BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549120.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 = 12,599,972 number of mapped reads = 7,207,143 (57.2%) number of secondary alignments = 0 number of mapped bases = 286,016,466 bp number of sequenced bases = 285,986,339 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 442,165 duplication rate = 4.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0358 >>>>>>> ACTG content number of A's = 84,557,701 bp (29.57%) number of C's = 58,410,011 bp (20.42%) number of T's = 84,656,681 bp (29.6%) number of G's = 58,350,661 bp (20.4%) number of N's = 11,285 bp (0%) GC percentage = 40.83% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 919,715 number of insertions = 7,267 mapped reads with insertion percentage = 0.1% number of deletions = 23,626 mapped reads with deletion percentage = 0.33% homopolymer indels = 44.58% >>>>>>> Coverage mean coverageData = 0.0924X std coverageData = 1.4337X There is a 6.14% of reference with a coverageData >= 1X There is a 1.94% of reference with a coverageData >= 2X There is a 0.65% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.08% 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% 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 23045779 0.0924602671300867 1.1792842080709938 chr2 243199373 24689227 0.1015184648522922 0.5988378204799485 chr3 198022430 19794136 0.09995906019333264 0.4418031218336059 chr4 191154276 19421244 0.10159984074852713 0.5231745264250967 chr5 180915260 17970833 0.09933287551309934 0.446610863981376 chr6 171115067 17000332 0.099350292747745 0.4589668722904774 chr7 159138663 16033687 0.10075293267984789 0.853989598105149 chr8 146364022 15593070 0.10653622240580407 5.955045876176868 chr9 141213431 12172211 0.08619726122226999 0.528795623626598 chr10 135534747 13664643 0.10082021992485808 0.6708883493869654 chr11 135006516 13320947 0.09866891906165477 0.5584548834650884 chr12 133851895 13076106 0.09769085450751369 0.446146060147242 chr13 115169878 9507048 0.08254804264010769 0.4011661346380823 chr14 107349540 8818555 0.08214804646577899 0.47258334026683957 chr15 102531392 8428424 0.08220335095031188 0.39430245605702613 chr16 90354753 7918011 0.08763247905729984 0.44440828241245084 chr17 81195210 7283232 0.08970026680145295 0.43547209604449966 chr18 78077248 7702543 0.09865284954715617 0.9629255868172968 chr19 59128983 5198547 0.08791876227602291 0.9340687685112599 chr20 63025520 5981524 0.0949063807803569 0.45920353856752305 chr21 48129895 3832039 0.07961868605780253 0.48301569738175776 chr22 51304566 3230992 0.06297669490080084 0.35521403658655726 chrMT 16571 86523 5.2213505521694525 6.664396097719836 chrX 155270560 9508312 0.06123705614251665 0.39021011177277126 chrY 59373566 2738501 0.04612323605424003 0.5557289230196047