads with deletion percentage = 4.28% homopolymer indels = 44.43% >>>>>>> Coverage mean coverageData = 0.0954X std coverageData = 1.2573X There is a 5.04% of reference with a coverageData >= 1X There is a 2.86% of reference with a coverageData >= 2X There is a 0.58% of reference with a coverageData >= 3X There is a 0.29% of reference with a coverageData >= 4X There is a 0.09% 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% 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 25821568 0.10359680508077851 0.9624975000846597 chr2 243199373 26128257 0.10743554425199937 1.7182123472587525 chr3 198022430 13839508 0.06988858787360604 0.3978203946476443 chr4 191154276 21032303 0.11002789704793212 1.3126988918721525 chr5 180915260 18853374 0.10421107650067772 0.4793276039438122 chr6 171115067 22582583 0.13197308335215158 0.8175202901945827 chr7 159138663 16410061 0.10311800219158558 1.0570278714983166 chr8 146364022 16091956 0.10994475131327014 0.6457029810329221 chr9 141213431 11530551 0.08165335916241565 2.135373354254191 chr10 135534747 16443843 0.12132566270994699 2.8841209554705896 chr11 135006516 9459893 0.0700698994410018 0.7219823820671559 chr12 133851895 13057000 0.09754811465313958 0.46018708916226503 chr13 115169878 9275133 0.08053436507070016 0.4193454562300882 chr14 107349540 8946789 0.08334259280477588 0.4578756927071179 chr15 102531392 8098159 0.07898223989780613 0.41278223564405575 chr16 90354753 9310394 0.10304265897334698 1.6612060217900804 chr17 81195210 5817464 0.07164787183874517 0.8973328566466353 chr18 78077248 9000921 0.1152822522638093 1.960864919142205 chr19 59128983 3766006 0.06369137111659776 0.6941945183481146 chr20 63025520 5642495 0.08952714709850866 0.6422895660396992 chr21 48129895 3814814 0.07926080038196634 0.7974484417380343 chr22 51304566 2774218 0.05407351072807048 0.3567969778037156 chrMT 16571 74300 4.483736648361596 4.3501467998433725 chrX 155270560 11010514 0.0709117942255119 0.4759246198521858 chrY 59373566 6477382 0.10909538429947091 2.945920987324702