BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472805.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 3,209,382 number of mapped reads = 2,246,424 (70%) number of supplementary alignments = 21,015 (0.65%) number of secondary alignments = 0 number of mapped bases = 140,010,866 bp number of sequenced bases = 139,940,660 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 195,181 duplication rate = 5.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.5005 >>>>>>> ACTG content number of A's = 38,000,767 bp (27.15%) number of C's = 27,364,584 bp (19.55%) number of T's = 41,615,793 bp (29.74%) number of G's = 32,956,425 bp (23.55%) number of N's = 3,091 bp (0%) GC percentage = 43.1% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 1,300,610 number of insertions = 11,224 mapped reads with insertion percentage = 0.49% number of deletions = 38,812 mapped reads with deletion percentage = 1.71% homopolymer indels = 46.14% >>>>>>> Coverage mean coverageData = 0.0452X std coverageData = 0.4154X There is a 3.22% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 11111801 0.04458083576850948 0.5010887267439327 chr2 243199373 11726559 0.04821788335778316 0.5237690901328096 chr3 198022430 9771630 0.049346076603544356 0.3262674089587703 chr4 191154276 7039627 0.036826939722760896 0.31959457243879885 chr5 180915260 7867574 0.04348761956288264 0.3150788597191064 chr6 171115067 9078716 0.053056204571395225 0.3708525121481181 chr7 159138663 7808982 0.0490703004083929 0.5738067209570329 chr8 146364022 7019863 0.047961670525834554 0.40371447959724793 chr9 141213431 6158348 0.043610214385344126 0.4330830854567691 chr10 135534747 6770430 0.04995346322519051 0.405376529020056 chr11 135006516 5612996 0.04157574142569533 0.4312470351781752 chr12 133851895 6826766 0.051002385883292874 0.3619840243027992 chr13 115169878 5985927 0.05197476201199067 0.3369164041404899 chr14 107349540 4289776 0.039960823306741694 0.3620959509382665 chr15 102531392 3920909 0.038241058894431086 0.35088888243302485 chr16 90354753 4120647 0.045605204631570403 0.34695819928382216 chr17 81195210 3661496 0.04509497543020087 0.35989443839496904 chr18 78077248 3036397 0.03888965195084745 0.7014367857803854 chr19 59128983 2999999 0.050736522899438335 0.4355917869902709 chr20 63025520 4019114 0.06376962855681317 0.40084385927585187 chr21 48129895 1920697 0.03990652794900134 0.3273897459660478 chr22 51304566 1781805 0.034729949767044126 0.28207355433514764 chrMT 16571 189839 11.456098002534548 8.490159393691695 chrX 155270560 6735541 0.04337938241479904 0.35732032010375125 chrY 59373566 555427 0.009354785932850994 0.17061881852146266