BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975222.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 = 54,271,510 number of mapped reads = 54,178,816 (99.83%) number of supplementary alignments = 133,879 (0.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 27,099,675 number of mapped paired reads (second in pair) = 27,079,141 number of mapped paired reads (both in pair) = 54,127,846 number of mapped paired reads (singletons) = 50,970 number of mapped bases = 5,298,352,650 bp number of sequenced bases = 5,296,275,097 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 28,852,232 duplication rate = 33.98% >>>>>>> Insert size mean insert size = 135,786.7004 std insert size = 3,699,494.9429 median insert size = 203 >>>>>>> Mapping quality mean mapping quality = 55.745 >>>>>>> ACTG content number of A's = 1,408,562,400 bp (26.6%) number of C's = 1,200,398,662 bp (22.66%) number of T's = 1,425,276,626 bp (26.91%) number of G's = 1,261,783,816 bp (23.82%) number of N's = 253,593 bp (0%) GC percentage = 46.49% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 32,443,597 number of insertions = 449,120 mapped reads with insertion percentage = 0.82% number of deletions = 1,404,413 mapped reads with deletion percentage = 2.55% homopolymer indels = 49.98% >>>>>>> Coverage mean coverageData = 1.7115X std coverageData = 22.2799X There is a 18.61% of reference with a coverageData >= 1X There is a 8.62% of reference with a coverageData >= 2X There is a 4.75% of reference with a coverageData >= 3X There is a 3.36% of reference with a coverageData >= 4X There is a 2.64% of reference with a coverageData >= 5X There is a 2.27% of reference with a coverageData >= 6X There is a 2.04% of reference with a coverageData >= 7X There is a 1.89% of reference with a coverageData >= 8X There is a 1.77% of reference with a coverageData >= 9X There is a 1.68% of reference with a coverageData >= 10X There is a 1.61% of reference with a coverageData >= 11X There is a 1.54% of reference with a coverageData >= 12X There is a 1.49% of reference with a coverageData >= 13X There is a 1.43% of reference with a coverageData >= 14X There is a 1.39% of reference with a coverageData >= 15X There is a 1.34% of reference with a coverageData >= 16X There is a 1.3% of reference with a coverageData >= 17X There is a 1.27% of reference with a coverageData >= 18X There is a 1.23% of reference with a coverageData >= 19X There is a 1.2% of reference with a coverageData >= 20X There is a 1.17% of reference with a coverageData >= 21X There is a 1.14% of reference with a coverageData >= 22X There is a 1.11% of reference with a coverageData >= 23X There is a 1.09% of reference with a coverageData >= 24X There is a 1.06% of reference with a coverageData >= 25X There is a 1.04% of reference with a coverageData >= 26X There is a 1.02% of reference with a coverageData >= 27X There is a 0.99% of reference with a coverageData >= 28X There is a 0.97% of reference with a coverageData >= 29X There is a 0.95% of reference with a coverageData >= 30X There is a 0.93% of reference with a coverageData >= 31X There is a 0.92% of reference with a coverageData >= 32X There is a 0.9% of reference with a coverageData >= 33X There is a 0.88% of reference with a coverageData >= 34X There is a 0.87% of reference with a coverageData >= 35X There is a 0.85% of reference with a coverageData >= 36X There is a 0.84% of reference with a coverageData >= 37X There is a 0.82% of reference with a coverageData >= 38X There is a 0.81% of reference with a coverageData >= 39X There is a 0.79% of reference with a coverageData >= 40X There is a 0.78% of reference with a coverageData >= 41X There is a 0.77% of reference with a coverageData >= 42X There is a 0.75% of reference with a coverageData >= 43X There is a 0.74% of reference with a coverageData >= 44X There is a 0.73% of reference with a coverageData >= 45X There is a 0.72% of reference with a coverageData >= 46X There is a 0.71% of reference with a coverageData >= 47X There is a 0.7% of reference with a coverageData >= 48X There is a 0.69% of reference with a coverageData >= 49X There is a 0.68% of reference with a coverageData >= 50X There is a 0.67% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 710448323 2.8503372234326347 32.96022406406703 chr2 243199373 414296512 1.7035262340088353 19.576035371752138 chr3 198022430 307978135 1.5552689409982496 18.354226799450302 chr4 191154276 150360298 0.7865913394477244 10.995505305772152 chr5 180915260 253935952 1.4036182022456258 17.98580304701005 chr6 171115067 390831045 2.2840247317321274 27.68010173323288 chr7 159138663 326440401 2.051295359946564 28.31277926524488 chr8 146364022 268049580 1.8313898206486838 22.606721079527436 chr9 141213431 213917072 1.5148493346925336 19.527890594866616 chr10 135534747 183785922 1.356005939938044 16.622118997580426 chr11 135006516 279426556 2.0697264419444763 24.774831380725974 chr12 133851895 289229898 2.160820345502019 25.215697967559038 chr13 115169878 68312894 0.593148965565458 8.931831004791146 chr14 107349540 166373721 1.5498317086407636 19.71984789445485 chr15 102531392 127771068 1.246165350022752 14.87301682401151 chr16 90354753 160079949 1.771682658465128 22.306147100812698 chr17 81195210 208003844 2.5617748140561494 28.826029706686654 chr18 78077248 129036846 1.6526817902188355 21.701549284126987 chr19 59128983 276166430 4.67057635677583 44.17537625204262 chr20 63025520 133481198 2.1178912605560414 25.75082862117632 chr21 48129895 52137944 1.0832756647401787 16.809517499914566 chr22 51304566 57401532 1.1188386624301627 15.040701364079354 chrMT 16571 68608 4.140245006336371 6.205755762244603 chrX 155270560 123045335 0.7924575978859096 12.460770492538954 chrY 59373566 7773587 0.13092673261363483 3.141905063590222