BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818921.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 = 2,390,210 number of mapped reads = 2,356,910 (98.61%) number of supplementary alignments = 34,395 (1.44%) number of secondary alignments = 0 number of mapped bases = 218,417,406 bp number of sequenced bases = 218,270,336 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 694,582 duplication rate = 25.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2969 >>>>>>> ACTG content number of A's = 63,425,063 bp (29.06%) number of C's = 44,820,746 bp (20.53%) number of T's = 61,248,093 bp (28.06%) number of G's = 48,773,376 bp (22.35%) number of N's = 3,058 bp (0%) GC percentage = 42.88% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,313,068 number of insertions = 32,002 mapped reads with insertion percentage = 1.31% number of deletions = 75,092 mapped reads with deletion percentage = 3.09% homopolymer indels = 39.66% >>>>>>> Coverage mean coverageData = 0.0706X std coverageData = 0.8641X There is a 4.32% of reference with a coverageData >= 1X There is a 1.47% of reference with a coverageData >= 2X There is a 0.58% of reference with a coverageData >= 3X There is a 0.25% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 20648160 0.08284095709434562 1.2063383182641598 chr2 243199373 16473259 0.06773561459798665 1.3745786956611432 chr3 198022430 13593048 0.06864398139140096 0.3879327931443067 chr4 191154276 10726837 0.056116123711509334 0.49602942525732047 chr5 180915260 9492158 0.05246742590978782 0.38740051621001365 chr6 171115067 10779821 0.06299749746759588 0.4235251586272703 chr7 159138663 19661748 0.12355104428645351 1.9425222335330017 chr8 146364022 19088070 0.1304150414778845 0.68653111502473 chr9 141213431 8156473 0.05775989537425799 0.6667227455054291 chr10 135534747 9978656 0.07362433782386446 1.0001889678215885 chr11 135006516 9548933 0.07072942316354568 0.5040176187285837 chr12 133851895 8639237 0.06454325506560815 0.3831753239954526 chr13 115169878 6596681 0.05727783266384983 0.3524747439119036 chr14 107349540 6469578 0.06026647156569092 0.4124731008494604 chr15 102531392 6124637 0.05973426167860864 0.3610563815973245 chr16 90354753 5517702 0.0610670918440782 1.0304672707495497 chr17 81195210 5544546 0.06828661444437424 0.5240650250612355 chr18 78077248 4205112 0.05385835320425228 0.7693794727492194 chr19 59128983 3867044 0.0654001439530932 1.0914049668029004 chr20 63025520 9127399 0.1448206853350833 0.6324306524046861 chr21 48129895 2116481 0.04397435315410516 0.3642564249991485 chr22 51304566 1991632 0.038819780679949616 0.3459603433538885 chrMT 16571 285956 17.256411803753544 11.429882890877728 chrX 155270560 8993353 0.05792052917178891 0.43444895398753863 chrY 59373566 790885 0.01332049013192167 1.1305777557796712