BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083635.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 = 2,968,426 number of mapped reads = 2,382,459 (80.26%) number of supplementary alignments = 16,831 (0.57%) number of secondary alignments = 0 number of mapped bases = 135,962,730 bp number of sequenced bases = 135,923,782 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 100,334 duplication rate = 3.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4599 >>>>>>> ACTG content number of A's = 40,846,688 bp (30.05%) number of C's = 27,577,649 bp (20.29%) number of T's = 38,865,789 bp (28.59%) number of G's = 28,626,214 bp (21.06%) number of N's = 7,442 bp (0.01%) GC percentage = 41.35% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,079,850 number of insertions = 8,769 mapped reads with insertion percentage = 0.37% number of deletions = 25,119 mapped reads with deletion percentage = 1.05% homopolymer indels = 45.46% >>>>>>> Coverage mean coverageData = 0.0439X std coverageData = 0.2985X There is a 3.71% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 11410355 0.045778642212490214 0.4373638157897219 chr2 243199373 12968058 0.053322744380595095 0.30907360514608906 chr3 198022430 8137750 0.04109509210648511 0.2324069857642451 chr4 191154276 9843095 0.05149293652212101 0.270111016725468 chr5 180915260 9219254 0.050958962776274375 0.259307682787051 chr6 171115067 8445050 0.049353047326919496 0.27632615386327586 chr7 159138663 7595996 0.047731932999839265 0.4190839016745712 chr8 146364022 6822093 0.04661045048352115 0.41692516704916094 chr9 141213431 6172692 0.04371179112559059 0.2684307710756534 chr10 135534747 5188068 0.038278508757610324 0.2674829426811896 chr11 135006516 7066421 0.05234133291759044 0.2735601811928626 chr12 133851895 6558446 0.04899778221294514 0.25807364761762125 chr13 115169878 4825504 0.04189901112858694 0.23545415499562933 chr14 107349540 2400032 0.022357170789926068 0.18538160016554003 chr15 102531392 1489776 0.014529950007896118 0.14123663178920462 chr16 90354753 2487007 0.0275249161491261 0.19644552169655233 chr17 81195210 3758962 0.04629536643848818 0.25349566605938495 chr18 78077248 3832647 0.04908788537218935 0.3680342286209804 chr19 59128983 1823849 0.03084526246629339 0.3564903325651757 chr20 63025520 2924368 0.046399744103658325 0.2533497635816682 chr21 48129895 1910227 0.0396889916339938 0.23527048432535005 chr22 51304566 961262 0.018736383034601636 0.154153807164938 chrMT 16571 47026 2.837849254722105 2.2722940815611388 chrX 155270560 9740586 0.06273298685855194 0.30741830603761017 chrY 59373566 334206 0.005628868577642785 0.10494150625084243