BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084823.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 = 2,001,890 number of mapped reads = 1,850,326 (92.43%) number of supplementary alignments = 18,688 (0.93%) number of secondary alignments = 0 number of mapped bases = 125,359,902 bp number of sequenced bases = 125,309,685 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,667 duplication rate = 3.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3134 >>>>>>> ACTG content number of A's = 35,173,151 bp (28.07%) number of C's = 22,880,289 bp (18.26%) number of T's = 40,153,092 bp (32.04%) number of G's = 27,085,276 bp (21.61%) number of N's = 17,877 bp (0.01%) GC percentage = 39.87% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 983,211 number of insertions = 10,139 mapped reads with insertion percentage = 0.54% number of deletions = 29,884 mapped reads with deletion percentage = 1.6% homopolymer indels = 49.09% >>>>>>> Coverage mean coverageData = 0.0405X std coverageData = 0.2916X There is a 3.39% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% 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 10292677 0.041294488891163085 0.3579265530517389 chr2 243199373 10397044 0.042751113507188195 0.41226933459042847 chr3 198022430 10797102 0.054524641476220645 0.2717998190265481 chr4 191154276 7847231 0.04105182036315003 0.23741286348276253 chr5 180915260 6742589 0.03726932155971807 0.22582890377500645 chr6 171115067 6045864 0.03533215459045462 0.23226054851103767 chr7 159138663 8074530 0.05073895838876062 0.32251924026726825 chr8 146364022 5955589 0.04069025241735978 0.33386944341114483 chr9 141213431 8918708 0.06315764681052187 0.3605727284105751 chr10 135534747 3472940 0.025623982608681154 0.2070094868044534 chr11 135006516 5146290 0.03811882679795989 0.2734871320808268 chr12 133851895 4430063 0.03309675219764352 0.2121529635011547 chr13 115169878 3378483 0.029334779706895235 0.1982497039019709 chr14 107349540 2727487 0.025407533185517143 0.18568933552926686 chr15 102531392 3725639 0.0363365689992778 0.22709251333856115 chr16 90354753 2198834 0.02433556539078802 0.18920708678453707 chr17 81195210 3064614 0.037743778235193925 0.23088291020129784 chr18 78077248 5514325 0.07062652874240649 0.5228883413301769 chr19 59128983 2543063 0.04300873904765113 0.30969937441956946 chr20 63025520 2746762 0.043581742760710265 0.24308835972514872 chr21 48129895 1059658 0.022016628126863773 0.17901727175095894 chr22 51304566 1244773 0.024262421399296116 0.17627629813565734 chrMT 16571 236688 14.283265946533099 7.8119524607806525 chrX 155270560 8523309 0.05489327146111923 0.2824745243491101 chrY 59373566 275640 0.004642470017717986 0.11073778160984978