BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926952.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 = 10,611,404 number of mapped reads = 10,196,657 (96.09%) number of supplementary alignments = 313,072 (2.95%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,103,045 number of mapped paired reads (second in pair) = 5,093,612 number of mapped paired reads (both in pair) = 9,992,314 number of mapped paired reads (singletons) = 204,343 number of mapped bases = 930,903,278 bp number of sequenced bases = 930,195,086 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 691,571 duplication rate = 5.66% >>>>>>> Insert size mean insert size = 303,750.1448 std insert size = 5,413,097.2093 median insert size = 194 >>>>>>> Mapping quality mean mapping quality = 52.7839 >>>>>>> ACTG content number of A's = 263,710,859 bp (28.35%) number of C's = 183,832,346 bp (19.76%) number of T's = 265,998,375 bp (28.6%) number of G's = 216,601,961 bp (23.29%) number of N's = 51,545 bp (0.01%) GC percentage = 43.05% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 9,315,982 number of insertions = 157,774 mapped reads with insertion percentage = 1.52% number of deletions = 486,376 mapped reads with deletion percentage = 4.65% homopolymer indels = 52.51% >>>>>>> Coverage mean coverageData = 0.3007X std coverageData = 1.2829X There is a 17.02% of reference with a coverageData >= 1X There is a 6.98% of reference with a coverageData >= 2X There is a 2.95% of reference with a coverageData >= 3X There is a 1.37% of reference with a coverageData >= 4X There is a 0.67% of reference with a coverageData >= 5X There is a 0.34% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 75443014 0.30267934217102715 1.552498574880653 chr2 243199373 84429545 0.347161853085863 2.3938612537137556 chr3 198022430 63916294 0.322773001018117 0.8609674235343081 chr4 191154276 58603844 0.3065787761922731 1.3035605685806346 chr5 180915260 59201771 0.3272348114802477 0.8623084165491318 chr6 171115067 54335811 0.3175396062580509 0.8954886364012307 chr7 159138663 45403188 0.28530582791185066 0.8860306129966822 chr8 146364022 46155779 0.31534921198052346 0.9073768363793889 chr9 141213431 36021944 0.255088653713116 1.1369564380767991 chr10 135534747 46417518 0.34247688528167614 2.2457756526563326 chr11 135006516 47634709 0.3528326662396058 1.1013860867984195 chr12 133851895 39956434 0.29851227731964497 1.1822959588848172 chr13 115169878 28098606 0.24397530402871487 0.7457903043423704 chr14 107349540 28366763 0.2642467121889856 0.7976047582189462 chr15 102531392 24768677 0.24157164471150455 0.7685719666985424 chr16 90354753 26591099 0.29429662654271216 0.9135260944562849 chr17 81195210 26889552 0.33117165409141747 0.927054470004839 chr18 78077248 26555866 0.3401229766704892 1.3487418324158678 chr19 59128983 17169433 0.2903725403158042 1.1331882657398078 chr20 63025520 20895500 0.33154030303914983 0.9369088669468413 chr21 48129895 12378482 0.2571890505890362 1.261051904800796 chr22 51304566 10419834 0.2030975956409026 0.7093528690736235 chrMT 16571 59907 3.6151710820107414 4.7534424597965375 chrX 155270560 49679969 0.3199574278601172 0.8856100318435961 chrY 59373566 1509739 0.025427797279348185 0.9232079237489879