BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013348.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,666,920 number of mapped reads = 1,053,324 (63.19%) number of supplementary alignments = 12,358 (0.74%) number of secondary alignments = 0 number of mapped bases = 64,878,545 bp number of sequenced bases = 64,836,049 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 278,084 duplication rate = 16.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3344 >>>>>>> ACTG content number of A's = 17,546,221 bp (27.06%) number of C's = 11,781,436 bp (18.17%) number of T's = 20,745,694 bp (32%) number of G's = 14,755,940 bp (22.76%) number of N's = 6,758 bp (0.01%) GC percentage = 40.93% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 580,535 number of insertions = 4,446 mapped reads with insertion percentage = 0.42% number of deletions = 24,871 mapped reads with deletion percentage = 2.33% homopolymer indels = 43.83% >>>>>>> Coverage mean coverageData = 0.021X std coverageData = 0.3609X There is a 0.77% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.1% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% 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 0.01% 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 5152730 0.02067288731047936 0.42867476163761564 chr2 243199373 11474483 0.047181383975031875 0.5880534494987532 chr3 198022430 4239723 0.021410317002977894 0.33956232252593893 chr4 191154276 3653958 0.019115230255168345 0.31894822044650445 chr5 180915260 3832619 0.02118460874997499 0.3352627060957179 chr6 171115067 2909273 0.01700185174225482 0.3213225617948257 chr7 159138663 3282237 0.02062501304287067 0.36028638192048745 chr8 146364022 4908099 0.03353350729867208 0.44556907966317777 chr9 141213431 2283542 0.01617085558950834 0.29940675054525123 chr10 135534747 2464250 0.01818168443550494 0.31899369908464353 chr11 135006516 2119380 0.01569835340392015 0.2832140404790066 chr12 133851895 2740310 0.020472702310266135 0.33113546828849366 chr13 115169878 1797361 0.015606172648719833 0.29336948464089846 chr14 107349540 1442134 0.013434002604948285 0.26517979186823337 chr15 102531392 1461414 0.014253332286759552 0.2822463094012979 chr16 90354753 2085008 0.02307579768382522 0.3449081311793598 chr17 81195210 1467459 0.01807322131441005 0.3042736859818721 chr18 78077248 1711135 0.02191592357353579 0.4373271404926013 chr19 59128983 1411857 0.02387757962960398 0.3967375827704159 chr20 63025520 989777 0.015704384509639905 0.2937454309361596 chr21 48129895 921583 0.01914782901562532 0.3247647584719996 chr22 51304566 509777 0.00993628910144177 0.22134836233582586 chrMT 16571 47357 2.857823909239032 6.086571405791206 chrX 155270560 1771384 0.011408370009098955 0.2322056653418103 chrY 59373566 201695 0.0033970504651851295 0.10980274035697488