BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819093.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 = 2,498,411 number of mapped reads = 2,239,058 (89.62%) number of supplementary alignments = 9,255 (0.37%) number of secondary alignments = 0 number of mapped bases = 129,143,875 bp number of sequenced bases = 129,105,014 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 101,063 duplication rate = 3.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3033 >>>>>>> ACTG content number of A's = 32,590,133 bp (25.24%) number of C's = 24,064,970 bp (18.64%) number of T's = 41,499,127 bp (32.14%) number of G's = 30,949,027 bp (23.97%) number of N's = 1,757 bp (0%) GC percentage = 42.61% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 669,781 number of insertions = 8,164 mapped reads with insertion percentage = 0.36% number of deletions = 23,398 mapped reads with deletion percentage = 1.04% homopolymer indels = 42.13% >>>>>>> Coverage mean coverageData = 0.0417X std coverageData = 0.3612X There is a 3.63% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% 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% 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 12667962 0.050824194335708395 0.6674938961477024 chr2 243199373 10277381 0.04225907687681415 0.43778135129249557 chr3 198022430 7026058 0.035481122012289215 0.21576839511529575 chr4 191154276 7214498 0.037741755774273134 0.248595769100679 chr5 180915260 7068359 0.039069998849184974 0.22329302575430648 chr6 171115067 5446008 0.03182658368710454 0.27102032290883665 chr7 159138663 6481273 0.04072720530522492 0.483425180846301 chr8 146364022 11743228 0.08023302338603404 0.3833277304698568 chr9 141213431 5417487 0.0383638224893778 0.3072982661673737 chr10 135534747 6687788 0.04934371552705964 0.3720357455562613 chr11 135006516 4412552 0.03268399282298345 0.31707467633897224 chr12 133851895 5997716 0.044808599833420365 0.24116596224984913 chr13 115169878 2892186 0.025112347518506533 0.1790730370331094 chr14 107349540 3114065 0.029008647824666972 0.19912339189825895 chr15 102531392 3446694 0.03361598757968681 0.21531454723728027 chr16 90354753 4064117 0.044979559625380194 0.26168213660701206 chr17 81195210 4578119 0.05638410196857672 0.284346396143663 chr18 78077248 3127138 0.040051847114283536 0.5956380371302378 chr19 59128983 2678337 0.045296517276476746 0.4673619527459001 chr20 63025520 3675136 0.05831187112775904 0.27622630736204706 chr21 48129895 1760570 0.03657955206426276 0.23797716462793087 chr22 51304566 1071086 0.02087701121962517 0.1614065678191042 chrMT 16571 30360 1.832116347836582 1.6571600685979821 chrX 155270560 7850798 0.05056205117055029 0.2979870266888783 chrY 59373566 414959 0.006988951952119567 0.1861312196775228