BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716255.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 = 1,623,162 number of mapped reads = 1,528,494 (94.17%) number of supplementary alignments = 33,641 (2.07%) number of secondary alignments = 0 number of mapped bases = 118,314,774 bp number of sequenced bases = 118,269,405 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 64,463 duplication rate = 3.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2965 >>>>>>> ACTG content number of A's = 29,218,590 bp (24.71%) number of C's = 23,733,515 bp (20.07%) number of T's = 34,643,932 bp (29.29%) number of G's = 30,668,707 bp (25.93%) number of N's = 4,661 bp (0%) GC percentage = 46% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 749,614 number of insertions = 9,913 mapped reads with insertion percentage = 0.64% number of deletions = 21,557 mapped reads with deletion percentage = 1.39% homopolymer indels = 38.35% >>>>>>> Coverage mean coverageData = 0.0382X std coverageData = 0.3118X There is a 3.23% of reference with a coverageData >= 1X There is a 0.42% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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% 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 12892866 0.05172651505650612 0.546825786908205 chr2 243199373 10679014 0.04391053261473663 0.3360958090375497 chr3 198022430 7459060 0.03766775309241483 0.22416295020170127 chr4 191154276 7229285 0.037819112139557895 0.30125789197167174 chr5 180915260 5948225 0.03287851450452549 0.20790260649432 chr6 171115067 7723867 0.04513843891958386 0.25525849548886737 chr7 159138663 7294407 0.04583679957145298 0.3945098392029946 chr8 146364022 7257117 0.049582656317001185 0.34629320691877036 chr9 141213431 3495217 0.024751307118938283 0.22872586320333038 chr10 135534747 6086678 0.04490861668115262 0.439495570167157 chr11 135006516 3553556 0.02632136659240951 0.23228397774230297 chr12 133851895 4342353 0.032441475707161264 0.206955079555223 chr13 115169878 2219894 0.0192749531261985 0.1567062068265747 chr14 107349540 2280697 0.021245521871821715 0.18598366961711682 chr15 102531392 2509727 0.024477644856318734 0.17831898176693145 chr16 90354753 3535094 0.03912460476760973 0.24486255164037016 chr17 81195210 2986068 0.03677640589882088 0.2416615749521777 chr18 78077248 3458293 0.04429322355214159 0.3314670077241207 chr19 59128983 2930690 0.049564356620170516 0.42429356730248696 chr20 63025520 3096369 0.04912881321724914 0.2680901020465311 chr21 48129895 1821392 0.03784325729362177 0.26643711261885517 chr22 51304566 1850059 0.036060318685865116 0.2266609226876345 chrMT 16571 15820 0.9546798624102347 1.2577890551948632 chrX 155270560 7250659 0.046696933404503725 0.2599405073835316 chrY 59373566 398367 0.0067095009924113365 0.2285115613352802