BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081036.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,847,777 number of mapped reads = 1,444,887 (78.2%) number of supplementary alignments = 9,125 (0.49%) number of secondary alignments = 0 number of mapped bases = 93,722,827 bp number of sequenced bases = 93,688,868 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,237 duplication rate = 1.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6987 >>>>>>> ACTG content number of A's = 27,688,395 bp (29.55%) number of C's = 17,718,568 bp (18.91%) number of T's = 27,974,348 bp (29.86%) number of G's = 20,306,326 bp (21.67%) number of N's = 1,231 bp (0%) GC percentage = 40.59% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 737,666 number of insertions = 6,174 mapped reads with insertion percentage = 0.42% number of deletions = 19,810 mapped reads with deletion percentage = 1.36% homopolymer indels = 46.82% >>>>>>> Coverage mean coverageData = 0.0303X std coverageData = 0.2597X There is a 2.73% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% 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 7485725 0.030032924170728545 0.4151821365979172 chr2 243199373 7693807 0.03163580113341822 0.2729145454970114 chr3 198022430 6478996 0.032718495576485956 0.19462293686216992 chr4 191154276 6586512 0.03445652452995611 0.2064992398877032 chr5 180915260 5704313 0.031530303192776554 0.19171526535484157 chr6 171115067 5392682 0.031514945437271166 0.2300170094090189 chr7 159138663 5179145 0.03254485680830434 0.37185583754250734 chr8 146364022 4726659 0.032293858390964415 0.31002738516001965 chr9 141213431 3937791 0.027885385774671815 0.236110800114248 chr10 135534747 4284305 0.03161038106338886 0.23338405497529274 chr11 135006516 4264570 0.031587882765599255 0.24311191549382466 chr12 133851895 4364665 0.03260816740771582 0.1964704645200619 chr13 115169878 2992121 0.025980065725171645 0.1731421542345319 chr14 107349540 2832452 0.026385320328340484 0.18361724854808956 chr15 102531392 2720705 0.02653533661183494 0.17897840182465516 chr16 90354753 2677543 0.02963367073783047 0.20588568585007974 chr17 81195210 2393530 0.02947870939677353 0.20720952629474754 chr18 78077248 2535474 0.032473916088845756 0.44978566198749975 chr19 59128983 1708349 0.028891905683546087 0.2930144290758029 chr20 63025520 1876602 0.02977527198506256 0.19007542961466262 chr21 48129895 1242242 0.025810195513619964 0.18518913403758575 chr22 51304566 1033407 0.020142593156328426 0.15337645766977037 chrMT 16571 20230 1.2208074346750346 1.3969221236100238 chrX 155270560 5370770 0.034589750948280214 0.2211590359627683 chrY 59373566 220232 0.003709260110804192 0.08478537127481996