BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089701.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 21,840,551 number of mapped reads = 17,313,733 (79.27%) number of supplementary alignments = 735 (0%) number of secondary alignments = 0 number of mapped bases = 798,722,664 bp number of sequenced bases = 798,554,801 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,912,115 duplication rate = 8.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.6885 >>>>>>> ACTG content number of A's = 257,663,395 bp (32.27%) number of C's = 162,179,802 bp (20.31%) number of T's = 209,263,132 bp (26.21%) number of G's = 169,404,353 bp (21.21%) number of N's = 44,119 bp (0.01%) GC percentage = 41.52% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 3,724,551 number of insertions = 37,358 mapped reads with insertion percentage = 0.22% number of deletions = 112,547 mapped reads with deletion percentage = 0.65% homopolymer indels = 43.03% >>>>>>> Coverage mean coverageData = 0.258X std coverageData = 1.3906X There is a 13.59% of reference with a coverageData >= 1X There is a 5.44% of reference with a coverageData >= 2X There is a 2.64% of reference with a coverageData >= 3X There is a 1.43% of reference with a coverageData >= 4X There is a 0.83% of reference with a coverageData >= 5X There is a 0.5% of reference with a coverageData >= 6X There is a 0.32% of reference with a coverageData >= 7X There is a 0.21% of reference with a coverageData >= 8X There is a 0.15% of reference with a coverageData >= 9X There is a 0.1% 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 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% 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 67473233 0.27070437268840347 1.4337509292146042 chr2 243199373 85014072 0.34956534201262107 1.88271706861529 chr3 198022430 79215125 0.4000310722376248 1.1949369063187025 chr4 191154276 35452896 0.1854674493391924 0.7712101532914555 chr5 180915260 28199759 0.15587274948503516 0.67851087197358 chr6 171115067 48193541 0.28164405300440315 1.0952114454816229 chr7 159138663 50430849 0.3168987853064971 2.0145889083446624 chr8 146364022 61644215 0.42117054558667427 3.155127271505244 chr9 141213431 26705864 0.1891170252778576 1.1007861530392624 chr10 135534747 34468420 0.2543142682075468 1.3096388438829827 chr11 135006516 42021902 0.3112583247463404 1.2635430910737109 chr12 133851895 28422370 0.21234193210338934 0.8140479746616383 chr13 115169878 23825367 0.20687151374771795 0.7949549459763776 chr14 107349540 26773864 0.24940827878722163 0.9152737264161187 chr15 102531392 19856100 0.19365873819405474 0.7552245535012513 chr16 90354753 15295553 0.1692833248074952 0.7967988119159065 chr17 81195210 18469182 0.227466398572034 0.9723169124508529 chr18 78077248 34841793 0.44624770842332967 1.71544663947111 chr19 59128983 12516288 0.21167771480189335 1.3994617610183437 chr20 63025520 17769264 0.2819376024188297 0.9656986459265453 chr21 48129895 12424508 0.25814533773655646 0.9928234635351363 chr22 51304566 6275017 0.12230913326505871 0.5850017378224502 chrMT 16571 1084719 65.45887393639491 48.625520424642325 chrX 155270560 20568847 0.1324710041620253 0.9452952055537008 chrY 59373566 1779916 0.029978256653811226 0.5474464049721733