BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926971.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 23,453,622 number of mapped reads = 23,058,854 (98.32%) number of supplementary alignments = 130,176 (0.56%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 11,584,625 number of mapped paired reads (second in pair) = 11,474,229 number of mapped paired reads (both in pair) = 22,872,860 number of mapped paired reads (singletons) = 185,994 number of mapped bases = 2,237,184,576 bp number of sequenced bases = 2,235,474,095 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,301,512 duplication rate = 4.32% >>>>>>> Insert size mean insert size = 60,305.2757 std insert size = 2,389,018.9291 median insert size = 183 >>>>>>> Mapping quality mean mapping quality = 53.5027 >>>>>>> ACTG content number of A's = 642,088,885 bp (28.72%) number of C's = 458,196,918 bp (20.5%) number of T's = 646,967,276 bp (28.94%) number of G's = 488,039,780 bp (21.83%) number of N's = 181,236 bp (0.01%) GC percentage = 42.33% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 20,708,695 number of insertions = 364,809 mapped reads with insertion percentage = 1.55% number of deletions = 1,205,144 mapped reads with deletion percentage = 5.09% homopolymer indels = 53.2% >>>>>>> Coverage mean coverageData = 0.7227X std coverageData = 3.2031X There is a 26.15% of reference with a coverageData >= 1X There is a 15.54% of reference with a coverageData >= 2X There is a 9.48% of reference with a coverageData >= 3X There is a 6.13% of reference with a coverageData >= 4X There is a 4.07% of reference with a coverageData >= 5X There is a 2.78% of reference with a coverageData >= 6X There is a 1.93% of reference with a coverageData >= 7X There is a 1.36% of reference with a coverageData >= 8X There is a 0.97% of reference with a coverageData >= 9X There is a 0.7% of reference with a coverageData >= 10X There is a 0.51% of reference with a coverageData >= 11X There is a 0.38% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.21% of reference with a coverageData >= 14X There is a 0.16% of reference with a coverageData >= 15X There is a 0.12% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 126493244 0.5074941979783473 3.5566973850592074 chr2 243199373 175062305 0.7198304125562034 5.872228882474361 chr3 198022430 203766913 1.0290092541536835 2.046017309380648 chr4 191154276 107342445 0.5615487513342364 2.3641773051542003 chr5 180915260 146343822 0.8089081153242684 1.8273452655853695 chr6 171115067 157631369 0.9212009892734928 2.565127292435359 chr7 159138663 142225616 0.8937213202551538 3.104271641965929 chr8 146364022 40000695 0.2732959538376173 1.4053693530691844 chr9 141213431 126011645 0.8923488658808949 5.1537335575772545 chr10 135534747 138585449 1.022508633892975 4.791157431809534 chr11 135006516 87177091 0.6457250626332732 2.012521192942394 chr12 133851895 130896796 0.9779226211179154 2.253564849030631 chr13 115169878 75864121 0.6587149549641791 1.726073963672958 chr14 107349540 83607464 0.7788339288645298 1.860232323885086 chr15 102531392 69376456 0.6766362442441043 1.8006649511431825 chr16 90354753 70486730 0.7801109256532415 3.3717604928921334 chr17 81195210 71057454 0.8751434228694033 2.890432646655647 chr18 78077248 36541765 0.46802065820762534 4.980075839665673 chr19 59128983 43218997 0.7309274539695703 2.44074521995248 chr20 63025520 69852049 1.1083137275186306 2.31745944830463 chr21 48129895 31092873 0.6460199632681517 2.575969158493953 chr22 51304566 22142643 0.43159205361955505 1.5188287424270477 chrMT 16571 39619 2.3908635568161247 2.4014247692191204 chrX 155270560 78782038 0.5073855468802329 1.6854677974848138 chrY 59373566 3584977 0.06038001827277816 2.1172483251228345