BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085020.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 = 2,705,773 number of mapped reads = 2,471,516 (91.34%) number of supplementary alignments = 18,201 (0.67%) number of secondary alignments = 0 number of mapped bases = 165,961,220 bp number of sequenced bases = 165,903,618 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 92,149 duplication rate = 2.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5114 >>>>>>> ACTG content number of A's = 46,515,637 bp (28.04%) number of C's = 32,102,835 bp (19.35%) number of T's = 50,833,005 bp (30.64%) number of G's = 36,433,862 bp (21.96%) number of N's = 18,279 bp (0.01%) GC percentage = 41.31% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,433,789 number of insertions = 11,496 mapped reads with insertion percentage = 0.46% number of deletions = 33,800 mapped reads with deletion percentage = 1.35% homopolymer indels = 46.07% >>>>>>> Coverage mean coverageData = 0.0536X std coverageData = 0.4057X There is a 4.49% of reference with a coverageData >= 1X There is a 0.64% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 14829619 0.059496818665900134 0.6194924635590547 chr2 243199373 17191220 0.0706877644787349 0.5105739506276358 chr3 198022430 10638246 0.05372242932277924 0.27212763700824827 chr4 191154276 9643909 0.05045091954940103 0.2650275532631163 chr5 180915260 8109689 0.044825898047516834 0.24404827831304318 chr6 171115067 11801452 0.06896793021738992 0.4158460141372703 chr7 159138663 14627977 0.0919196927022065 0.4796609885958287 chr8 146364022 9344837 0.06384654420059596 0.6923495702732752 chr9 141213431 5294551 0.03749325374014884 0.3309691250450477 chr10 135534747 11501829 0.08486258509044917 0.5564032843367432 chr11 135006516 6695803 0.04959614690005037 0.42066606224690634 chr12 133851895 7101526 0.05305510243243101 0.2724812426674147 chr13 115169878 3160732 0.02744408568358473 0.18837945977589052 chr14 107349540 5352642 0.049861806580633695 0.26730594305034994 chr15 102531392 2993290 0.029193888248391284 0.2041994132922153 chr16 90354753 4360501 0.04825978551454842 0.2677631012381324 chr17 81195210 2924597 0.036019329219051224 0.25738821684706104 chr18 78077248 4023518 0.051532528400591165 0.5378663868958862 chr19 59128983 2433436 0.04115470749767504 0.4239727917982474 chr20 63025520 3608481 0.05725428366160248 0.27826814311328063 chr21 48129895 1957759 0.04067656910533464 0.24212972184952936 chr22 51304566 819853 0.015980117637092964 0.14255019252792278 chrMT 16571 10664 0.6435338844970129 0.9640802741078011 chrX 155270560 7209384 0.04643110709460956 0.2846756699122294 chrY 59373566 325705 0.005485690382821203 0.10825207571738471