BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238039.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 = 2,005,845 number of mapped reads = 1,787,283 (89.1%) number of supplementary alignments = 13,146 (0.66%) number of secondary alignments = 0 number of mapped bases = 117,176,659 bp number of sequenced bases = 117,116,634 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 91,948 duplication rate = 3.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5843 >>>>>>> ACTG content number of A's = 31,250,802 bp (26.68%) number of C's = 21,503,325 bp (18.36%) number of T's = 36,940,854 bp (31.54%) number of G's = 27,194,423 bp (23.22%) number of N's = 227,230 bp (0.19%) GC percentage = 41.58% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,013,328 number of insertions = 9,576 mapped reads with insertion percentage = 0.53% number of deletions = 36,231 mapped reads with deletion percentage = 2% homopolymer indels = 46.03% >>>>>>> Coverage mean coverageData = 0.0379X std coverageData = 0.369X There is a 3.22% of reference with a coverageData >= 1X There is a 0.4% 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 9239384 0.03706864987108698 0.6753607176572832 chr2 243199373 7896826 0.03247058535796472 0.5247137945025258 chr3 198022430 5319854 0.026864906162397867 0.19016319724542827 chr4 191154276 3825970 0.020015089801077742 0.2121585170643314 chr5 180915260 10141049 0.05605413827446065 0.27504655114574705 chr6 171115067 8956574 0.05234240419050883 0.33135505466176945 chr7 159138663 7072888 0.04444481225784837 0.4917582054408111 chr8 146364022 6847875 0.0467866003299636 0.3568894085963191 chr9 141213431 5482886 0.03882694415944047 0.31273687141020085 chr10 135534747 4896504 0.03612729656698293 0.31518007117733293 chr11 135006516 4217206 0.03123705525442935 0.24191095926801393 chr12 133851895 4498434 0.03360754810382027 0.21684153222071734 chr13 115169878 1916876 0.01664390058657525 0.16393053299493496 chr14 107349540 3499737 0.0326013227443732 0.22019279256798133 chr15 102531392 3019418 0.029448717520581404 0.20281606854428688 chr16 90354753 3574518 0.039560929351442085 0.24600314656827119 chr17 81195210 2517787 0.03100905829297073 0.22338362607513484 chr18 78077248 4129676 0.05289218185558999 0.6083249668687913 chr19 59128983 3169620 0.05360518377256717 0.46539829429221763 chr20 63025520 3379877 0.05362711803091827 0.26987627343850196 chr21 48129895 2065182 0.04290850831899799 0.26146559061133995 chr22 51304566 1036416 0.020201242906917875 0.16177658986384819 chrMT 16571 198257 11.964093898980146 7.214201994236636 chrX 155270560 9914065 0.06385025596610201 0.3171950203719743 chrY 59373566 359780 0.006059598980462114 0.16484176520236835