BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068936.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 = 2,120,337 number of mapped reads = 1,754,693 (82.76%) number of supplementary alignments = 8,893 (0.42%) number of secondary alignments = 0 number of mapped bases = 113,643,568 bp number of sequenced bases = 113,594,795 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 61,833 duplication rate = 2.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8933 >>>>>>> ACTG content number of A's = 29,903,030 bp (26.32%) number of C's = 19,660,432 bp (17.31%) number of T's = 37,386,847 bp (32.91%) number of G's = 26,373,414 bp (23.22%) number of N's = 271,072 bp (0.24%) GC percentage = 40.52% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 1,086,258 number of insertions = 11,020 mapped reads with insertion percentage = 0.62% number of deletions = 29,286 mapped reads with deletion percentage = 1.65% homopolymer indels = 48.07% >>>>>>> Coverage mean coverageData = 0.0367X std coverageData = 0.4147X There is a 3.26% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 12308909 0.049383664323949666 0.7387366251952495 chr2 243199373 9724243 0.039984654894648926 0.4085706219095646 chr3 198022430 7541415 0.03808364032296745 0.2751496504291733 chr4 191154276 6212284 0.032498796940331066 0.2250552596733049 chr5 180915260 4483952 0.02478481914682045 0.17213765671827558 chr6 171115067 7065893 0.04129322521902762 0.30189396147078684 chr7 159138663 7857582 0.049375694453333445 0.5468392557419279 chr8 146364022 7047506 0.048150535245608375 0.5257992956542327 chr9 141213431 6869488 0.04864613763261655 0.43493023268564934 chr10 135534747 7853862 0.05794722146048644 0.7935866178842899 chr11 135006516 3267709 0.02420408360141669 0.2844393638283734 chr12 133851895 6190661 0.04625008110643484 0.24867024273901367 chr13 115169878 2673743 0.023215644979670814 0.16264487499357225 chr14 107349540 3192528 0.029739559200719443 0.24315875880951104 chr15 102531392 2166548 0.021130582134298928 0.1572852159389 chr16 90354753 2229722 0.024677417910710243 0.24044256758524118 chr17 81195210 2233585 0.027508827183278423 0.19812619278917562 chr18 78077248 2186984 0.028010515944414435 0.6944166992371094 chr19 59128983 1824914 0.030863273937926514 0.4633942269043262 chr20 63025520 1288640 0.020446320791958558 0.17877118978768652 chr21 48129895 1053714 0.02189312900017754 0.20877780306557694 chr22 51304566 660541 0.012874896943870454 0.1338183711779235 chrMT 16571 83233 5.0228109347655545 4.827723834543479 chrX 155270560 7308962 0.04707242635049426 0.2858336696320727 chrY 59373566 316950 0.0053382341899423725 0.13787653975476966