BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238640.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 = 2,229,860 number of mapped reads = 1,985,725 (89.05%) number of supplementary alignments = 18,325 (0.82%) number of secondary alignments = 0 number of mapped bases = 121,771,403 bp number of sequenced bases = 121,719,736 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 674,175 duplication rate = 19.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.8862 >>>>>>> ACTG content number of A's = 30,762,252 bp (25.27%) number of C's = 21,574,518 bp (17.72%) number of T's = 40,938,533 bp (33.63%) number of G's = 28,438,347 bp (23.36%) number of N's = 6,086 bp (0.01%) GC percentage = 41.09% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 697,283 number of insertions = 7,059 mapped reads with insertion percentage = 0.35% number of deletions = 31,420 mapped reads with deletion percentage = 1.57% homopolymer indels = 40.09% >>>>>>> Coverage mean coverageData = 0.0393X std coverageData = 0.7443X There is a 1.35% of reference with a coverageData >= 1X There is a 0.72% of reference with a coverageData >= 2X There is a 0.5% of reference with a coverageData >= 3X There is a 0.36% of reference with a coverageData >= 4X There is a 0.26% of reference with a coverageData >= 5X There is a 0.18% of reference with a coverageData >= 6X There is a 0.13% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% 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 0.01% 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 20516026 0.08231083203600123 0.7416102873217184 chr2 243199373 14704697 0.060463548152321925 1.8169596180996064 chr3 198022430 4429986 0.022371132401516333 0.36964042840619404 chr4 191154276 16999993 0.08893336500617961 0.7405293023302901 chr5 180915260 10171423 0.05622202903171352 0.5826810604690685 chr6 171115067 3569902 0.020862581317868403 0.6438725844452258 chr7 159138663 2278617 0.01431843750000589 0.3201224632482078 chr8 146364022 4046695 0.02764815386119958 0.4377953159473847 chr9 141213431 5228790 0.037027568574550106 0.4706369493059113 chr10 135534747 2070662 0.015277720627611457 0.4163046997648886 chr11 135006516 3262243 0.024163596666697183 0.3576694843539265 chr12 133851895 1550018 0.011580097539896615 0.2514762639705629 chr13 115169878 865173 0.007512146535398778 0.4394097085477406 chr14 107349540 662251 0.006169108875548046 0.1891470740125811 chr15 102531392 2391376 0.02332335447079466 0.5145557545810883 chr16 90354753 1062076 0.011754511685732792 0.28016617537160227 chr17 81195210 1927283 0.02373641252975391 0.36645292740961216 chr18 78077248 2006689 0.025701328509939284 1.4066257997839493 chr19 59128983 816765 0.013813276646412133 0.30022059539076423 chr20 63025520 2426509 0.03850042014726733 0.48964591168208205 chr21 48129895 664486 0.013806097021404264 0.2723712415656386 chr22 51304566 405465 0.007903097747674155 0.1923144846107573 chrMT 16571 6666 0.4022690241989017 0.974532155645737 chrX 155270560 19189878 0.12358993230912543 0.903681050574702 chrY 59373566 517734 0.008719941126662327 0.26496885824461064