BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238625.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 967,432 number of mapped reads = 755,203 (78.06%) number of supplementary alignments = 5,930 (0.61%) number of secondary alignments = 0 number of mapped bases = 45,953,679 bp number of sequenced bases = 45,921,881 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 151,202 duplication rate = 15.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.0622 >>>>>>> ACTG content number of A's = 11,461,178 bp (24.96%) number of C's = 7,928,856 bp (17.27%) number of T's = 15,560,062 bp (33.88%) number of G's = 10,969,692 bp (23.89%) number of N's = 2,093 bp (0%) GC percentage = 41.15% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 318,245 number of insertions = 2,838 mapped reads with insertion percentage = 0.37% number of deletions = 18,667 mapped reads with deletion percentage = 2.44% homopolymer indels = 40.82% >>>>>>> Coverage mean coverageData = 0.0148X std coverageData = 0.2716X There is a 0.93% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.12% 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% 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 2810805 0.011277023057045863 0.19839073583175765 chr2 243199373 10086906 0.04147587173261339 0.5612790413520644 chr3 198022430 868850 0.004387634269511792 0.09700561098448642 chr4 191154276 2630136 0.0137592318363833 0.17817191006919528 chr5 180915260 1903555 0.01052180451776152 0.15649138338294247 chr6 171115067 3378286 0.0197427734402839 0.33628494926522545 chr7 159138663 7324492 0.04602584853939611 0.5585695782850602 chr8 146364022 2442334 0.016686710071413587 0.2626316203091948 chr9 141213431 1664721 0.011788687437245258 0.1694751883093275 chr10 135534747 604558 0.004460538816662269 0.10512857920047342 chr11 135006516 6070237 0.04496254832618597 0.38593360876683147 chr12 133851895 1039943 0.007769355824211528 0.13251291896736103 chr13 115169878 367789 0.003193447856218099 0.12182626461149118 chr14 107349540 335398 0.0031243543288587915 0.11506358660374803 chr15 102531392 340065 0.003316691535798129 0.17007786309803857 chr16 90354753 670816 0.007424246956881172 0.13200088217279698 chr17 81195210 545297 0.0067158764661117325 0.1403967318825777 chr18 78077248 351058 0.004496290647949067 0.2809039093541703 chr19 59128983 760567 0.012862845958301025 0.17487053867618216 chr20 63025520 268726 0.0042637649003133965 0.09685041946894371 chr21 48129895 161225 0.003349789148719315 0.08283744466324251 chr22 51304566 144599 0.002818443099197058 0.07624142941874391 chrMT 16571 28523 1.7212600325870497 2.2375700212537395 chrX 155270560 1060941 0.006832853568635291 0.13483354602585104 chrY 59373566 93852 0.0015807034396418096 0.08731752331365548