BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716392.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 = 1,578,242 number of mapped reads = 1,456,625 (92.29%) number of supplementary alignments = 5,659 (0.36%) number of secondary alignments = 0 number of mapped bases = 85,396,161 bp number of sequenced bases = 85,367,844 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,751 duplication rate = 2.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8529 >>>>>>> ACTG content number of A's = 20,328,954 bp (23.81%) number of C's = 16,051,750 bp (18.8%) number of T's = 27,370,691 bp (32.06%) number of G's = 21,614,630 bp (25.32%) number of N's = 1,819 bp (0%) GC percentage = 44.12% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 433,027 number of insertions = 6,197 mapped reads with insertion percentage = 0.42% number of deletions = 17,558 mapped reads with deletion percentage = 1.2% homopolymer indels = 42.99% >>>>>>> Coverage mean coverageData = 0.0276X std coverageData = 0.26X There is a 2.49% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.02% 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 7333526 0.029422297808437557 0.4132227524370628 chr2 243199373 6740106 0.027714323095726072 0.3505131543528182 chr3 198022430 4916376 0.024827369303568287 0.17174905634234863 chr4 191154276 5326081 0.027862735333213262 0.2191844390168491 chr5 180915260 4979345 0.02752307903711384 0.17905229421651542 chr6 171115067 4597001 0.02686496917305359 0.2002904917057462 chr7 159138663 4923230 0.030936730943881312 0.3350301768169862 chr8 146364022 4495927 0.03071743273083873 0.3434113823512971 chr9 141213431 2885791 0.020435669465463237 0.18825438659388138 chr10 135534747 3811603 0.028122699782661638 0.2792980942109026 chr11 135006516 3059812 0.022664180149645517 0.1970725694293113 chr12 133851895 4253256 0.031775837017473677 0.19421030455353855 chr13 115169878 2581103 0.022411267987971648 0.16201385123562917 chr14 107349540 2512173 0.023401804982117295 0.16867675530764425 chr15 102531392 3180439 0.031019173132848913 0.1913411895639501 chr16 90354753 3011679 0.0333317163735703 0.21019533177270697 chr17 81195210 3205706 0.03948146694860448 0.22490693762466676 chr18 78077248 1610966 0.02063297620325962 0.31213883252536023 chr19 59128983 2236412 0.037822602157726946 0.3275971843677245 chr20 63025520 2891287 0.045874861484681125 0.24286000330519514 chr21 48129895 1120313 0.023276863579278533 0.20931425958863395 chr22 51304566 808210 0.01575317877165163 0.13628904627512686 chrMT 16571 7557 0.45603765614627967 0.7187476109482022 chrX 155270560 4579140 0.029491360113597837 0.19784134162549238 chrY 59373566 329122 0.00554324124644964 0.23590134942024543