BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777250.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 = 18,612,898 number of mapped reads = 18,491,385 (99.35%) number of supplementary alignments = 609,676 (3.28%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,247,287 number of mapped paired reads (second in pair) = 9,244,098 number of mapped paired reads (both in pair) = 18,447,228 number of mapped paired reads (singletons) = 44,157 number of mapped bases = 1,680,860,099 bp number of sequenced bases = 1,680,232,865 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,098,256 duplication rate = 35.15% >>>>>>> Insert size mean insert size = 405,945.4254 std insert size = 6,332,747.3825 median insert size = 197 >>>>>>> Mapping quality mean mapping quality = 53.8501 >>>>>>> ACTG content number of A's = 433,856,807 bp (25.82%) number of C's = 351,218,839 bp (20.9%) number of T's = 489,745,661 bp (29.15%) number of G's = 405,353,317 bp (24.12%) number of N's = 58,241 bp (0%) GC percentage = 45.03% >>>>>>> Mismatches and indels general error rate = 0.0045 number of mismatches = 7,407,746 number of insertions = 100,916 mapped reads with insertion percentage = 0.53% number of deletions = 355,703 mapped reads with deletion percentage = 1.9% homopolymer indels = 49.54% >>>>>>> Coverage mean coverageData = 0.543X std coverageData = 8.3534X There is a 7.61% of reference with a coverageData >= 1X There is a 3.75% of reference with a coverageData >= 2X There is a 2.15% of reference with a coverageData >= 3X There is a 1.58% of reference with a coverageData >= 4X There is a 1.25% of reference with a coverageData >= 5X There is a 1.07% of reference with a coverageData >= 6X There is a 0.95% of reference with a coverageData >= 7X There is a 0.87% of reference with a coverageData >= 8X There is a 0.81% of reference with a coverageData >= 9X There is a 0.76% of reference with a coverageData >= 10X There is a 0.72% of reference with a coverageData >= 11X There is a 0.68% of reference with a coverageData >= 12X There is a 0.65% of reference with a coverageData >= 13X There is a 0.62% of reference with a coverageData >= 14X There is a 0.6% of reference with a coverageData >= 15X There is a 0.58% of reference with a coverageData >= 16X There is a 0.55% of reference with a coverageData >= 17X There is a 0.53% of reference with a coverageData >= 18X There is a 0.52% of reference with a coverageData >= 19X There is a 0.5% of reference with a coverageData >= 20X There is a 0.48% of reference with a coverageData >= 21X There is a 0.47% of reference with a coverageData >= 22X There is a 0.45% of reference with a coverageData >= 23X There is a 0.44% of reference with a coverageData >= 24X There is a 0.43% of reference with a coverageData >= 25X There is a 0.42% of reference with a coverageData >= 26X There is a 0.4% of reference with a coverageData >= 27X There is a 0.39% of reference with a coverageData >= 28X There is a 0.38% of reference with a coverageData >= 29X There is a 0.37% of reference with a coverageData >= 30X There is a 0.36% of reference with a coverageData >= 31X There is a 0.35% of reference with a coverageData >= 32X There is a 0.35% of reference with a coverageData >= 33X There is a 0.34% of reference with a coverageData >= 34X There is a 0.33% of reference with a coverageData >= 35X There is a 0.32% of reference with a coverageData >= 36X There is a 0.31% of reference with a coverageData >= 37X There is a 0.31% of reference with a coverageData >= 38X There is a 0.3% of reference with a coverageData >= 39X There is a 0.29% of reference with a coverageData >= 40X There is a 0.29% of reference with a coverageData >= 41X There is a 0.28% of reference with a coverageData >= 42X There is a 0.27% of reference with a coverageData >= 43X There is a 0.27% of reference with a coverageData >= 44X There is a 0.26% of reference with a coverageData >= 45X There is a 0.26% of reference with a coverageData >= 46X There is a 0.25% of reference with a coverageData >= 47X There is a 0.25% of reference with a coverageData >= 48X There is a 0.24% of reference with a coverageData >= 49X There is a 0.24% of reference with a coverageData >= 50X There is a 0.23% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 166935788 0.6697507405608429 10.539133762259505 chr2 243199373 147138105 0.6050102152195926 8.35909901129402 chr3 198022430 101123726 0.5106680389691208 7.869454480316133 chr4 191154276 79580715 0.4163166875743862 6.6836935609714985 chr5 180915260 89103499 0.4925151090073883 7.730286933861086 chr6 171115067 78539131 0.4589843102477937 7.461265854482891 chr7 159138663 109113544 0.6856507522625096 11.679412414100048 chr8 146364022 56228648 0.384169874752417 6.255561634172666 chr9 141213431 58055128 0.41111619191520105 6.385436299797497 chr10 135534747 69615105 0.5136328988757399 7.695778731998047 chr11 135006516 112015364 0.8297033900200788 10.748076770608067 chr12 133851895 91706611 0.6851349470995536 9.21095353499461 chr13 115169878 50539432 0.43882508931719105 7.082486487064924 chr14 107349540 36450069 0.3395456468653708 6.077731322553254 chr15 102531392 76772496 0.7487706399226493 9.99661603371072 chr16 90354753 52992926 0.5864984877995295 8.130147680072424 chr17 81195210 70824612 0.872275741389178 10.084886838345357 chr18 78077248 26365096 0.3376796272327631 6.141333529464787 chr19 59128983 84190156 1.4238390672134509 14.029822940319562 chr20 63025520 46834235 0.7430995412651891 9.591358339095214 chr21 48129895 10941673 0.22733631561007978 4.006061888588905 chr22 51304566 19131694 0.3729043142086028 5.687764047944831 chrMT 16571 469366 28.324542876108865 17.862095069091914 chrX 155270560 45415057 0.29248981262127216 5.573568008337504 chrY 59373566 777923 0.013102177490905633 0.5296301841233279