BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708571.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 4,016,816 number of mapped reads = 3,286,957 (81.83%) number of supplementary alignments = 82 (0%) number of secondary alignments = 0 number of mapped bases = 163,914,353 bp number of sequenced bases = 163,899,383 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,654 duplication rate = 0.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8559 >>>>>>> ACTG content number of A's = 50,729,360 bp (30.95%) number of C's = 31,154,468 bp (19.01%) number of T's = 50,599,956 bp (30.87%) number of G's = 31,411,484 bp (19.17%) number of N's = 4,115 bp (0%) GC percentage = 38.17% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 259,237 number of insertions = 11,192 mapped reads with insertion percentage = 0.34% number of deletions = 8,750 mapped reads with deletion percentage = 0.27% homopolymer indels = 47.36% >>>>>>> Coverage mean coverageData = 0.0529X std coverageData = 0.239X There is a 4.97% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 18435035 0.07396184180419756 0.2841799841738669 chr2 243199373 11567628 0.04756438249534467 0.22347916535085782 chr3 198022430 5750434 0.029039306304846375 0.17677563691692602 chr4 191154276 5759331 0.030129229230530005 0.17913524532357772 chr5 180915260 7243145 0.04003611967282362 0.20754626304408125 chr6 171115067 8912791 0.05208653543057082 0.23377463747158692 chr7 159138663 12534236 0.07876298420327937 0.2909807581878778 chr8 146364022 11680409 0.07980382638022888 0.2919229502563211 chr9 141213431 7708317 0.05458628790061761 0.2440404399893949 chr10 135534747 7911505 0.058372521992459986 0.24916998997274595 chr11 135006516 8013322 0.059355075869078795 0.2522735870874532 chr12 133851895 8621729 0.0644124537796047 0.26271764921911916 chr13 115169878 9537158 0.08280948252806172 0.29883990601976856 chr14 107349540 7858238 0.07320234441619405 0.28176276896347047 chr15 102531392 6190967 0.06038118550072938 0.2557309061654735 chr16 90354753 3784106 0.04188054169103866 0.21233692622426137 chr17 81195210 1351430 0.016644208445301144 0.13313022235594238 chr18 78077248 4510246 0.0577664571374237 0.24679489794825898 chr19 59128983 1758180 0.029734656521997003 0.17674056022928403 chr20 63025520 2675738 0.04245483416876211 0.2129051557303526 chr21 48129895 2554489 0.05307489243431759 0.2404439365454493 chr22 51304566 825984 0.016099619671278383 0.13086143135000528 chrMT 16571 100 0.006034638826866212 0.07744818888195831 chrX 155270560 8501970 0.054755840385968854 0.2402342402050131 chrY 59373566 227865 0.003837819005178163 0.06521736159086786