BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238307.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 = 1,520,305 number of mapped reads = 1,365,655 (89.83%) number of supplementary alignments = 7,445 (0.49%) number of secondary alignments = 0 number of mapped bases = 90,600,681 bp number of sequenced bases = 90,554,532 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 48,344 duplication rate = 2.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0167 >>>>>>> ACTG content number of A's = 24,660,593 bp (27.23%) number of C's = 16,139,181 bp (17.82%) number of T's = 29,137,529 bp (32.18%) number of G's = 20,567,616 bp (22.71%) number of N's = 49,613 bp (0.05%) GC percentage = 40.54% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 727,818 number of insertions = 6,593 mapped reads with insertion percentage = 0.48% number of deletions = 26,942 mapped reads with deletion percentage = 1.95% homopolymer indels = 46.12% >>>>>>> Coverage mean coverageData = 0.0293X std coverageData = 0.3421X There is a 2.62% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.03% 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 8521886 0.034190029159445905 0.6646913762203901 chr2 243199373 6069161 0.02495549608180939 0.4264006053257657 chr3 198022430 5957451 0.030084728280528626 0.1877602490164392 chr4 191154276 7482105 0.03914170876303076 0.2249689105385437 chr5 180915260 6338593 0.03503625398985138 0.20450309401831335 chr6 171115067 5479581 0.03202278499531546 0.22177246180670157 chr7 159138663 4234169 0.02660679007966782 0.39075049986306015 chr8 146364022 4327277 0.029565168686058654 0.5726173071726475 chr9 141213431 2864115 0.020282171318392512 0.3057449142593828 chr10 135534747 4122104 0.030413632601535016 0.25450741686872586 chr11 135006516 3372717 0.024981883096664756 0.2841618326286789 chr12 133851895 4316008 0.032244653689811414 0.20061692546972953 chr13 115169878 2141854 0.018597345392690267 0.1471843277970653 chr14 107349540 2317037 0.021584042185928323 0.1710241826212421 chr15 102531392 2977949 0.029044265779596554 0.20431276536494505 chr16 90354753 2563207 0.02836825861280369 0.1985864655227096 chr17 81195210 2511016 0.030925666674179425 0.22794166370235966 chr18 78077248 2496358 0.031972925070309854 0.5123166213423901 chr19 59128983 1725805 0.029187124696529957 0.43104996879569596 chr20 63025520 2068983 0.03282770217524584 0.2033973522496295 chr21 48129895 1210006 0.025140424677843158 0.18305350859331132 chr22 51304566 1149623 0.02240781064203915 0.16109547198167823 chrMT 16571 4235 0.2555669543177841 0.5287391992430064 chrX 155270560 6107061 0.039331738096391226 0.24504073511715488 chrY 59373566 242380 0.004082288067386756 0.09686022051337397