BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926903.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 = 29,221,822 number of mapped reads = 27,331,032 (93.53%) number of supplementary alignments = 198,865 (0.68%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 13,750,372 number of mapped paired reads (second in pair) = 13,580,660 number of mapped paired reads (both in pair) = 27,023,114 number of mapped paired reads (singletons) = 307,918 number of mapped bases = 2,565,684,128 bp number of sequenced bases = 2,563,702,607 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,810,359 duplication rate = 5.35% >>>>>>> Insert size mean insert size = 110,390.4532 std insert size = 3,289,651.4275 median insert size = 235 >>>>>>> Mapping quality mean mapping quality = 53.5435 >>>>>>> ACTG content number of A's = 730,313,652 bp (28.49%) number of C's = 510,942,847 bp (19.93%) number of T's = 735,133,510 bp (28.67%) number of G's = 587,069,077 bp (22.9%) number of N's = 243,521 bp (0.01%) GC percentage = 42.83% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 26,521,015 number of insertions = 407,932 mapped reads with insertion percentage = 1.47% number of deletions = 1,407,809 mapped reads with deletion percentage = 5.01% homopolymer indels = 53.26% >>>>>>> Coverage mean coverageData = 0.8288X std coverageData = 2.6465X There is a 32.99% of reference with a coverageData >= 1X There is a 17.78% of reference with a coverageData >= 2X There is a 10.48% of reference with a coverageData >= 3X There is a 6.57% of reference with a coverageData >= 4X There is a 4.29% of reference with a coverageData >= 5X There is a 2.88% of reference with a coverageData >= 6X There is a 1.97% of reference with a coverageData >= 7X There is a 1.38% 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 0.37% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.2% of reference with a coverageData >= 14X There is a 0.15% 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 0.04% 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% 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 213682777 0.8573008811079351 2.762593623070706 chr2 243199373 221880117 0.912338359523649 3.493810404275839 chr3 198022430 173754525 0.8774487061894958 1.8054367075279765 chr4 191154276 150256495 0.7860483068660206 1.8596364328090484 chr5 180915260 155497399 0.8595040517864552 1.781583314984026 chr6 171115067 145425055 0.8498670371323876 1.7873314169808745 chr7 159138663 132386579 0.8318945032232676 1.8665215407301503 chr8 146364022 130041621 0.8884807838910029 1.9253012972314747 chr9 141213431 111400722 0.7888819159135082 3.0651248230552826 chr10 135534747 126810717 0.935632520861975 6.561979615520259 chr11 135006516 122385110 0.9065126160281034 2.1008221699148706 chr12 133851895 116310189 0.868946898361058 1.8710936462392542 chr13 115169878 75840193 0.6585071923059604 1.5601309076728496 chr14 107349540 77450800 0.7214823649919693 1.7070502764393323 chr15 102531392 76709052 0.748151863577547 1.783630533076833 chr16 90354753 81306677 0.8998605419241199 3.9738020679824735 chr17 81195210 69748795 0.8590259819513983 2.018187286099779 chr18 78077248 67598260 0.8657869191291169 2.9838291745220458 chr19 59128983 42349171 0.71621680014351 1.9937746479223661 chr20 63025520 61679081 0.9786366062509282 2.170798751521725 chr21 48129895 32453642 0.6742928069965662 2.523645590549974 chr22 51304566 34817930 0.6786516818015769 1.7641625969668628 chrMT 16571 137423 8.292981715044355 6.753730359957911 chrX 155270560 142364105 0.9168776424841901 1.9055383483417105 chrY 59373566 3397693 0.05722568524854983 1.0930017348988093