BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083641.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,124,738 number of mapped reads = 1,680,627 (79.1%) number of supplementary alignments = 11,318 (0.53%) number of secondary alignments = 0 number of mapped bases = 100,347,840 bp number of sequenced bases = 100,315,286 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 60,415 duplication rate = 2.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0054 >>>>>>> ACTG content number of A's = 29,364,696 bp (29.27%) number of C's = 19,483,174 bp (19.42%) number of T's = 29,388,523 bp (29.3%) number of G's = 22,065,222 bp (22%) number of N's = 13,671 bp (0.01%) GC percentage = 41.42% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 834,071 number of insertions = 7,196 mapped reads with insertion percentage = 0.42% number of deletions = 20,579 mapped reads with deletion percentage = 1.21% homopolymer indels = 45.47% >>>>>>> Coverage mean coverageData = 0.0324X std coverageData = 0.2748X There is a 2.91% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 8038509 0.032250708013281136 0.4881821264752873 chr2 243199373 8843688 0.036363942434999616 0.2649164404583027 chr3 198022430 7151000 0.03611207073865319 0.20547324044841453 chr4 191154276 6907895 0.03613780002493902 0.21383428439617577 chr5 180915260 6781511 0.03748446095702485 0.2100484761487291 chr6 171115067 6262427 0.03659775325337073 0.2304898737978786 chr7 159138663 5663207 0.03558661919888066 0.3711554890701463 chr8 146364022 5066334 0.034614613145845366 0.374542053304336 chr9 141213431 4270199 0.030239326172876575 0.24014774243670933 chr10 135534747 4595467 0.03390619086041456 0.2703267944118184 chr11 135006516 4786484 0.03545372580387157 0.22969600660423556 chr12 133851895 4604562 0.034400424439265505 0.20411169212551514 chr13 115169878 3406100 0.029574573309871875 0.18604580530411 chr14 107349540 3202645 0.02983380273450636 0.19256791343141777 chr15 102531392 2849666 0.027793107500188822 0.1810595467590421 chr16 90354753 2764113 0.03059178303547573 0.20156858448380185 chr17 81195210 2618801 0.032253146460240696 0.20807200639109205 chr18 78077248 2767576 0.035446638693003116 0.4088947684190988 chr19 59128983 1794230 0.030344340608733283 0.35415997737660326 chr20 63025520 2129125 0.03378195054955516 0.20553530666350942 chr21 48129895 1328699 0.02760652189247452 0.1882360936700908 chr22 51304566 1050836 0.02048230950828041 0.15388419912964063 chrMT 16571 13249 0.7995292981715044 0.9556527573573292 chrX 155270560 3201027 0.02061580121820904 0.17130767500296562 chrY 59373566 250490 0.004218880840002098 0.11247928793946343