BamQC report ----------------------------------- >>>>>>> Input bam file = SRR620538.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP016866/SRP016866.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 = 15,501,626 number of mapped reads = 6,847,362 (44.17%) number of supplementary alignments = 219 (0%) number of secondary alignments = 0 number of mapped bases = 313,358,779 bp number of sequenced bases = 313,288,268 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 688,925 duplication rate = 4.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.0244 >>>>>>> ACTG content number of A's = 78,736,184 bp (25.13%) number of C's = 65,665,907 bp (20.96%) number of T's = 92,084,175 bp (29.39%) number of G's = 76,765,967 bp (24.5%) number of N's = 36,035 bp (0.01%) GC percentage = 45.46% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 2,243,916 number of insertions = 19,213 mapped reads with insertion percentage = 0.28% number of deletions = 45,131 mapped reads with deletion percentage = 0.65% homopolymer indels = 40.68% >>>>>>> Coverage mean coverageData = 0.1012X std coverageData = 1.1474X There is a 7.18% of reference with a coverageData >= 1X There is a 1.49% of reference with a coverageData >= 2X There is a 0.47% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 0.01% 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 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% 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 26096020 0.10469791367139664 1.8042872888877013 chr2 243199373 25722947 0.10576896923167643 1.4034328837467391 chr3 198022430 19194691 0.09693190311824777 0.5588514211284125 chr4 191154276 19919846 0.10420821556719977 1.3122765336434017 chr5 180915260 17244415 0.09531763655536851 0.5042647597058814 chr6 171115067 16557620 0.09676307463912573 0.6708462062580923 chr7 159138663 17132157 0.10765552931659354 1.216461116322336 chr8 146364022 14816765 0.10123228917554616 0.7825028481996602 chr9 141213431 12787974 0.09055777421058482 0.7093729804691191 chr10 135534747 17468422 0.12888519281332336 2.70457919232744 chr11 135006516 14074238 0.10424858308320467 0.9764968103518724 chr12 133851895 13890229 0.10377312177761847 0.5756729845560322 chr13 115169878 8757490 0.07603976102154072 0.5552971665886245 chr14 107349540 9096409 0.08473635751024178 0.587629728952703 chr15 102531392 9308529 0.0907871123021523 0.5717727113571839 chr16 90354753 10850204 0.12008448520688225 0.8308613324048373 chr17 81195210 10136039 0.12483543056296055 0.7381180918494591 chr18 78077248 7826235 0.10023707546659431 1.4661670746289601 chr19 59128983 8591344 0.14529835563043592 1.387103720451276 chr20 63025520 7289731 0.11566316311233926 0.7133798599977923 chr21 48129895 4094572 0.08507336240812494 0.8303958235284552 chr22 51304566 4642999 0.09049874820108604 0.5676145377484824 chrMT 16571 60906 3.6754571238911353 3.534964789868806 chrX 155270560 15987638 0.10296631892098541 0.6899546065462482 chrY 59373566 1811359 0.030507835759772287 0.9986174051684829