BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082902.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 = 1,776,748 number of mapped reads = 1,562,010 (87.91%) number of supplementary alignments = 19,150 (1.08%) number of secondary alignments = 0 number of mapped bases = 103,158,754 bp number of sequenced bases = 103,121,573 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 86,242 duplication rate = 4.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.086 >>>>>>> ACTG content number of A's = 27,975,811 bp (27.13%) number of C's = 19,160,076 bp (18.58%) number of T's = 32,632,979 bp (31.65%) number of G's = 23,348,178 bp (22.64%) number of N's = 4,529 bp (0%) GC percentage = 41.22% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 742,043 number of insertions = 8,247 mapped reads with insertion percentage = 0.52% number of deletions = 23,132 mapped reads with deletion percentage = 1.47% homopolymer indels = 47.41% >>>>>>> Coverage mean coverageData = 0.0333X std coverageData = 0.2628X There is a 2.69% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% 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 9778712 0.03923244789027025 0.3368403460281613 chr2 243199373 10893852 0.044793914826416925 0.4024768293134693 chr3 198022430 8454071 0.042692491956593 0.2487290824470604 chr4 191154276 5263871 0.02753729139702844 0.20209143298459767 chr5 180915260 6365573 0.03518538458281518 0.22625418513109852 chr6 171115067 6924388 0.0404662670646063 0.2935170472878678 chr7 159138663 4939919 0.031041601750795154 0.23875960189215897 chr8 146364022 8023765 0.05482061021799469 0.3225254240641826 chr9 141213431 3040340 0.021530105022375668 0.22031533072875342 chr10 135534747 3565610 0.026307718713637324 0.2109521333779904 chr11 135006516 3887205 0.02879272138242572 0.22617636016576553 chr12 133851895 3075614 0.022977739687585298 0.18523115138356597 chr13 115169878 2586236 0.022455836933334253 0.17981841649977473 chr14 107349540 1984623 0.018487484902124405 0.1756165121630768 chr15 102531392 2162755 0.021093588586020562 0.17702250367362946 chr16 90354753 3758108 0.04159280917961228 0.251793793741113 chr17 81195210 2810408 0.034612977785265904 0.2397042435408211 chr18 78077248 3108309 0.03981068851197214 0.39083105062165685 chr19 59128983 1961907 0.03318012420406419 0.26733675508332383 chr20 63025520 2120824 0.03365024199721002 0.22480940039714306 chr21 48129895 1612429 0.0335016105894268 0.2206851681619764 chr22 51304566 1609177 0.03136518102501832 0.21547165037696775 chrMT 16571 9531 0.5751614265886187 0.8700987401245011 chrX 155270560 5040846 0.03246491801150199 0.2288094278243129 chrY 59373566 180681 0.0030431219172518628 0.06859184584700403