BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081251.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 = 3,544,756 number of mapped reads = 2,861,560 (80.73%) number of supplementary alignments = 27,613 (0.78%) number of secondary alignments = 0 number of mapped bases = 194,206,237 bp number of sequenced bases = 194,122,749 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 154,400 duplication rate = 4.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1145 >>>>>>> ACTG content number of A's = 54,113,837 bp (27.88%) number of C's = 35,641,226 bp (18.36%) number of T's = 61,992,703 bp (31.93%) number of G's = 42,323,223 bp (21.8%) number of N's = 51,760 bp (0.03%) GC percentage = 40.16% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,694,379 number of insertions = 15,860 mapped reads with insertion percentage = 0.55% number of deletions = 49,719 mapped reads with deletion percentage = 1.72% homopolymer indels = 50.07% >>>>>>> Coverage mean coverageData = 0.0627X std coverageData = 0.5072X There is a 4.92% of reference with a coverageData >= 1X There is a 0.96% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 18363837 0.0736761935690423 1.0232197155578195 chr2 243199373 12164367 0.05001808536735002 0.44960655084265827 chr3 198022430 13454784 0.0679457574578799 0.3221879448738989 chr4 191154276 7766448 0.04062921407000072 0.28076367928693347 chr5 180915260 15838711 0.08754767839926825 0.3644790701349555 chr6 171115067 10617576 0.06204933432308448 0.34327579470769715 chr7 159138663 14243859 0.08950596122577704 0.8364875061714621 chr8 146364022 11143069 0.0761325689724487 0.5592433363698232 chr9 141213431 8907569 0.06307876621169271 0.41963535656664214 chr10 135534747 5549902 0.040948185781466064 0.5275993753944521 chr11 135006516 9003769 0.06669136621524253 0.43221153899898973 chr12 133851895 5672774 0.0423809763769127 0.25484529760285646 chr13 115169878 6222636 0.05403006504877951 0.28119734688451653 chr14 107349540 7421719 0.06913601120228367 0.3288598929051435 chr15 102531392 6249757 0.06095457086937823 0.2994574077519494 chr16 90354753 6039300 0.0668398706153289 0.33412952642855753 chr17 81195210 3335632 0.04108163523439375 0.28070286162293123 chr18 78077248 6241994 0.07994638847926608 0.6488375346500497 chr19 59128983 5376905 0.09093518486526311 0.7790656392339562 chr20 63025520 4025374 0.06386895340173314 0.3126417987454562 chr21 48129895 2957210 0.0614422699239215 0.3330689967722156 chr22 51304566 1267128 0.024698152597178193 0.18608930227598416 chrMT 16571 103794 6.263593023957516 3.8471527261238023 chrX 155270560 11734675 0.07557565967431303 0.36114658209317874 chrY 59373566 503448 0.008479328999710073 0.19609422006718766