BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777282.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 33,661,894 number of mapped reads = 33,291,489 (98.9%) number of supplementary alignments = 1,247,035 (3.7%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 16,647,214 number of mapped paired reads (second in pair) = 16,644,275 number of mapped paired reads (both in pair) = 33,131,928 number of mapped paired reads (singletons) = 159,561 number of mapped bases = 3,291,293,861 bp number of sequenced bases = 3,288,097,564 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,267,186 duplication rate = 36.49% >>>>>>> Insert size mean insert size = 274,137.3029 std insert size = 5,236,916.4989 median insert size = 225 >>>>>>> Mapping quality mean mapping quality = 53.3499 >>>>>>> ACTG content number of A's = 867,580,665 bp (26.39%) number of C's = 777,333,674 bp (23.64%) number of T's = 865,221,003 bp (26.31%) number of G's = 777,826,799 bp (23.66%) number of N's = 135,423 bp (0%) GC percentage = 47.3% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 16,182,613 number of insertions = 1,105,654 mapped reads with insertion percentage = 3.02% number of deletions = 860,593 mapped reads with deletion percentage = 2.35% homopolymer indels = 30.5% >>>>>>> Coverage mean coverageData = 1.0632X std coverageData = 38.882X There is a 12.34% of reference with a coverageData >= 1X There is a 6.53% of reference with a coverageData >= 2X There is a 4.07% of reference with a coverageData >= 3X There is a 3.11% of reference with a coverageData >= 4X There is a 2.54% of reference with a coverageData >= 5X There is a 2.21% of reference with a coverageData >= 6X There is a 1.98% of reference with a coverageData >= 7X There is a 1.81% of reference with a coverageData >= 8X There is a 1.68% of reference with a coverageData >= 9X There is a 1.57% of reference with a coverageData >= 10X There is a 1.47% of reference with a coverageData >= 11X There is a 1.39% of reference with a coverageData >= 12X There is a 1.32% of reference with a coverageData >= 13X There is a 1.26% of reference with a coverageData >= 14X There is a 1.2% of reference with a coverageData >= 15X There is a 1.15% of reference with a coverageData >= 16X There is a 1.1% of reference with a coverageData >= 17X There is a 1.06% of reference with a coverageData >= 18X There is a 1.02% of reference with a coverageData >= 19X There is a 0.98% of reference with a coverageData >= 20X There is a 0.94% of reference with a coverageData >= 21X There is a 0.91% of reference with a coverageData >= 22X There is a 0.88% of reference with a coverageData >= 23X There is a 0.85% of reference with a coverageData >= 24X There is a 0.82% of reference with a coverageData >= 25X There is a 0.8% of reference with a coverageData >= 26X There is a 0.77% of reference with a coverageData >= 27X There is a 0.75% of reference with a coverageData >= 28X There is a 0.73% of reference with a coverageData >= 29X There is a 0.71% of reference with a coverageData >= 30X There is a 0.69% of reference with a coverageData >= 31X There is a 0.67% of reference with a coverageData >= 32X There is a 0.65% of reference with a coverageData >= 33X There is a 0.63% of reference with a coverageData >= 34X There is a 0.61% of reference with a coverageData >= 35X There is a 0.6% of reference with a coverageData >= 36X There is a 0.58% of reference with a coverageData >= 37X There is a 0.57% of reference with a coverageData >= 38X There is a 0.55% of reference with a coverageData >= 39X There is a 0.54% of reference with a coverageData >= 40X There is a 0.53% of reference with a coverageData >= 41X There is a 0.52% of reference with a coverageData >= 42X There is a 0.5% of reference with a coverageData >= 43X There is a 0.49% of reference with a coverageData >= 44X There is a 0.48% of reference with a coverageData >= 45X There is a 0.47% of reference with a coverageData >= 46X There is a 0.46% of reference with a coverageData >= 47X There is a 0.45% of reference with a coverageData >= 48X There is a 0.44% of reference with a coverageData >= 49X There is a 0.43% of reference with a coverageData >= 50X There is a 0.42% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 351518544 1.410301577543512 18.095002988981836 chr2 243199373 312035460 1.2830438506105852 89.42803030509555 chr3 198022430 170094566 0.8589661585306271 11.688777656077805 chr4 191154276 119187095 0.6235125757793668 22.78639429028409 chr5 180915260 150619196 0.8325400300671154 19.743831466747586 chr6 171115067 161330278 0.9428174901746087 22.63346399500165 chr7 159138663 176335390 1.1080612760960546 30.27030916018089 chr8 146364022 101612069 0.6942421205123757 11.765764923759773 chr9 141213431 117186721 0.8298553485326761 19.366838091193756 chr10 135534747 146968086 1.0843572534207777 82.33316251314156 chr11 135006516 233403018 1.7288277996893129 33.749011762366884 chr12 133851895 186963000 1.3967900865355698 15.795019267953894 chr13 115169878 75202439 0.6529696853547071 10.442905899695372 chr14 107349540 65092963 0.6063646197272946 19.957137591006536 chr15 102531392 151054239 1.4732486905083664 14.09691692388762 chr16 90354753 139713437 1.5462765638903357 63.81263822541393 chr17 81195210 176860221 2.1782100323405778 24.771754239009926 chr18 78077248 42944035 0.5500198342031727 11.78131096503984 chr19 59128983 149738260 2.532400396604149 27.44935056398252 chr20 63025520 98515585 1.5631062623521392 18.0199005062502 chr21 48129895 18294404 0.38010479765226995 5.767081028958204 chr22 51304566 47683966 0.9294292831558111 15.602840252329978 chrMT 16571 670837 40.48259006698449 11.729577431241099 chrX 155270560 81259845 0.5233435430386804 11.516225638647983 chrY 59373566 17010207 0.28649461613944494 86.02793495985937