BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716356.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 = 461,603 number of mapped reads = 407,096 (88.19%) number of supplementary alignments = 2,689 (0.58%) number of secondary alignments = 0 number of mapped bases = 22,686,127 bp number of sequenced bases = 22,678,720 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,550 duplication rate = 3.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8545 >>>>>>> ACTG content number of A's = 5,596,230 bp (24.68%) number of C's = 4,490,335 bp (19.8%) number of T's = 7,029,881 bp (31%) number of G's = 5,562,095 bp (24.53%) number of N's = 179 bp (0%) GC percentage = 44.33% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 124,485 number of insertions = 1,522 mapped reads with insertion percentage = 0.37% number of deletions = 4,775 mapped reads with deletion percentage = 1.17% homopolymer indels = 40.46% >>>>>>> Coverage mean coverageData = 0.0073X std coverageData = 0.1037X There is a 0.66% 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 2747420 0.011022720781907299 0.14061025279116976 chr2 243199373 2218016 0.009120155091847215 0.12524282498617997 chr3 198022430 1460396 0.007374901923989116 0.09353294168056256 chr4 191154276 1029045 0.005383321898590435 0.0871186426845792 chr5 180915260 1661987 0.009186549548114405 0.10490379438329014 chr6 171115067 875016 0.005113611649405485 0.08069815869828703 chr7 159138663 1536521 0.009655233813294008 0.1376636484692958 chr8 146364022 1021937 0.006982159864396183 0.10380627491503144 chr9 141213431 571128 0.004044431156127068 0.07671974332757255 chr10 135534747 931679 0.006874097016612278 0.10000933550080802 chr11 135006516 946600 0.007011513429470323 0.1001894902488901 chr12 133851895 888734 0.006639681866289603 0.08952747254807461 chr13 115169878 669516 0.005813290867599946 0.08294632272273605 chr14 107349540 498137 0.004640327289711721 0.07502095820917147 chr15 102531392 963258 0.009394761752576225 0.10646769803621249 chr16 90354753 685484 0.007586584847395908 0.09627677275679156 chr17 81195210 756811 0.009320882352542718 0.10831022461155035 chr18 78077248 723972 0.009272509194996217 0.13630672916869396 chr19 59128983 361742 0.006117845794844806 0.09972834594943829 chr20 63025520 627849 0.009961821814401531 0.10932027641341777 chr21 48129895 278904 0.005794818376395793 0.0848705168607099 chr22 51304566 265328 0.005171625465070692 0.0785216472330761 chrMT 16571 616 0.037173375173495865 0.21004598766170648 chrX 155270560 900851 0.00580181458738862 0.0854739169765647 chrY 59373566 65180 0.001097794934533661 0.04140339144134546