BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549140.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 = 11,749,171 number of mapped reads = 10,345,268 (88.05%) number of secondary alignments = 0 number of mapped bases = 410,692,690 bp number of sequenced bases = 410,653,147 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 499,341 duplication rate = 3.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.0527 >>>>>>> ACTG content number of A's = 117,310,402 bp (28.57%) number of C's = 87,596,159 bp (21.33%) number of T's = 118,359,930 bp (28.82%) number of G's = 87,295,479 bp (21.26%) number of N's = 91,177 bp (0.02%) GC percentage = 42.59% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 1,309,304 number of insertions = 10,437 mapped reads with insertion percentage = 0.1% number of deletions = 31,281 mapped reads with deletion percentage = 0.3% homopolymer indels = 46.41% >>>>>>> Coverage mean coverageData = 0.1327X std coverageData = 0.7958X There is a 9.78% of reference with a coverageData >= 1X There is a 2.37% of reference with a coverageData >= 2X There is a 0.63% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.01% 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% of reference with a coverageData >= 11X There is a 0% 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 33461174 0.13424710384171923 1.4399502978709424 chr2 243199373 35379138 0.14547380432596757 0.7639667494922373 chr3 198022430 27532157 0.1390355476397295 0.48273244161526513 chr4 191154276 25147275 0.13155486513940184 0.48235631864198025 chr5 180915260 25143852 0.13898137724811052 0.501243794372143 chr6 171115067 23918307 0.13977908210736345 0.5823614183430682 chr7 159138663 22788603 0.14319966355379019 1.2977363403939963 chr8 146364022 21399748 0.14620907315596998 0.716810023780739 chr9 141213431 17704839 0.12537645232909891 0.7130714131465462 chr10 135534747 20014704 0.1476721242560773 0.7263352612812661 chr11 135006516 19121644 0.1416349711594661 0.7024717937021082 chr12 133851895 19456670 0.14535969027558407 0.5225302292507116 chr13 115169878 12948318 0.11242799093700524 0.42703601945039443 chr14 107349540 12969239 0.12081317721529128 0.6125545398606345 chr15 102531392 12416786 0.12110228641000016 0.44074855257237966 chr16 90354753 12962490 0.1434621817847258 0.5475933568325836 chr17 81195210 12005498 0.14785968285567586 0.550219717719358 chr18 78077248 10906479 0.13968831227248174 1.5597938238516622 chr19 59128983 9036669 0.15282977216097224 1.2907904887656019 chr20 63025520 9286113 0.1473389350853432 0.5307548841184091 chr21 48129895 5263775 0.10936601877066218 0.5150678742268333 chr22 51304566 5516376 0.10752212580845144 0.4562891519165309 chrMT 16571 159153 9.604308732122382 12.814016346576741 chrX 155270560 13028321 0.0839072197588519 0.5096315762761379 chrY 59373566 3125362 0.052638947103160354 0.40105300388897713