BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716499.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 778,912 number of mapped reads = 708,943 (91.02%) number of supplementary alignments = 3,307 (0.42%) number of secondary alignments = 0 number of mapped bases = 41,064,814 bp number of sequenced bases = 41,054,365 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,737 duplication rate = 1.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6435 >>>>>>> ACTG content number of A's = 9,929,582 bp (24.19%) number of C's = 7,278,707 bp (17.73%) number of T's = 13,615,104 bp (33.16%) number of G's = 10,229,977 bp (24.92%) number of N's = 995 bp (0%) GC percentage = 42.65% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 201,011 number of insertions = 2,650 mapped reads with insertion percentage = 0.37% number of deletions = 6,726 mapped reads with deletion percentage = 0.94% homopolymer indels = 44.22% >>>>>>> Coverage mean coverageData = 0.0133X std coverageData = 0.1623X There is a 1.24% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 4122895 0.016541162398949448 0.29304523568258567 chr2 243199373 3613190 0.014856905079274197 0.18110326704270724 chr3 198022430 3680479 0.01858617228361454 0.14404631213766736 chr4 191154276 1945388 0.010177057195414242 0.10923575394349999 chr5 180915260 1845644 0.010201704378060757 0.10704927452721477 chr6 171115067 3065674 0.01791586242957787 0.17894194275423547 chr7 159138663 2358783 0.014822186862283744 0.18508546491848557 chr8 146364022 3208854 0.02192378944054981 0.1646309712483911 chr9 141213431 1528049 0.010820847487233705 0.1326700498049066 chr10 135534747 2139130 0.01578288997728383 0.19038580182452475 chr11 135006516 1354551 0.010033226840695601 0.12787390720119038 chr12 133851895 1810244 0.013524231390224248 0.12318204047384881 chr13 115169878 947954 0.008230919546515452 0.09471823419984501 chr14 107349540 882717 0.008222829832340222 0.10004642861488512 chr15 102531392 1212550 0.011826134185323457 0.11404016705647638 chr16 90354753 862509 0.009545806627350306 0.11334894273760886 chr17 81195210 864698 0.010649618370344753 0.11030002645603405 chr18 78077248 817689 0.01047282045596689 0.21563354235131185 chr19 59128983 748291 0.012655232037391884 0.1993936782711106 chr20 63025520 625520 0.009924868529446485 0.10437997829306574 chr21 48129895 382640 0.007950152394888874 0.10243215966979459 chr22 51304566 631840 0.012315473051657819 0.11626920777860399 chrMT 16571 90735 5.475529539557058 3.6470161007190796 chrX 155270560 2223599 0.014320802346562026 0.13449566736541715 chrY 59373566 101191 0.001704310635477074 0.05192910613247226