BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716227.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 = 2,595,338 number of mapped reads = 2,334,759 (89.96%) number of supplementary alignments = 12,424 (0.48%) number of secondary alignments = 0 number of mapped bases = 133,739,287 bp number of sequenced bases = 133,701,266 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 102,040 duplication rate = 3.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9392 >>>>>>> ACTG content number of A's = 34,840,078 bp (26.06%) number of C's = 24,629,285 bp (18.42%) number of T's = 40,860,676 bp (30.56%) number of G's = 33,369,151 bp (24.96%) number of N's = 2,076 bp (0%) GC percentage = 43.38% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 727,809 number of insertions = 7,895 mapped reads with insertion percentage = 0.34% number of deletions = 22,497 mapped reads with deletion percentage = 0.96% homopolymer indels = 43.03% >>>>>>> Coverage mean coverageData = 0.0432X std coverageData = 0.4111X There is a 3.76% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.06% 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 9560864 0.03835843602572208 0.7545367702219876 chr2 243199373 11237828 0.04620829347286187 0.4677180735248164 chr3 198022430 8074250 0.04077442136226689 0.22459037906514145 chr4 191154276 8288007 0.043357685600504174 0.2628539561574312 chr5 180915260 7334565 0.04054143912459347 0.2304415193255697 chr6 171115067 6955314 0.040646999249925785 0.26469242171598256 chr7 159138663 8540223 0.053665293141239974 0.555015267964043 chr8 146364022 5843640 0.03992538548851848 0.37159777287655804 chr9 141213431 6210582 0.04398010837935097 0.448791613294102 chr10 135534747 5142507 0.03794235141782498 0.3944950809250741 chr11 135006516 5089382 0.03769730640260356 0.33256301990464976 chr12 133851895 9942839 0.07428239249059566 0.3518884832993204 chr13 115169878 5067917 0.044003841004329275 0.23017912553764244 chr14 107349540 4719590 0.04396469700755122 0.27297452544322043 chr15 102531392 3435853 0.03351025410832226 0.2035575727990289 chr16 90354753 3724275 0.04121836291224215 0.2616568216764657 chr17 81195210 4024489 0.04956559629564355 0.2627061017521799 chr18 78077248 4272779 0.05472502053351061 0.8419344610795634 chr19 59128983 2312039 0.03910161958983803 0.5875379658246341 chr20 63025520 3964354 0.06290077416259318 0.29228004952100517 chr21 48129895 1607244 0.033393881287295556 0.25700572316521625 chr22 51304566 915398 0.01784242751415147 0.14520531390339003 chrMT 16571 51903 3.13215859030837 2.4733556229794775 chrX 155270560 7041288 0.045348506503744175 0.3167120664433338 chrY 59373566 382157 0.006436483872301017 0.14610063578260357