BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926900.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 43,698,852 number of mapped reads = 41,024,737 (93.88%) number of supplementary alignments = 583,325 (1.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 20,577,558 number of mapped paired reads (second in pair) = 20,447,179 number of mapped paired reads (both in pair) = 40,601,748 number of mapped paired reads (singletons) = 422,989 number of mapped bases = 3,921,330,746 bp number of sequenced bases = 3,918,295,936 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,395,443 duplication rate = 6.73% >>>>>>> Insert size mean insert size = 121,829.1629 std insert size = 3,435,439.9471 median insert size = 171 >>>>>>> Mapping quality mean mapping quality = 53.3457 >>>>>>> ACTG content number of A's = 1,129,520,693 bp (28.83%) number of C's = 794,285,897 bp (20.27%) number of T's = 1,132,676,552 bp (28.91%) number of G's = 861,542,737 bp (21.99%) number of N's = 270,057 bp (0.01%) GC percentage = 42.26% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 36,408,000 number of insertions = 627,920 mapped reads with insertion percentage = 1.51% number of deletions = 2,157,218 mapped reads with deletion percentage = 5.12% homopolymer indels = 53.24% >>>>>>> Coverage mean coverageData = 1.2667X std coverageData = 4.8291X There is a 38.05% of reference with a coverageData >= 1X There is a 24.8% of reference with a coverageData >= 2X There is a 16.37% of reference with a coverageData >= 3X There is a 11.46% of reference with a coverageData >= 4X There is a 8.21% of reference with a coverageData >= 5X There is a 6.02% of reference with a coverageData >= 6X There is a 4.48% of reference with a coverageData >= 7X There is a 3.39% of reference with a coverageData >= 8X There is a 2.58% of reference with a coverageData >= 9X There is a 1.99% of reference with a coverageData >= 10X There is a 1.54% of reference with a coverageData >= 11X There is a 1.21% of reference with a coverageData >= 12X There is a 0.95% of reference with a coverageData >= 13X There is a 0.75% of reference with a coverageData >= 14X There is a 0.6% of reference with a coverageData >= 15X There is a 0.48% of reference with a coverageData >= 16X There is a 0.38% of reference with a coverageData >= 17X There is a 0.31% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.2% of reference with a coverageData >= 20X There is a 0.17% of reference with a coverageData >= 21X There is a 0.14% of reference with a coverageData >= 22X There is a 0.11% of reference with a coverageData >= 23X There is a 0.09% of reference with a coverageData >= 24X There is a 0.08% of reference with a coverageData >= 25X There is a 0.07% of reference with a coverageData >= 26X There is a 0.06% of reference with a coverageData >= 27X There is a 0.05% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 317767173 1.2748901957600338 4.5012522745515735 chr2 243199373 340311652 1.3993113872049332 6.8851433940234985 chr3 198022430 265233812 1.339412974580708 2.7513725053927125 chr4 191154276 233873572 1.2234807240200056 2.900919385170326 chr5 180915260 235069895 1.2993370211003759 2.599840126959937 chr6 171115067 224865145 1.3141165704595728 2.6494302213987844 chr7 159138663 201717783 1.2675598700989463 3.3568354986275746 chr8 146364022 197902185 1.3521231672630587 3.0611952552009343 chr9 141213431 167318799 1.1848646252352582 4.851999844793647 chr10 135534747 198333634 1.4633416034635014 14.007958529458058 chr11 135006516 189439973 1.4031913318909732 3.450978188993189 chr12 133851895 177871585 1.3288686349939236 2.9827814857563446 chr13 115169878 116711498 1.013385618069336 2.4170340921055926 chr14 107349540 120363968 1.1212341291821093 2.5208748019632643 chr15 102531392 117208319 1.143145691419073 2.630574153539051 chr16 90354753 124877468 1.3820796787524836 7.61952820452565 chr17 81195210 104178971 1.2830679420620994 3.176232860094109 chr18 78077248 104047031 1.3326165261357572 5.142390319332606 chr19 59128983 62430813 1.0558411430820651 3.073142444016576 chr20 63025520 94484720 1.4991501855121545 3.134575865301219 chr21 48129895 50118705 1.0413217190687825 3.9163517868820334 chr22 51304566 50398238 0.9823343598696459 2.530423105410847 chrMT 16571 629427 37.98364612877919 24.3673816775972 chrX 155270560 220854490 1.4223848358632827 3.0143071711839577 chrY 59373566 5321890 0.08963399638148735 1.7886338750215633