BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504640.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 438,671,610 number of mapped reads = 399,305,174 (91.03%) number of supplementary alignments = 3,168,036 (0.72%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 204,377,088 number of mapped paired reads (second in pair) = 194,928,086 number of mapped paired reads (both in pair) = 386,232,908 number of mapped paired reads (singletons) = 13,072,266 number of mapped bases = 31,922,220,183 bp number of sequenced bases = 31,914,351,512 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 108,851,517 duplication rate = 24.06% >>>>>>> Insert size mean insert size = 63,201.9271 std insert size = 2,449,505.9051 median insert size = 348 >>>>>>> Mapping quality mean mapping quality = 53.0384 >>>>>>> ACTG content number of A's = 8,172,746,578 bp (25.61%) number of C's = 7,275,813,180 bp (22.8%) number of T's = 8,319,274,260 bp (26.07%) number of G's = 7,646,541,288 bp (23.96%) number of N's = 499,976,206 bp (1.57%) GC percentage = 46.76% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 286,057,698 number of insertions = 4,168,198 mapped reads with insertion percentage = 1.02% number of deletions = 4,056,734 mapped reads with deletion percentage = 0.99% homopolymer indels = 35.07% >>>>>>> Coverage mean coverageData = 10.3118X std coverageData = 25.4028X There is a 71.91% of reference with a coverageData >= 1X There is a 63.16% of reference with a coverageData >= 2X There is a 56.32% of reference with a coverageData >= 3X There is a 50.63% of reference with a coverageData >= 4X There is a 45.77% of reference with a coverageData >= 5X There is a 41.57% of reference with a coverageData >= 6X There is a 37.91% of reference with a coverageData >= 7X There is a 34.68% of reference with a coverageData >= 8X There is a 31.84% of reference with a coverageData >= 9X There is a 29.31% of reference with a coverageData >= 10X There is a 27.07% of reference with a coverageData >= 11X There is a 25.05% of reference with a coverageData >= 12X There is a 23.25% of reference with a coverageData >= 13X There is a 21.62% of reference with a coverageData >= 14X There is a 20.16% of reference with a coverageData >= 15X There is a 18.83% of reference with a coverageData >= 16X There is a 17.62% of reference with a coverageData >= 17X There is a 16.52% of reference with a coverageData >= 18X There is a 15.51% of reference with a coverageData >= 19X There is a 14.6% of reference with a coverageData >= 20X There is a 13.75% of reference with a coverageData >= 21X There is a 12.97% of reference with a coverageData >= 22X There is a 12.26% of reference with a coverageData >= 23X There is a 11.6% of reference with a coverageData >= 24X There is a 10.99% of reference with a coverageData >= 25X There is a 10.42% of reference with a coverageData >= 26X There is a 9.89% of reference with a coverageData >= 27X There is a 9.4% of reference with a coverageData >= 28X There is a 8.95% of reference with a coverageData >= 29X There is a 8.52% of reference with a coverageData >= 30X There is a 8.12% of reference with a coverageData >= 31X There is a 7.75% of reference with a coverageData >= 32X There is a 7.4% of reference with a coverageData >= 33X There is a 7.07% of reference with a coverageData >= 34X There is a 6.77% of reference with a coverageData >= 35X There is a 6.48% of reference with a coverageData >= 36X There is a 6.2% of reference with a coverageData >= 37X There is a 5.95% of reference with a coverageData >= 38X There is a 5.7% of reference with a coverageData >= 39X There is a 5.47% of reference with a coverageData >= 40X There is a 5.26% of reference with a coverageData >= 41X There is a 5.05% of reference with a coverageData >= 42X There is a 4.86% of reference with a coverageData >= 43X There is a 4.67% of reference with a coverageData >= 44X There is a 4.5% of reference with a coverageData >= 45X There is a 4.33% of reference with a coverageData >= 46X There is a 4.17% of reference with a coverageData >= 47X There is a 4.02% of reference with a coverageData >= 48X There is a 3.88% of reference with a coverageData >= 49X There is a 3.74% of reference with a coverageData >= 50X There is a 3.61% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2694502401 10.810413992910373 22.338325823788267 chr2 243199373 1793960082 7.376499617867025 36.968519193117075 chr3 198022430 1578356771 7.970595911786357 15.763784326971559 chr4 191154276 1231445615 6.442155732890851 11.389700356776334 chr5 180915260 2164091594 11.961907436663994 20.056475115983947 chr6 171115067 844250149 4.933815378163047 11.08684863875946 chr7 159138663 1638549606 10.296364033170242 18.501349461640157 chr8 146364022 1857659195 12.69204801573436 33.461382535315295 chr9 141213431 880531027 6.235462312363191 13.922645279607147 chr10 135534747 1840589330 13.580202647222265 22.747095821977027 chr11 135006516 1411486293 10.454949396664677 19.988738976980496 chr12 133851895 1527561711 11.412327864316003 23.71900177811647 chr13 115169878 416406789 3.615587653917633 7.12614413849576 chr14 107349540 962938335 8.970120738291007 18.500756864913303 chr15 102531392 1299299190 12.672208624652242 23.8183883395618 chr16 90354753 1892366474 20.94374021475107 33.63162841158748 chr17 81195210 1414438635 17.420222633822856 30.528980644391364 chr18 78077248 430633260 5.515476928695028 43.94229232616929 chr19 59128983 1660235498 28.078201480312963 56.389971094865416 chr20 63025520 1600998635 25.402386763330156 36.127866384084214 chr21 48129895 483957072 10.055228086410743 19.505261505922387 chr22 51304566 651376456 12.696266761129994 26.982835410148628 chrMT 16571 369348 22.288817814253818 18.458891246008104 chrX 155270560 1600425268 10.30733236229714 18.558267678540656 chrY 59373566 45791449 0.7712430309474758 26.635134071750603