BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080716.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 = 2,232,367 number of mapped reads = 2,022,455 (90.6%) number of supplementary alignments = 14,749 (0.66%) number of secondary alignments = 0 number of mapped bases = 136,391,878 bp number of sequenced bases = 136,340,574 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 105,306 duplication rate = 4.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.205 >>>>>>> ACTG content number of A's = 38,273,921 bp (28.07%) number of C's = 25,056,365 bp (18.38%) number of T's = 43,558,830 bp (31.95%) number of G's = 29,449,617 bp (21.6%) number of N's = 1,841 bp (0%) GC percentage = 39.98% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,114,805 number of insertions = 9,592 mapped reads with insertion percentage = 0.47% number of deletions = 28,993 mapped reads with deletion percentage = 1.42% homopolymer indels = 47.94% >>>>>>> Coverage mean coverageData = 0.0441X std coverageData = 0.3589X There is a 3.68% of reference with a coverageData >= 1X There is a 0.55% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 16849750 0.06760163698849922 0.459566239747429 chr2 243199373 8625419 0.03546645245668458 0.34201044790466006 chr3 198022430 8609753 0.04347867562275647 0.24004343174253379 chr4 191154276 6040338 0.031599282665275036 0.20909886547531276 chr5 180915260 6278750 0.03470547481732608 0.21207195732700193 chr6 171115067 7916622 0.04626490313678806 0.3572936702379444 chr7 159138663 8866551 0.05571588219262594 0.904308873967865 chr8 146364022 15951564 0.10898555384054696 0.5119513386859219 chr9 141213431 4429266 0.03136575585363406 0.24975427132173328 chr10 135534747 6397361 0.04720089232910878 0.3228133952409487 chr11 135006516 5700347 0.04222275464096859 0.2529704650349488 chr12 133851895 4467353 0.033375343696105314 0.2111810241686839 chr13 115169878 2965301 0.025747192334440085 0.1847880535910992 chr14 107349540 2890369 0.026924838243368346 0.19369552151523595 chr15 102531392 2396517 0.023373495212081 0.1761937719924697 chr16 90354753 3160503 0.03497882396955919 0.22908115260873593 chr17 81195210 2116781 0.026070269416139203 0.18991828496460397 chr18 78077248 4726407 0.06053501014789866 0.4165778362928207 chr19 59128983 2079050 0.03516126769844832 0.30462233940442734 chr20 63025520 3405604 0.054035317756997485 0.2718473764199167 chr21 48129895 2100657 0.043645576205807224 0.24513441763233354 chr22 51304566 1249650 0.024357481164541964 0.17727539529506697 chrMT 16571 21496 1.2972059622231609 1.3729994901740108 chrX 155270560 8852240 0.05701170910956977 0.2891315802129987 chrY 59373566 294229 0.004955555473962941 0.10295776288140214