BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006440.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 4,644,701 number of mapped reads = 4,422,208 (95.21%) number of supplementary alignments = 12,219 (0.26%) number of secondary alignments = 0 number of mapped bases = 247,806,983 bp number of sequenced bases = 247,730,256 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 170,525 duplication rate = 3.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3775 >>>>>>> ACTG content number of A's = 69,694,800 bp (28.13%) number of C's = 51,984,420 bp (20.98%) number of T's = 71,901,600 bp (29.02%) number of G's = 54,144,324 bp (21.86%) number of N's = 5,112 bp (0%) GC percentage = 42.84% >>>>>>> Mismatches and indels general error rate = 0.0041 number of mismatches = 990,289 number of insertions = 15,781 mapped reads with insertion percentage = 0.36% number of deletions = 46,383 mapped reads with deletion percentage = 1.04% homopolymer indels = 45.24% >>>>>>> Coverage mean coverageData = 0.08X std coverageData = 0.5778X There is a 6.55% of reference with a coverageData >= 1X There is a 1.06% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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% 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 19968288 0.08011329287721212 0.7924783979194707 chr2 243199373 21096210 0.08674450817765883 0.47764465538129025 chr3 198022430 16566723 0.08366084084515073 0.33597046634479244 chr4 191154276 16659873 0.08715406920847536 0.3847406828354008 chr5 180915260 14953198 0.08265304983117511 0.33419945513064336 chr6 171115067 14470531 0.08456608324268722 0.3658000620772461 chr7 159138663 12262410 0.07705487635019279 0.5348226678387855 chr8 146364022 12640220 0.08636152400895351 1.6680195816290138 chr9 141213431 10757316 0.07617771145295663 0.42137470001668725 chr10 135534747 12093431 0.08922753218405315 0.553688915023965 chr11 135006516 11353307 0.08409451140861972 0.4295212066720954 chr12 133851895 11541711 0.08622747552434726 0.3471728836268456 chr13 115169878 8217977 0.07135526356987197 0.3094227152874313 chr14 107349540 7504926 0.06991111466336977 0.3284693326602795 chr15 102531392 7375183 0.07193097505201139 0.31291248622048023 chr16 90354753 7565217 0.0837279362603094 0.41956230280004797 chr17 81195210 7004360 0.08626567995821428 0.3981382084121755 chr18 78077248 6802969 0.08713126005670692 0.6629484175395832 chr19 59128983 5241062 0.08863778360605323 0.6187075300679545 chr20 63025520 5575182 0.08845911941702346 0.35799724963177676 chr21 48129895 4812312 0.09998592350970223 0.4423156261800514 chr22 51304566 3093055 0.06028810379177557 0.32945324805862536 chrMT 16571 135145 8.155512642568342 5.524532863157723 chrX 155270560 7923889 0.05103278432176711 0.28756764776689947 chrY 59373566 2192488 0.036927005529699866 0.4324846127839253