BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818797.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 = 1,814,430 number of mapped reads = 1,766,647 (97.37%) number of supplementary alignments = 13,037 (0.72%) number of secondary alignments = 0 number of mapped bases = 119,988,891 bp number of sequenced bases = 119,937,880 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 787,625 duplication rate = 37.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6216 >>>>>>> ACTG content number of A's = 35,552,292 bp (29.64%) number of C's = 27,410,785 bp (22.85%) number of T's = 32,773,686 bp (27.33%) number of G's = 24,193,438 bp (20.17%) number of N's = 7,679 bp (0.01%) GC percentage = 43.03% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 636,075 number of insertions = 13,747 mapped reads with insertion percentage = 0.77% number of deletions = 30,934 mapped reads with deletion percentage = 1.73% homopolymer indels = 40.24% >>>>>>> Coverage mean coverageData = 0.0388X std coverageData = 0.5211X There is a 1.86% of reference with a coverageData >= 1X There is a 0.86% of reference with a coverageData >= 2X There is a 0.46% of reference with a coverageData >= 3X There is a 0.26% of reference with a coverageData >= 4X There is a 0.15% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% 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 9983578 0.04005437563182641 0.703793106973235 chr2 243199373 10633499 0.04372338163881697 0.9146505393469757 chr3 198022430 8121495 0.041013005445898226 0.36983630714957305 chr4 191154276 7782687 0.040714166394059635 0.41331418236748985 chr5 180915260 7489984 0.041400509829850725 0.39946692682305934 chr6 171115067 6971269 0.04074024060078824 0.4055949152865133 chr7 159138663 6461515 0.040603049429917604 0.431631994042405 chr8 146364022 6187673 0.042275915320228084 0.4213784936635677 chr9 141213431 5120463 0.036260453157603685 0.4423680521580855 chr10 135534747 5752851 0.04244558039422909 0.5767079309678306 chr11 135006516 5695765 0.0421888155383552 0.42844872809869866 chr12 133851895 5503005 0.04111264169999237 0.4198057535095523 chr13 115169878 3816790 0.03314052308017553 0.3390913852827306 chr14 107349540 3741998 0.034858072051356714 0.3920523102116963 chr15 102531392 3417344 0.03332973378533669 0.33165108626055667 chr16 90354753 3622214 0.04008880418277498 0.6100159238513085 chr17 81195210 3230381 0.03978536418589225 0.3904325623704431 chr18 78077248 3341995 0.042803698716430166 0.5295210827713008 chr19 59128983 2459585 0.041596944090853044 0.5918936214833417 chr20 63025520 2619637 0.041564702679168695 0.40554846825435237 chr21 48129895 1635344 0.033977718006656776 0.3651345027926678 chr22 51304566 1523257 0.02969047628236442 0.3565566869910424 chrMT 16571 17761 1.0718122020397078 1.9605183735596685 chrX 155270560 3663298 0.02359299792568533 0.31416012678439104 chrY 59373566 1195503 0.02013527366707265 0.9346523896964157