BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124856.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 123,936,082 number of mapped reads = 119,454,487 (96.38%) number of supplementary alignments = 2,247,753 (1.81%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 60,451,926 number of mapped paired reads (second in pair) = 59,002,561 number of mapped paired reads (both in pair) = 117,369,660 number of mapped paired reads (singletons) = 2,084,827 number of mapped bases = 16,125,538,644 bp number of sequenced bases = 16,110,913,264 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,050,896 duplication rate = 27.97% >>>>>>> Insert size mean insert size = 71,079.0365 std insert size = 2,521,835.848 median insert size = 260 >>>>>>> Mapping quality mean mapping quality = 53.4451 >>>>>>> ACTG content number of A's = 4,606,124,274 bp (28.59%) number of C's = 3,208,749,316 bp (19.92%) number of T's = 4,686,399,821 bp (29.09%) number of G's = 3,609,604,285 bp (22.4%) number of N's = 35,568 bp (0%) GC percentage = 42.32% >>>>>>> Mismatches and indels general error rate = 0.0149 number of mismatches = 226,896,388 number of insertions = 3,708,181 mapped reads with insertion percentage = 2.81% number of deletions = 6,242,036 mapped reads with deletion percentage = 4.93% homopolymer indels = 43.43% >>>>>>> Coverage mean coverageData = 5.209X std coverageData = 70.2959X There is a 45.33% of reference with a coverageData >= 1X There is a 38.57% of reference with a coverageData >= 2X There is a 33.43% of reference with a coverageData >= 3X There is a 29.7% of reference with a coverageData >= 4X There is a 26.46% of reference with a coverageData >= 5X There is a 23.78% of reference with a coverageData >= 6X There is a 21.44% of reference with a coverageData >= 7X There is a 19.42% of reference with a coverageData >= 8X There is a 17.64% of reference with a coverageData >= 9X There is a 16.07% of reference with a coverageData >= 10X There is a 14.67% of reference with a coverageData >= 11X There is a 13.43% of reference with a coverageData >= 12X There is a 12.32% of reference with a coverageData >= 13X There is a 11.32% of reference with a coverageData >= 14X There is a 10.42% of reference with a coverageData >= 15X There is a 9.61% of reference with a coverageData >= 16X There is a 8.87% of reference with a coverageData >= 17X There is a 8.2% of reference with a coverageData >= 18X There is a 7.59% of reference with a coverageData >= 19X There is a 7.03% of reference with a coverageData >= 20X There is a 6.52% of reference with a coverageData >= 21X There is a 6.06% of reference with a coverageData >= 22X There is a 5.63% of reference with a coverageData >= 23X There is a 5.24% of reference with a coverageData >= 24X There is a 4.88% of reference with a coverageData >= 25X There is a 4.55% of reference with a coverageData >= 26X There is a 4.25% of reference with a coverageData >= 27X There is a 3.97% of reference with a coverageData >= 28X There is a 3.71% of reference with a coverageData >= 29X There is a 3.47% of reference with a coverageData >= 30X There is a 3.25% of reference with a coverageData >= 31X There is a 3.04% of reference with a coverageData >= 32X There is a 2.85% of reference with a coverageData >= 33X There is a 2.68% of reference with a coverageData >= 34X There is a 2.51% of reference with a coverageData >= 35X There is a 2.36% of reference with a coverageData >= 36X There is a 2.22% of reference with a coverageData >= 37X There is a 2.09% of reference with a coverageData >= 38X There is a 1.96% of reference with a coverageData >= 39X There is a 1.85% of reference with a coverageData >= 40X There is a 1.74% of reference with a coverageData >= 41X There is a 1.64% of reference with a coverageData >= 42X There is a 1.55% of reference with a coverageData >= 43X There is a 1.46% of reference with a coverageData >= 44X There is a 1.38% of reference with a coverageData >= 45X There is a 1.31% of reference with a coverageData >= 46X There is a 1.24% of reference with a coverageData >= 47X There is a 1.17% of reference with a coverageData >= 48X There is a 1.11% of reference with a coverageData >= 49X There is a 1.05% of reference with a coverageData >= 50X There is a 0.99% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1558599955 6.253143718346042 51.14896995229358 chr2 243199373 1319883089 5.427164851284382 95.06183065746016 chr3 198022430 1091375755 5.5113744185444045 11.832947672538566 chr4 191154276 795102415 4.159480141579464 107.83867075421779 chr5 180915260 850931139 4.703479070809173 12.944996247495757 chr6 171115067 828630542 4.842534070947709 24.318677123735775 chr7 159138663 1108099648 6.963107689298608 53.42426494303832 chr8 146364022 1030860564 7.043128153447436 21.74925999654864 chr9 141213431 603166249 4.27130935583599 83.99130179469087 chr10 135534747 893446174 6.592008276667237 188.1889412930373 chr11 135006516 563030531 4.1703952348492574 19.563635673357663 chr12 133851895 803982856 6.006510823025703 13.317482519559727 chr13 115169878 354645212 3.079322633301739 8.03677834452625 chr14 107349540 508620286 4.737982910779124 13.860538971896013 chr15 102531392 554761541 5.410650632734997 11.76338834559989 chr16 90354753 634441406 7.021671632481802 102.84698991324024 chr17 81195210 379449358 4.673297328746363 60.87858245883957 chr18 78077248 245220612 3.1407435364525145 64.78615969260939 chr19 59128983 286350978 4.8428192651309425 29.519466896850076 chr20 63025520 363454626 5.7667850419956865 33.995934638936546 chr21 48129895 162656306 3.3795275472759707 49.17797476433649 chr22 51304566 135859727 2.648102061715131 11.45501338967989 chrMT 16571 12589944 759.757648904713 364.264102231921 chrX 155270560 697898055 4.494722341440644 15.230612601877061 chrY 59373566 342481676 5.768251750282272 171.41592569679315