BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549144.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 = 12,589,379 number of mapped reads = 11,017,746 (87.52%) number of secondary alignments = 0 number of mapped bases = 437,312,523 bp number of sequenced bases = 437,267,375 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 570,621 duplication rate = 4.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.668 >>>>>>> ACTG content number of A's = 126,847,994 bp (29.01%) number of C's = 90,530,521 bp (20.7%) number of T's = 128,904,262 bp (29.48%) number of G's = 90,898,912 bp (20.79%) number of N's = 85,686 bp (0.02%) GC percentage = 41.49% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 1,340,707 number of insertions = 10,920 mapped reads with insertion percentage = 0.1% number of deletions = 35,295 mapped reads with deletion percentage = 0.32% homopolymer indels = 45.56% >>>>>>> Coverage mean coverageData = 0.1413X std coverageData = 0.7963X There is a 10.07% of reference with a coverageData >= 1X There is a 2.72% of reference with a coverageData >= 2X There is a 0.78% of reference with a coverageData >= 3X There is a 0.24% 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 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 35461449 0.1422722593738292 1.4648133348658214 chr2 243199373 38040079 0.15641520177767892 0.7609389578602419 chr3 198022430 29629956 0.14962929199485128 0.5083127436696997 chr4 191154276 27830639 0.14559255268765214 0.5475459169866893 chr5 180915260 28223318 0.1560029706725679 0.5362172710210258 chr6 171115067 26532333 0.1550555042590142 0.5725656015921907 chr7 159138663 23885028 0.1500894097621016 1.0921871624481723 chr8 146364022 23036513 0.15739191015125287 1.006355251291321 chr9 141213431 19318328 0.13680234141467748 0.7033666847099094 chr10 135534747 21426307 0.15808718778218547 0.7806744336203659 chr11 135006516 20817748 0.1541980981125385 0.6996086890010037 chr12 133851895 19677602 0.14701026085585117 0.5295304038510698 chr13 115169878 13986202 0.12143975701702141 0.46007120099247784 chr14 107349540 13531669 0.12605241717849933 0.5948191097309128 chr15 102531392 12928033 0.12608853491426314 0.45971801783396965 chr16 90354753 12256331 0.13564677665601055 0.5417549506844395 chr17 81195210 11660424 0.1436097523486915 0.5370107324646924 chr18 78077248 11514294 0.14747310253558119 1.364342196420816 chr19 59128983 8625100 0.14586924317639624 1.2195851773351376 chr20 63025520 9488365 0.15054798437204484 0.5452844352413481 chr21 48129895 5821321 0.12095021192130172 0.5505167880416342 chr22 51304566 5250650 0.10234274274925159 0.4455054000137499 chrMT 16571 230494 13.909480417597006 16.585673983541607 chrX 155270560 14825597 0.09548234385191887 0.5214607407404437 chrY 59373566 3314743 0.055828598875129046 0.4995567220847408