BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085053.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,391,903 number of mapped reads = 1,244,163 (89.39%) number of supplementary alignments = 16,349 (1.17%) number of secondary alignments = 0 number of mapped bases = 84,106,847 bp number of sequenced bases = 84,081,698 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 47,286 duplication rate = 2.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.0959 >>>>>>> ACTG content number of A's = 24,341,621 bp (28.95%) number of C's = 15,978,399 bp (19%) number of T's = 24,840,991 bp (29.54%) number of G's = 18,911,382 bp (22.49%) number of N's = 9,305 bp (0.01%) GC percentage = 41.5% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 815,356 number of insertions = 7,169 mapped reads with insertion percentage = 0.57% number of deletions = 15,515 mapped reads with deletion percentage = 1.23% homopolymer indels = 42.88% >>>>>>> Coverage mean coverageData = 0.0272X std coverageData = 0.4398X There is a 2.48% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% 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 7321992 0.02937602309925639 0.9378879628825113 chr2 243199373 8194806 0.03369583522733836 0.47762941016416444 chr3 198022430 5206876 0.02629437483420439 0.1894212977031366 chr4 191154276 5149347 0.026938173227158153 0.17772698533806602 chr5 180915260 4350463 0.024046965413531175 0.16815921787925256 chr6 171115067 5670882 0.033140752006367735 0.39944787595508685 chr7 159138663 6991347 0.04393242263195337 0.4725634287021637 chr8 146364022 5003379 0.03418448694994184 0.5175058140719907 chr9 141213431 2819664 0.019967392478410922 0.38972809610703485 chr10 135534747 5722619 0.042222523202850706 0.6150109238854248 chr11 135006516 3668045 0.027169392327700687 0.45466409309131367 chr12 133851895 3486591 0.026048125803523364 0.1829769350896161 chr13 115169878 1794953 0.015585264403944232 0.12853304566883964 chr14 107349540 2614954 0.024359247370785195 0.20813985972158225 chr15 102531392 1467699 0.014314630586503693 0.1268459744475872 chr16 90354753 2150131 0.02379654560065036 0.23087965179012862 chr17 81195210 1412027 0.017390520943292097 0.21881613655712187 chr18 78077248 2225803 0.028507703037893958 0.7526346227232734 chr19 59128983 1309284 0.02214284659690494 0.624093773400624 chr20 63025520 1745991 0.027702920975503257 0.18147747361199895 chr21 48129895 976986 0.02029894309970965 0.1914389706237196 chr22 51304566 503527 0.009814467585594623 0.10353279751557908 chrMT 16571 14243 0.8595136081105546 1.104053232093654 chrX 155270560 4120135 0.026535197657559812 0.24792858699506803 chrY 59373566 185103 0.0031175995054768986 0.077200393286882