BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548958.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 6,291,488 number of mapped reads = 5,488,074 (87.23%) number of secondary alignments = 0 number of mapped bases = 217,055,977 bp number of sequenced bases = 217,034,347 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 246,523 duplication rate = 2.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 37.3548 >>>>>>> ACTG content number of A's = 62,040,428 bp (28.59%) number of C's = 45,712,361 bp (21.06%) number of T's = 63,370,461 bp (29.2%) number of G's = 45,910,792 bp (21.15%) number of N's = 305 bp (0%) GC percentage = 42.22% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 673,215 number of insertions = 7,275 mapped reads with insertion percentage = 0.13% number of deletions = 16,643 mapped reads with deletion percentage = 0.3% homopolymer indels = 39.67% >>>>>>> Coverage mean coverageData = 0.0701X std coverageData = 0.7358X There is a 5.93% of reference with a coverageData >= 1X There is a 0.73% of reference with a coverageData >= 2X There is a 0.12% 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 0.01% of reference with a coverageData >= 6X There is a 0.01% 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% 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 17342815 0.06957982664364154 1.3305275872581868 chr2 243199373 18627561 0.07659378710651528 0.7400195417959523 chr3 198022430 14772199 0.07459861491448216 0.31511551870317595 chr4 191154276 14768147 0.07725773814235785 0.3693884286679847 chr5 180915260 13607270 0.0752135005084701 0.33422534362871836 chr6 171115067 12683924 0.07412511488541217 0.3430541372241707 chr7 159138663 12627304 0.07934780751551243 1.108721194296665 chr8 146364022 11346109 0.07751979513107395 1.2365959414997894 chr9 141213431 9266132 0.06561792270311738 0.7743360442931823 chr10 135534747 10336177 0.07626219274973081 0.6247829497035051 chr11 135006516 10035896 0.07433638240097981 0.5291257973071261 chr12 133851895 10007043 0.07476205697349297 0.34400243043138506 chr13 115169878 7012270 0.060886319598254676 0.27428302063854787 chr14 107349540 6723728 0.0626339712308036 0.420395095258461 chr15 102531392 6060124 0.05910505925833914 0.28124252351354667 chr16 90354753 5963483 0.06600076699894249 0.3981488205628206 chr17 81195210 5635918 0.06941195176414963 0.3267448426238254 chr18 78077248 5904727 0.07562673059378322 1.5399530522767015 chr19 59128983 4601976 0.07782944617870394 1.3137497138532936 chr20 63025520 4281036 0.06792543718798354 0.33745562732884005 chr21 48129895 2783553 0.057834179775376617 0.4265699570705479 chr22 51304566 2371531 0.046224560207760064 0.3325319784895156 chrMT 16571 6729 0.4060708466598274 0.7390317722957631 chrX 155270560 8214334 0.05290335785483095 0.43574393062658245 chrY 59373566 2075991 0.03496490340499339 0.36029188938798384