BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038478.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 11,410,332 number of mapped reads = 10,632,386 (93.18%) number of supplementary alignments = 215,189 (1.89%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,388,866 number of mapped paired reads (second in pair) = 5,243,520 number of mapped paired reads (both in pair) = 10,466,002 number of mapped paired reads (singletons) = 166,384 number of mapped bases = 1,505,400,213 bp number of sequenced bases = 1,504,202,203 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,548,689 duplication rate = 8.78% >>>>>>> Insert size mean insert size = 91,303.9485 std insert size = 2,855,499.8848 median insert size = 261 >>>>>>> Mapping quality mean mapping quality = 53.7281 >>>>>>> ACTG content number of A's = 436,071,994 bp (28.99%) number of C's = 307,853,972 bp (20.47%) number of T's = 437,574,557 bp (29.09%) number of G's = 322,669,563 bp (21.45%) number of N's = 32,117 bp (0%) GC percentage = 41.92% >>>>>>> Mismatches and indels general error rate = 0.015 number of mismatches = 21,639,970 number of insertions = 294,599 mapped reads with insertion percentage = 2.57% number of deletions = 558,480 mapped reads with deletion percentage = 5.02% homopolymer indels = 45.99% >>>>>>> Coverage mean coverageData = 0.4863X std coverageData = 7.2942X There is a 22.02% of reference with a coverageData >= 1X There is a 10.96% of reference with a coverageData >= 2X There is a 5.33% of reference with a coverageData >= 3X There is a 2.9% of reference with a coverageData >= 4X There is a 1.56% of reference with a coverageData >= 5X There is a 0.88% of reference with a coverageData >= 6X There is a 0.51% of reference with a coverageData >= 7X There is a 0.31% of reference with a coverageData >= 8X There is a 0.19% of reference with a coverageData >= 9X There is a 0.12% of reference with a coverageData >= 10X There is a 0.09% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% 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 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% 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 118909301 0.47706722062690465 7.038079255332611 chr2 243199373 139385980 0.5731346190600581 8.201930343565232 chr3 198022430 101215965 0.5111338397372459 1.258419364302509 chr4 191154276 99915840 0.5226973839706311 6.865480080144687 chr5 180915260 92314603 0.5102643248557364 1.3280565161733093 chr6 171115067 91120576 0.5325105357320755 7.3881605968296515 chr7 159138663 79152083 0.4973780821571939 6.560287777101948 chr8 146364022 75022902 0.5125774830101348 1.8966341585595372 chr9 141213431 65924932 0.46684604667667906 12.705425160398596 chr10 135534747 85552779 0.6312239546955438 19.179656256882417 chr11 135006516 68763670 0.5093359345707432 3.8436398728753236 chr12 133851895 65586902 0.4899960661744834 1.2235434278293862 chr13 115169878 46667546 0.40520617726103697 1.057068338460391 chr14 107349540 43957414 0.40947929539334776 1.2040289129405655 chr15 102531392 41936394 0.4090102863325995 1.0856069889194473 chr16 90354753 54453743 0.6026660600798721 12.137037723045726 chr17 81195210 35438280 0.43645776641257533 4.585482254607018 chr18 78077248 44162533 0.5656261475814311 10.786809993294536 chr19 59128983 20196067 0.34155951912787 3.7482301143845387 chr20 63025520 30462917 0.48334257297678784 2.331594985981481 chr21 48129895 20064653 0.41688545133954685 3.2453766212744317 chr22 51304566 14442834 0.2815116689613942 1.0629531376543304 chrMT 16571 1870993 112.90767002594895 42.768756468932786 chrX 155270560 44629578 0.2874310365081442 1.3521511289544699 chrY 59373566 24251728 0.4084600207439115 11.612804328786359