BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237829.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,589,255 number of mapped reads = 1,418,672 (89.27%) number of supplementary alignments = 15,211 (0.96%) number of secondary alignments = 0 number of mapped bases = 95,504,120 bp number of sequenced bases = 95,455,139 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 248,745 duplication rate = 11.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8582 >>>>>>> ACTG content number of A's = 27,040,690 bp (28.33%) number of C's = 17,176,660 bp (17.99%) number of T's = 30,884,997 bp (32.36%) number of G's = 20,192,479 bp (21.15%) number of N's = 160,313 bp (0.17%) GC percentage = 39.15% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 823,922 number of insertions = 7,334 mapped reads with insertion percentage = 0.51% number of deletions = 27,450 mapped reads with deletion percentage = 1.91% homopolymer indels = 46.28% >>>>>>> Coverage mean coverageData = 0.0309X std coverageData = 0.4627X There is a 1.12% of reference with a coverageData >= 1X There is a 0.61% of reference with a coverageData >= 2X There is a 0.41% of reference with a coverageData >= 3X There is a 0.28% of reference with a coverageData >= 4X There is a 0.19% of reference with a coverageData >= 5X There is a 0.13% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% 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 6624664 0.026578324954303723 0.6073828996969987 chr2 243199373 6359058 0.026147509845759347 0.4366392388023267 chr3 198022430 6889589 0.03479196270846691 0.4220463207246854 chr4 191154276 5044611 0.026390259771118068 0.37647184008805085 chr5 180915260 6239435 0.03448816313228635 0.4353578621421492 chr6 171115067 6282026 0.036712290215799644 0.45685705462066756 chr7 159138663 6661658 0.04186071363437306 0.5308043939066666 chr8 146364022 5790042 0.039559188937838836 0.6567485067162177 chr9 141213431 4058117 0.028737471862715382 0.41963058245450624 chr10 135534747 5728414 0.04226527976622851 0.5512910769283537 chr11 135006516 3581495 0.026528312159392366 0.3899540455394402 chr12 133851895 4515642 0.033736108106650266 0.4246596529644714 chr13 115169878 2549064 0.022133078928849782 0.33846847254248397 chr14 107349540 2983871 0.027795843372966478 0.39373591219532084 chr15 102531392 2841721 0.027715619036948216 0.3840256941852726 chr16 90354753 2946241 0.032607482198529165 0.4117107588980703 chr17 81195210 2297112 0.028291225553822696 0.38002133997800014 chr18 78077248 2237072 0.02865203445695217 0.6585178377918521 chr19 59128983 1776436 0.030043405278930638 0.4924950270593529 chr20 63025520 2161531 0.034296123221196746 0.4332877797373863 chr21 48129895 1537797 0.03195097350617532 0.40909633857339645 chr22 51304566 926811 0.01806488334780963 0.2862639005416347 chrMT 16571 9780 0.5901876772675155 1.3093196922923165 chrX 155270560 5192929 0.033444388942759015 0.4228244833651787 chrY 59373566 269004 0.0045307031078443225 0.14358910705126593