BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618571.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 79,638,923 number of mapped reads = 75,053,217 (94.24%) number of supplementary alignments = 237,558 (0.3%) number of secondary alignments = 0 number of mapped bases = 7,281,501,933 bp number of sequenced bases = 7,276,111,064 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,163,848 duplication rate = 38.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.6981 >>>>>>> ACTG content number of A's = 1,926,967,192 bp (26.48%) number of C's = 1,715,360,340 bp (23.58%) number of T's = 2,049,193,931 bp (28.16%) number of G's = 1,584,100,098 bp (21.77%) number of N's = 489,503 bp (0.01%) GC percentage = 45.35% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 67,262,006 number of insertions = 1,306,243 mapped reads with insertion percentage = 1.71% number of deletions = 3,445,826 mapped reads with deletion percentage = 4.48% homopolymer indels = 51.92% >>>>>>> Coverage mean coverageData = 2.3521X std coverageData = 48.6468X There is a 21.2% of reference with a coverageData >= 1X There is a 15.13% of reference with a coverageData >= 2X There is a 11.98% of reference with a coverageData >= 3X There is a 9.93% of reference with a coverageData >= 4X There is a 8.47% of reference with a coverageData >= 5X There is a 7.34% of reference with a coverageData >= 6X There is a 6.45% of reference with a coverageData >= 7X There is a 5.73% of reference with a coverageData >= 8X There is a 5.12% of reference with a coverageData >= 9X There is a 4.62% of reference with a coverageData >= 10X There is a 4.19% of reference with a coverageData >= 11X There is a 3.82% of reference with a coverageData >= 12X There is a 3.51% of reference with a coverageData >= 13X There is a 3.23% of reference with a coverageData >= 14X There is a 2.99% of reference with a coverageData >= 15X There is a 2.77% of reference with a coverageData >= 16X There is a 2.58% of reference with a coverageData >= 17X There is a 2.41% of reference with a coverageData >= 18X There is a 2.26% of reference with a coverageData >= 19X There is a 2.12% of reference with a coverageData >= 20X There is a 2% of reference with a coverageData >= 21X There is a 1.88% of reference with a coverageData >= 22X There is a 1.78% of reference with a coverageData >= 23X There is a 1.68% of reference with a coverageData >= 24X There is a 1.6% of reference with a coverageData >= 25X There is a 1.52% of reference with a coverageData >= 26X There is a 1.44% of reference with a coverageData >= 27X There is a 1.37% of reference with a coverageData >= 28X There is a 1.31% of reference with a coverageData >= 29X There is a 1.25% of reference with a coverageData >= 30X There is a 1.2% of reference with a coverageData >= 31X There is a 1.15% of reference with a coverageData >= 32X There is a 1.1% of reference with a coverageData >= 33X There is a 1.05% of reference with a coverageData >= 34X There is a 1.01% of reference with a coverageData >= 35X There is a 0.97% of reference with a coverageData >= 36X There is a 0.93% of reference with a coverageData >= 37X There is a 0.9% of reference with a coverageData >= 38X There is a 0.87% of reference with a coverageData >= 39X There is a 0.84% of reference with a coverageData >= 40X There is a 0.81% of reference with a coverageData >= 41X There is a 0.78% of reference with a coverageData >= 42X There is a 0.75% of reference with a coverageData >= 43X There is a 0.73% of reference with a coverageData >= 44X There is a 0.7% of reference with a coverageData >= 45X There is a 0.68% of reference with a coverageData >= 46X There is a 0.66% of reference with a coverageData >= 47X There is a 0.64% of reference with a coverageData >= 48X There is a 0.62% of reference with a coverageData >= 49X There is a 0.6% of reference with a coverageData >= 50X There is a 0.58% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 702943102 2.820226080800818 51.886367330644916 chr2 243199373 641450002 2.637547926572985 64.33861809694746 chr3 198022430 467441907 2.3605503023066627 59.88483898932655 chr4 191154276 336567732 1.7607125461321096 30.042491836064944 chr5 180915260 416864696 2.304198639738848 51.47445054536254 chr6 171115067 380798798 2.2253960722231434 31.132513469806238 chr7 159138663 374909272 2.355865412794124 46.5237695226263 chr8 146364022 365681398 2.4984377513211546 51.43445854893755 chr9 141213431 321058203 2.273567044766443 36.839453894049484 chr10 135534747 381347663 2.813652376537804 75.26307365573999 chr11 135006516 399335515 2.9578980839709987 46.65442057571296 chr12 133851895 351826528 2.628476257284217 55.32677829407108 chr13 115169878 192728384 1.6734270049326614 40.15892037806937 chr14 107349540 229230864 2.1353688520696035 34.18682025554802 chr15 102531392 247692887 2.4157761068922188 39.53222861151759 chr16 90354753 301429555 3.3360675005110134 72.2201343281094 chr17 81195210 266332290 3.2801478067486984 39.99459216099621 chr18 78077248 184664749 2.3651544301356524 43.252471533131384 chr19 59128983 184306396 3.117022932729961 39.511024870887475 chr20 63025520 222444718 3.5294388368394265 54.07994386404626 chr21 48129895 93903235 1.9510376035518049 29.50095614608166 chr22 51304566 142443307 2.7764255329632843 38.52941987859922 chrMT 16571 3986 0.24054070363888722 0.8913996020730715 chrX 155270560 17997953 0.11591349319536169 14.574235820380572 chrY 59373566 58098793 0.9785296204038005 36.23469422141665