BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818844.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 = 2,114,774 number of mapped reads = 2,088,326 (98.75%) number of supplementary alignments = 33,337 (1.58%) number of secondary alignments = 0 number of mapped bases = 193,387,689 bp number of sequenced bases = 193,266,339 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 526,721 duplication rate = 21.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3139 >>>>>>> ACTG content number of A's = 54,762,773 bp (28.34%) number of C's = 40,673,889 bp (21.05%) number of T's = 55,757,342 bp (28.85%) number of G's = 42,069,328 bp (21.77%) number of N's = 3,007 bp (0%) GC percentage = 42.81% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 1,141,122 number of insertions = 27,089 mapped reads with insertion percentage = 1.26% number of deletions = 62,089 mapped reads with deletion percentage = 2.9% homopolymer indels = 40.52% >>>>>>> Coverage mean coverageData = 0.0625X std coverageData = 0.7216X There is a 4.09% of reference with a coverageData >= 1X There is a 1.24% of reference with a coverageData >= 2X There is a 0.43% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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 0.01% 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 17120563 0.06868814581609407 1.0748231076736616 chr2 243199373 14748381 0.060643170325936656 1.048284042633604 chr3 198022430 12104855 0.06112870648037195 0.34955999326775294 chr4 191154276 9922509 0.05190838106075116 0.44439654482982793 chr5 180915260 8660664 0.047871384647154694 0.3259737956135262 chr6 171115067 9680960 0.056575730996265804 0.37415481378921983 chr7 159138663 17326011 0.1088736745262212 1.5503014405468551 chr8 146364022 16983133 0.11603352222720417 0.629311811055248 chr9 141213431 7221784 0.05114091449275813 0.622129398937354 chr10 135534747 8912875 0.06576081187505371 0.9556397344256028 chr11 135006516 8609435 0.06377051460242111 0.44657017655680886 chr12 133851895 7595175 0.05674312642342494 0.3374444961782199 chr13 115169878 5997302 0.05207352915664285 0.3176474065411355 chr14 107349540 5723028 0.05331208685197906 0.3560361235089135 chr15 102531392 5393435 0.05260276774551154 0.31918854291626125 chr16 90354753 4893210 0.05415553512718916 0.7421046581041548 chr17 81195210 4831756 0.059507894615950865 0.47744589968488993 chr18 78077248 3768758 0.048269606018900665 0.6855901001796095 chr19 59128983 3303335 0.05586659591287068 0.8440597039516591 chr20 63025520 8095137 0.12844220880684523 0.5493342653112157 chr21 48129895 1880225 0.03906563685626158 0.3368625388162665 chr22 51304566 1763305 0.034369358080136574 0.30416705241718817 chrMT 16571 231933 13.996318870315612 9.381269644283716 chrX 155270560 7903271 0.05089999675405305 0.38592432783275704 chrY 59373566 716649 0.012070169408386218 0.9109355437930635