BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716493.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 = 3,126,721 number of mapped reads = 2,814,364 (90.01%) number of supplementary alignments = 14,161 (0.45%) number of secondary alignments = 0 number of mapped bases = 161,920,803 bp number of sequenced bases = 161,875,295 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 134,802 duplication rate = 3.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3201 >>>>>>> ACTG content number of A's = 40,847,658 bp (25.23%) number of C's = 29,963,274 bp (18.51%) number of T's = 51,750,812 bp (31.97%) number of G's = 39,310,842 bp (24.28%) number of N's = 2,709 bp (0%) GC percentage = 42.79% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 864,289 number of insertions = 12,522 mapped reads with insertion percentage = 0.44% number of deletions = 27,137 mapped reads with deletion percentage = 0.96% homopolymer indels = 41.07% >>>>>>> Coverage mean coverageData = 0.0523X std coverageData = 0.4554X There is a 4.44% of reference with a coverageData >= 1X There is a 0.55% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 10918620 0.04380578855207747 0.7744073672170999 chr2 243199373 13760213 0.05657996906102221 0.5280724085880012 chr3 198022430 9317024 0.047050346771322825 0.24529773157066753 chr4 191154276 10464753 0.054745063615526966 0.3147894950177384 chr5 180915260 9244976 0.051101139837512875 0.26527370131043454 chr6 171115067 8698855 0.05083628901013141 0.30794664919074893 chr7 159138663 10299630 0.06472110426113106 0.6606243084889651 chr8 146364022 7026722 0.04800853313528102 0.4106896212777047 chr9 141213431 7798301 0.05522350774127144 0.5231627847047352 chr10 135534747 6357122 0.046904001672722344 0.4530823339552397 chr11 135006516 6506626 0.048194903422291116 0.3937163706702463 chr12 133851895 12635103 0.09439614582968736 0.41717516977291025 chr13 115169878 5897243 0.051204734279565706 0.25719715088815737 chr14 107349540 5910184 0.055055513046446215 0.31785262161450395 chr15 102531392 2994947 0.029210049152556126 0.19609513766831918 chr16 90354753 4585165 0.05074625127911091 0.29351387566059606 chr17 81195210 5091893 0.06271174124680508 0.30390942642065 chr18 78077248 5264490 0.06742668491594375 0.9163210310040318 chr19 59128983 2879068 0.04869131606745206 0.6067184793685929 chr20 63025520 3955307 0.0627572291351186 0.29993876960741445 chr21 48129895 1460385 0.030342576064211237 0.2647764866394105 chr22 51304566 1655373 0.03226560770439029 0.20104391159039942 chrMT 16571 24699 1.4904954438476856 1.478612658246575 chrX 155270560 8727304 0.05620707492779056 0.3724124848955908 chrY 59373566 446800 0.007525234377871122 0.16601358332226893