BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716853.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 = 3,808,688 number of mapped reads = 3,467,962 (91.05%) number of supplementary alignments = 17,533 (0.46%) number of secondary alignments = 0 number of mapped bases = 202,344,385 bp number of sequenced bases = 202,289,923 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 199,300 duplication rate = 4.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4281 >>>>>>> ACTG content number of A's = 48,815,693 bp (24.13%) number of C's = 38,971,740 bp (19.27%) number of T's = 63,732,848 bp (31.51%) number of G's = 50,766,867 bp (25.1%) number of N's = 2,775 bp (0%) GC percentage = 44.36% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 974,767 number of insertions = 10,645 mapped reads with insertion percentage = 0.31% number of deletions = 34,604 mapped reads with deletion percentage = 0.99% homopolymer indels = 44.54% >>>>>>> Coverage mean coverageData = 0.0654X std coverageData = 0.5213X There is a 5.33% of reference with a coverageData >= 1X There is a 0.85% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% 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 22669781 0.09095175333585227 0.9467645641786936 chr2 243199373 16966558 0.06976398742606955 0.6879852887725406 chr3 198022430 17806663 0.08992245474414186 0.35956004150587184 chr4 191154276 9211840 0.048190603907809 0.2842221287248831 chr5 180915260 8798083 0.04863096125777339 0.2642663466908331 chr6 171115067 14716083 0.0860010942227548 0.7398959818132933 chr7 159138663 11583738 0.07279021817595639 0.678706180014812 chr8 146364022 16071104 0.1098022846078936 0.46761443048991524 chr9 141213431 7370327 0.05219281868450601 0.4071310372632317 chr10 135534747 10861683 0.0801394715408293 0.507311567512631 chr11 135006516 6698730 0.049617827335089515 0.4164597707876271 chr12 133851895 8883332 0.06636687511969853 0.31845438437458107 chr13 115169878 4479273 0.038892747633196244 0.23469548250168504 chr14 107349540 4375202 0.04075659755971008 0.2858161373651617 chr15 102531392 6004969 0.05856712644650333 0.29644293486795315 chr16 90354753 4362035 0.048276763038685964 0.3020018141709551 chr17 81195210 4477573 0.05514577768811731 0.2989811514209233 chr18 78077248 3861148 0.04945292129148814 0.8209441036742423 chr19 59128983 3942250 0.06667204135745071 0.6468631020241878 chr20 63025520 3124812 0.04958010659808915 0.27138900258533927 chr21 48129895 1845550 0.038345190655412816 0.2674765841465132 chr22 51304566 3276497 0.06386365299338075 0.3023930501777958 chrMT 16571 5007 0.3021543660611912 0.6012334739931997 chrX 155270560 10489596 0.06755688908444718 0.37747225999723316 chrY 59373566 462551 0.007790520784956727 0.15746270989652356