BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504605.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 = 437,166,046 number of mapped reads = 375,488,696 (85.89%) number of supplementary alignments = 1,931,911 (0.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 187,986,104 number of mapped paired reads (second in pair) = 187,502,592 number of mapped paired reads (both in pair) = 373,163,068 number of mapped paired reads (singletons) = 2,325,628 number of mapped bases = 37,277,218,703 bp number of sequenced bases = 37,267,600,629 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 93,541,564 duplication rate = 22.22% >>>>>>> Insert size mean insert size = 29,653.4872 std insert size = 1,680,575.1181 median insert size = 213 >>>>>>> Mapping quality mean mapping quality = 53.9647 >>>>>>> ACTG content number of A's = 9,811,335,694 bp (26.33%) number of C's = 8,698,488,640 bp (23.34%) number of T's = 9,837,199,913 bp (26.4%) number of G's = 8,856,659,002 bp (23.77%) number of N's = 63,917,380 bp (0.17%) GC percentage = 47.11% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 316,673,903 number of insertions = 2,808,643 mapped reads with insertion percentage = 0.73% number of deletions = 3,746,592 mapped reads with deletion percentage = 0.97% homopolymer indels = 40.09% >>>>>>> Coverage mean coverageData = 12.0416X std coverageData = 24.9808X There is a 78.64% of reference with a coverageData >= 1X There is a 70.13% of reference with a coverageData >= 2X There is a 62.91% of reference with a coverageData >= 3X There is a 56.88% of reference with a coverageData >= 4X There is a 51.68% of reference with a coverageData >= 5X There is a 47.18% of reference with a coverageData >= 6X There is a 43.23% of reference with a coverageData >= 7X There is a 39.76% of reference with a coverageData >= 8X There is a 36.67% of reference with a coverageData >= 9X There is a 33.91% of reference with a coverageData >= 10X There is a 31.45% of reference with a coverageData >= 11X There is a 29.23% of reference with a coverageData >= 12X There is a 27.22% of reference with a coverageData >= 13X There is a 25.41% of reference with a coverageData >= 14X There is a 23.76% of reference with a coverageData >= 15X There is a 22.25% of reference with a coverageData >= 16X There is a 20.88% of reference with a coverageData >= 17X There is a 19.62% of reference with a coverageData >= 18X There is a 18.46% of reference with a coverageData >= 19X There is a 17.4% of reference with a coverageData >= 20X There is a 16.42% of reference with a coverageData >= 21X There is a 15.51% of reference with a coverageData >= 22X There is a 14.67% of reference with a coverageData >= 23X There is a 13.89% of reference with a coverageData >= 24X There is a 13.17% of reference with a coverageData >= 25X There is a 12.49% of reference with a coverageData >= 26X There is a 11.87% of reference with a coverageData >= 27X There is a 11.28% of reference with a coverageData >= 28X There is a 10.74% of reference with a coverageData >= 29X There is a 10.23% of reference with a coverageData >= 30X There is a 9.75% of reference with a coverageData >= 31X There is a 9.3% of reference with a coverageData >= 32X There is a 8.88% of reference with a coverageData >= 33X There is a 8.48% of reference with a coverageData >= 34X There is a 8.11% of reference with a coverageData >= 35X There is a 7.76% of reference with a coverageData >= 36X There is a 7.43% of reference with a coverageData >= 37X There is a 7.12% of reference with a coverageData >= 38X There is a 6.82% of reference with a coverageData >= 39X There is a 6.54% of reference with a coverageData >= 40X There is a 6.28% of reference with a coverageData >= 41X There is a 6.03% of reference with a coverageData >= 42X There is a 5.8% of reference with a coverageData >= 43X There is a 5.57% of reference with a coverageData >= 44X There is a 5.36% of reference with a coverageData >= 45X There is a 5.16% of reference with a coverageData >= 46X There is a 4.97% of reference with a coverageData >= 47X There is a 4.79% of reference with a coverageData >= 48X There is a 4.61% of reference with a coverageData >= 49X There is a 4.45% of reference with a coverageData >= 50X There is a 4.29% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3831972159 15.373972364145082 26.003442054638008 chr2 243199373 2558711591 10.521045179668288 19.115943281706656 chr3 198022430 2758887669 13.932197827286535 23.148309381991133 chr4 191154276 1557605016 8.148418380136054 13.004095427049577 chr5 180915260 1515075272 8.37450236093959 14.134504378191556 chr6 171115067 1904490452 11.12988169533896 18.216232408746574 chr7 159138663 3031884854 19.051843196646686 28.468554602253818 chr8 146364022 2841351917 19.41291225927093 47.83395321963665 chr9 141213431 1464755990 10.372639341933418 20.247321428133557 chr10 135534747 1754175378 12.942624801594237 24.51476297493734 chr11 135006516 1902480336 14.091766770723867 23.963278855974764 chr12 133851895 1270917235 9.49495137891025 16.107843250282354 chr13 115169878 845417651 7.340614279369125 13.826690521298149 chr14 107349540 1244186856 11.590052980199077 20.23258524584338 chr15 102531392 830791501 8.102801344977351 15.163268030002403 chr16 90354753 1088825424 12.050560572059778 20.704618434238434 chr17 81195210 1354362492 16.680325009320132 51.5752642366568 chr18 78077248 487237612 6.240455759916128 28.248485664630955 chr19 59128983 1100283290 18.60818898238111 32.38735987718374 chr20 63025520 1678689052 26.635068651555752 39.87013471518123 chr21 48129895 353549028 7.345726143803139 18.723913594947643 chr22 51304566 767599853 14.961628425041155 27.89845815692369 chrMT 16571 246866 14.897471486331543 11.916635464832428 chrX 155270560 1096568801 7.062309822286981 12.534038572073234 chrY 59373566 37152408 0.6257398789218758 14.717614245745388