BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038412.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 = 12,247,794 number of mapped reads = 11,997,553 (97.96%) number of supplementary alignments = 252,759 (2.06%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,059,926 number of mapped paired reads (second in pair) = 5,937,627 number of mapped paired reads (both in pair) = 11,859,446 number of mapped paired reads (singletons) = 138,107 number of mapped bases = 1,707,480,465 bp number of sequenced bases = 1,706,194,315 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,768,062 duplication rate = 8.25% >>>>>>> Insert size mean insert size = 91,376.2107 std insert size = 2,846,670.1055 median insert size = 254 >>>>>>> Mapping quality mean mapping quality = 53.5481 >>>>>>> ACTG content number of A's = 485,573,500 bp (28.46%) number of C's = 360,304,531 bp (21.12%) number of T's = 484,988,803 bp (28.43%) number of G's = 375,291,887 bp (22%) number of N's = 35,594 bp (0%) GC percentage = 43.11% >>>>>>> Mismatches and indels general error rate = 0.0151 number of mismatches = 24,873,273 number of insertions = 322,567 mapped reads with insertion percentage = 2.5% number of deletions = 583,256 mapped reads with deletion percentage = 4.65% homopolymer indels = 45.85% >>>>>>> Coverage mean coverageData = 0.5516X std coverageData = 9.4153X There is a 25.65% of reference with a coverageData >= 1X There is a 12.46% of reference with a coverageData >= 2X There is a 5.73% of reference with a coverageData >= 3X There is a 3.01% of reference with a coverageData >= 4X There is a 1.55% of reference with a coverageData >= 5X There is a 0.85% of reference with a coverageData >= 6X There is a 0.48% of reference with a coverageData >= 7X There is a 0.28% of reference with a coverageData >= 8X There is a 0.17% of reference with a coverageData >= 9X There is a 0.11% of reference with a coverageData >= 10X There is a 0.08% 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 0.03% 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 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% 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 108684816 0.43604631982040276 12.452246143622707 chr2 243199373 176209414 0.7245471558020834 10.080055740565403 chr3 198022430 106473826 0.5376856854044262 1.2524363778094456 chr4 191154276 92870827 0.4858422680536846 8.990301517184587 chr5 180915260 95197954 0.526201902481858 1.2481371245641637 chr6 171115067 113856063 0.6653771932310321 14.05405525238863 chr7 159138663 88961831 0.5590208521482929 6.388178148982044 chr8 146364022 76017664 0.5193739756618604 2.1943932062647566 chr9 141213431 67104840 0.47520154085060085 12.82599967722954 chr10 135534747 96567754 0.7124944424768064 23.402330920853412 chr11 135006516 93659361 0.6937395599483509 8.016963345905156 chr12 133851895 52774776 0.39427739144074125 1.0220453957948457 chr13 115169878 106306292 0.9230390258814027 1.7316908780254419 chr14 107349540 31863826 0.2968231256510275 1.0137686465180544 chr15 102531392 31189942 0.30419895206338365 0.8322730442032845 chr16 90354753 60024418 0.6643194298810158 11.563888109733762 chr17 81195210 53421093 0.6579340456167303 9.548171679241976 chr18 78077248 33312096 0.42665561163221327 11.904811662704967 chr19 59128983 27368283 0.46285732666837853 7.30172763833626 chr20 63025520 62290476 0.9883373592157589 3.137663748387165 chr21 48129895 14372987 0.29862909528474973 3.7090580453886783 chr22 51304566 12876935 0.25099003858642915 0.8656016647327222 chrMT 16571 4661796 281.32255144529597 194.9838370470901 chrX 155270560 73634019 0.4742303949956772 2.0599903250975062 chrY 59373566 27779176 0.46787110614174665 12.666866287132546