BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975239.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 2,409,852 number of mapped reads = 2,387,376 (99.07%) number of supplementary alignments = 9,918 (0.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,193,350 number of mapped paired reads (second in pair) = 1,194,026 number of mapped paired reads (both in pair) = 2,379,376 number of mapped paired reads (singletons) = 8,000 number of mapped bases = 218,331,255 bp number of sequenced bases = 218,204,307 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 76,285 duplication rate = 1.94% >>>>>>> Insert size mean insert size = 53,291.2385 std insert size = 2,218,162.6682 median insert size = 173 >>>>>>> Mapping quality mean mapping quality = 52.8639 >>>>>>> ACTG content number of A's = 63,517,823 bp (29.11%) number of C's = 42,130,577 bp (19.31%) number of T's = 65,599,957 bp (30.06%) number of G's = 46,953,124 bp (21.52%) number of N's = 2,826 bp (0%) GC percentage = 40.83% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 1,607,718 number of insertions = 35,493 mapped reads with insertion percentage = 1.45% number of deletions = 71,074 mapped reads with deletion percentage = 2.91% homopolymer indels = 45.54% >>>>>>> Coverage mean coverageData = 0.0705X std coverageData = 0.6084X There is a 5.32% of reference with a coverageData >= 1X There is a 1.23% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.06% 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 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 15950777 0.06399493383809864 0.7279714996051595 chr2 243199373 21532085 0.08853676197594473 0.9667431100172404 chr3 198022430 13544852 0.06840059482150583 0.3185412451375055 chr4 191154276 10416259 0.05449137324032448 0.5390405202703578 chr5 180915260 12307385 0.06802845155240084 0.32022574880952437 chr6 171115067 11158057 0.06520791649516171 0.3741299084014794 chr7 159138663 10262358 0.06448689342073963 0.6227492436186227 chr8 146364022 12922036 0.08828696986749927 0.429973699114776 chr9 141213431 9796801 0.06937584428495332 0.8879818100324258 chr10 135534747 10210576 0.07533548574078941 0.9910519123799455 chr11 135006516 13512735 0.10008950234668673 0.5130721611375529 chr12 133851895 12612313 0.09422588301794307 0.3749218863029096 chr13 115169878 4885849 0.04242297625773295 0.24502629104458923 chr14 107349540 7833431 0.07297125819076634 0.344738917815366 chr15 102531392 5274962 0.051447287480501584 0.27029528466140157 chr16 90354753 5261039 0.05822647758220312 0.6856249748296067 chr17 81195210 6872621 0.08464318276903281 0.9044770413103247 chr18 78077248 6873980 0.08804075676437777 0.8043754747244694 chr19 59128983 3927341 0.06641989766676691 0.4300945160128706 chr20 63025520 10802453 0.17139807811185057 0.5324114569687125 chr21 48129895 1950820 0.04053239675673508 0.28656824565134487 chr22 51304566 2176464 0.0424224229866792 0.2676274375453504 chrMT 16571 21118 1.2743950274576066 1.3505198575929105 chrX 155270560 5522650 0.03556791448423964 0.2798414013584427 chrY 59373566 2702293 0.045513402378425445 0.8607971881175872