BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818823.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,600,064 number of mapped reads = 1,559,067 (97.44%) number of supplementary alignments = 13,259 (0.83%) number of secondary alignments = 0 number of mapped bases = 105,802,353 bp number of sequenced bases = 105,757,596 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 699,835 duplication rate = 37.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6084 >>>>>>> ACTG content number of A's = 29,756,269 bp (28.14%) number of C's = 22,755,298 bp (21.52%) number of T's = 30,420,818 bp (28.76%) number of G's = 22,819,015 bp (21.58%) number of N's = 6,196 bp (0.01%) GC percentage = 43.09% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 548,508 number of insertions = 13,194 mapped reads with insertion percentage = 0.83% number of deletions = 27,350 mapped reads with deletion percentage = 1.74% homopolymer indels = 38.96% >>>>>>> Coverage mean coverageData = 0.0342X std coverageData = 0.4602X There is a 1.64% of reference with a coverageData >= 1X There is a 0.76% of reference with a coverageData >= 2X There is a 0.41% of reference with a coverageData >= 3X There is a 0.23% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% 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% 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 8731723 0.03503190068280713 0.6122277563538023 chr2 243199373 9387264 0.03859904688158879 0.7816714017067523 chr3 198022430 7216453 0.03644260400198099 0.3437592734229114 chr4 191154276 6915318 0.0361766325331901 0.40536533895704846 chr5 180915260 6433865 0.03556286517787388 0.35368843694919777 chr6 171115067 6295403 0.03679046568120153 0.37753437600278783 chr7 159138663 5825572 0.03660689294593357 0.397436147157135 chr8 146364022 5431220 0.03710761651521164 0.37960951718193986 chr9 141213431 4523141 0.03203052973056083 0.3764565409843261 chr10 135534747 5139335 0.03791894782523923 0.5016856980073465 chr11 135006516 4910556 0.036372733298295025 0.389029178497471 chr12 133851895 4781634 0.03572331941957191 0.3649925748865531 chr13 115169878 3345278 0.029046466472769903 0.3057097991155893 chr14 107349540 3233433 0.030120604149770927 0.36746387190714747 chr15 102531392 3040589 0.029655200623824554 0.31363772327264366 chr16 90354753 3224822 0.03569067362731875 0.5288336467066149 chr17 81195210 2783400 0.034280347325907526 0.353394743662965 chr18 78077248 2822354 0.03614822592107755 0.46917993258367136 chr19 59128983 2175458 0.03679173714183449 0.5209964007038423 chr20 63025520 2420543 0.0384057600794091 0.37763904552877914 chr21 48129895 1424636 0.02959981524996055 0.33016886022140063 chr22 51304566 1285872 0.02506350019606442 0.3067637759069954 chrMT 16571 82351 4.969585420312594 5.168401546587227 chrX 155270560 3302434 0.021268899912514003 0.28700313783934756 chrY 59373566 1069699 0.018016418282843245 0.7826062644940144