BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238542.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 = 3,990,975 number of mapped reads = 3,563,039 (89.28%) number of supplementary alignments = 28,210 (0.71%) number of secondary alignments = 0 number of mapped bases = 219,986,814 bp number of sequenced bases = 219,845,214 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 658,767 duplication rate = 15.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.7298 >>>>>>> ACTG content number of A's = 56,271,406 bp (25.6%) number of C's = 38,543,823 bp (17.53%) number of T's = 72,881,588 bp (33.15%) number of G's = 52,132,978 bp (23.71%) number of N's = 15,419 bp (0.01%) GC percentage = 41.25% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,422,991 number of insertions = 14,371 mapped reads with insertion percentage = 0.4% number of deletions = 81,098 mapped reads with deletion percentage = 2.25% homopolymer indels = 41.11% >>>>>>> Coverage mean coverageData = 0.0711X std coverageData = 0.7941X There is a 4.51% of reference with a coverageData >= 1X There is a 1.5% of reference with a coverageData >= 2X There is a 0.55% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% 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 7983295 0.03202918800350752 0.6009737168486761 chr2 243199373 24348681 0.10011818986062929 1.651506031751255 chr3 198022430 16491671 0.0832818332751497 0.42481640794059716 chr4 191154276 19074291 0.09978479895474585 0.4818110589864126 chr5 180915260 8503521 0.047002784618610946 0.3341275399567921 chr6 171115067 24927117 0.1456745886672855 0.9381102072906323 chr7 159138663 10629101 0.0667914433841888 0.8788203917083358 chr8 146364022 14875769 0.10163542103263601 1.0805106704939862 chr9 141213431 12321776 0.08725640268594564 0.8600405977289992 chr10 135534747 12880244 0.09503278151985631 0.5925208109487672 chr11 135006516 4110754 0.030448559979134638 0.37781819871411854 chr12 133851895 3975410 0.029700065135424492 0.35063202652577413 chr13 115169878 3391134 0.029444626137400266 0.3606032586891261 chr14 107349540 7135149 0.0664665074484716 0.5655087198494082 chr15 102531392 5732092 0.0559057269016693 0.4294925160740782 chr16 90354753 4736845 0.05242496761625811 0.515614846518806 chr17 81195210 2909633 0.035835032633082665 0.29345732762157317 chr18 78077248 10185255 0.13045099899012835 1.8736244876733819 chr19 59128983 1598617 0.027036098354676588 0.4926128937888328 chr20 63025520 4246196 0.06737264523957914 0.44368909387597166 chr21 48129895 5015028 0.10419777562365345 0.5329094569507804 chr22 51304566 2765416 0.053901947050872624 0.3404427351143126 chrMT 16571 62729 3.785468589704906 3.033706919677139 chrX 155270560 11458487 0.07379690650951475 0.49190443999396055 chrY 59373566 628603 0.010587253593627844 0.29859418602687354