BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240187.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 = 1,320,799 number of mapped reads = 1,057,589 (80.07%) number of supplementary alignments = 9,960 (0.75%) number of secondary alignments = 0 number of mapped bases = 70,500,594 bp number of sequenced bases = 70,462,577 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 134,372 duplication rate = 8.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.913 >>>>>>> ACTG content number of A's = 20,520,261 bp (29.12%) number of C's = 13,041,496 bp (18.51%) number of T's = 22,303,848 bp (31.65%) number of G's = 14,543,317 bp (20.64%) number of N's = 53,655 bp (0.08%) GC percentage = 39.15% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 664,542 number of insertions = 5,390 mapped reads with insertion percentage = 0.5% number of deletions = 21,482 mapped reads with deletion percentage = 2.01% homopolymer indels = 49.01% >>>>>>> Coverage mean coverageData = 0.0228X std coverageData = 0.3893X There is a 1.12% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 5279963 0.02118334942884656 0.4802447577487459 chr2 243199373 6733965 0.02768907220825771 0.3924408524571488 chr3 198022430 4468215 0.02256418628940166 0.34616523230487345 chr4 191154276 4640361 0.024275475794221835 0.35677788404517485 chr5 180915260 4229267 0.023377060619430335 0.3583080595825699 chr6 171115067 4137374 0.024178899453664124 0.3791084589771523 chr7 159138663 4140590 0.026018755731283226 0.4453213162426796 chr8 146364022 3903890 0.026672470096510466 0.6403396949232713 chr9 141213431 2566424 0.01817407863987102 0.3335313312416456 chr10 135534747 3587752 0.026471086414467576 0.39116496973685894 chr11 135006516 3035944 0.02248738868278032 0.3822119739345608 chr12 133851895 3232942 0.02415312835130201 0.33716671913254964 chr13 115169878 2234983 0.019405968286256237 0.34066326406527575 chr14 107349540 2353167 0.021920606273673832 0.32394786140955456 chr15 102531392 1990125 0.01940990911349375 0.3287805022255356 chr16 90354753 2147960 0.02377251808767603 0.3385355200561517 chr17 81195210 1501048 0.018486903353042625 0.27413531175046907 chr18 78077248 1624071 0.02080082279539361 0.4679981809751105 chr19 59128983 1148678 0.019426649025910018 0.34035285724780906 chr20 63025520 1330348 0.021108084471179293 0.29886160581841165 chr21 48129895 1083738 0.02251694087427367 0.3197774417309401 chr22 51304566 747591 0.014571627016589518 0.2603587229912579 chrMT 16571 14772 0.8914368475046769 1.5988586810262884 chrX 155270560 4160642 0.026796077762584226 0.39468702274332673 chrY 59373566 206784 0.003482762008938456 0.11987755563280111