BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549131.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 13,476,699 number of mapped reads = 11,815,430 (87.67%) number of secondary alignments = 0 number of mapped bases = 468,997,501 bp number of sequenced bases = 468,952,289 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 608,816 duplication rate = 4.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1982 >>>>>>> ACTG content number of A's = 134,563,773 bp (28.69%) number of C's = 98,994,351 bp (21.11%) number of T's = 136,122,470 bp (29.03%) number of G's = 99,161,511 bp (21.15%) number of N's = 110,184 bp (0.02%) GC percentage = 42.26% >>>>>>> Mismatches and indels general error rate = 0.0033 number of mismatches = 1,522,207 number of insertions = 11,781 mapped reads with insertion percentage = 0.1% number of deletions = 35,774 mapped reads with deletion percentage = 0.3% homopolymer indels = 45.87% >>>>>>> Coverage mean coverageData = 0.1515X std coverageData = 0.8349X There is a 10.85% of reference with a coverageData >= 1X There is a 2.84% of reference with a coverageData >= 2X There is a 0.83% of reference with a coverageData >= 3X There is a 0.27% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% 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 38855228 0.15588818934176296 1.5548810774835793 chr2 243199373 39876691 0.16396707979999603 0.8047328729098489 chr3 198022430 31915213 0.16116968668650314 0.5302631372374906 chr4 191154276 29808339 0.15593864612267422 0.5423449373009184 chr5 180915260 28605531 0.15811563380557284 0.5389443596069053 chr6 171115067 27019269 0.1579011683407166 0.6053173836627539 chr7 159138663 26510660 0.16658842986509192 1.2703166972143387 chr8 146364022 24419451 0.16684052997669058 0.789591970808285 chr9 141213431 20377671 0.1443040570269835 0.7545219641711739 chr10 135534747 22299352 0.1645286724886866 0.7840498458434039 chr11 135006516 21977259 0.16278665394194752 0.7203845849422331 chr12 133851895 21721161 0.16227757552479927 0.5586166646292611 chr13 115169878 14892173 0.1293061454836307 0.46473738956152416 chr14 107349540 14566426 0.1356915548962762 0.6590373107026496 chr15 102531392 14408760 0.14053022902488244 0.48947528298203924 chr16 90354753 14278146 0.15802318667176257 0.5863098333396275 chr17 81195210 13468050 0.16587246957055718 0.5927476598258844 chr18 78077248 12389625 0.15868419184036814 1.5183254361936782 chr19 59128983 10112448 0.17102354018163984 1.3202153491078448 chr20 63025520 10456898 0.1659152990725027 0.571401974033257 chr21 48129895 6229435 0.1294296403513866 0.5718802240139433 chr22 51304566 6059830 0.1181148282201627 0.5011048896292013 chrMT 16571 145843 8.801098304266489 10.996408424328935 chrX 155270560 15096048 0.09722414860872532 0.5290122876229031 chrY 59373566 3507994 0.05908343116867867 0.43374141250551096