BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008786.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 = 1,549,805 number of mapped reads = 1,200,886 (77.49%) number of supplementary alignments = 5,963 (0.38%) number of secondary alignments = 0 number of mapped bases = 80,893,888 bp number of sequenced bases = 80,856,025 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,129 duplication rate = 1.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2965 >>>>>>> ACTG content number of A's = 23,771,334 bp (29.4%) number of C's = 14,196,496 bp (17.56%) number of T's = 25,130,849 bp (31.08%) number of G's = 17,741,471 bp (21.94%) number of N's = 15,875 bp (0.02%) GC percentage = 39.5% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 711,419 number of insertions = 7,196 mapped reads with insertion percentage = 0.59% number of deletions = 22,834 mapped reads with deletion percentage = 1.88% homopolymer indels = 46.99% >>>>>>> Coverage mean coverageData = 0.0261X std coverageData = 0.2607X There is a 2.4% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% 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 6591858 0.026446706425658214 0.44065177062152316 chr2 243199373 7653609 0.03147051287833707 0.29238565635508884 chr3 198022430 6187711 0.031247525848460703 0.18960059700690307 chr4 191154276 3882128 0.020308873446283775 0.15472579738533646 chr5 180915260 3891161 0.021508196710437803 0.1547532905169992 chr6 171115067 4705484 0.0274989460746902 0.19485286363535673 chr7 159138663 4504371 0.028304692995944045 0.3516616969314614 chr8 146364022 8084518 0.05523569173304079 0.41554511670804367 chr9 141213431 2421603 0.017148531714380626 0.22553763437741095 chr10 135534747 4240124 0.03128440561445103 0.29576685442739004 chr11 135006516 3770166 0.027925807669905354 0.2614406996192296 chr12 133851895 3712840 0.027738419392568183 0.17712618435904173 chr13 115169878 2023148 0.01756664186099077 0.13842198866409464 chr14 107349540 2962074 0.027592796392047883 0.17990062430502127 chr15 102531392 2274689 0.022185293261209212 0.15766556653338135 chr16 90354753 1798558 0.019905516204554285 0.1696714669743703 chr17 81195210 2161686 0.026623319282011833 0.21608010457818327 chr18 78077248 1367809 0.017518663055337197 0.4035118065710705 chr19 59128983 1384508 0.02341504842050133 0.2626977986193001 chr20 63025520 1691893 0.026844570262966494 0.17546734020891977 chr21 48129895 755173 0.01569031056477476 0.14074699083965972 chr22 51304566 851877 0.01660431159285121 0.13471344810068606 chrMT 16571 33529 2.0233540522599722 1.8831457629731396 chrX 155270560 3761059 0.024222615027600855 0.18216633467458693 chrY 59373566 182312 0.0030705920543832588 0.0887564721311233