BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618583.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 = 64,441,766 number of mapped reads = 60,141,089 (93.33%) number of supplementary alignments = 178,281 (0.28%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 30,750,869 number of mapped paired reads (second in pair) = 29,390,220 number of mapped paired reads (both in pair) = 57,746,104 number of mapped paired reads (singletons) = 2,394,985 number of mapped bases = 5,687,563,799 bp number of sequenced bases = 5,683,718,511 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,126,489 duplication rate = 34.39% >>>>>>> Insert size mean insert size = 87,372.5425 std insert size = 2,969,908.2441 median insert size = 225 >>>>>>> Mapping quality mean mapping quality = 52.3103 >>>>>>> ACTG content number of A's = 1,543,000,273 bp (27.15%) number of C's = 1,268,260,228 bp (22.31%) number of T's = 1,557,527,499 bp (27.4%) number of G's = 1,313,187,637 bp (23.1%) number of N's = 1,742,874 bp (0.03%) GC percentage = 45.42% >>>>>>> Mismatches and indels general error rate = 0.0154 number of mismatches = 85,826,498 number of insertions = 1,047,439 mapped reads with insertion percentage = 1.71% number of deletions = 2,881,136 mapped reads with deletion percentage = 4.67% homopolymer indels = 52.22% >>>>>>> Coverage mean coverageData = 1.8373X std coverageData = 7.8568X There is a 25.99% of reference with a coverageData >= 1X There is a 18.91% of reference with a coverageData >= 2X There is a 15.02% of reference with a coverageData >= 3X There is a 12.43% of reference with a coverageData >= 4X There is a 10.51% of reference with a coverageData >= 5X There is a 9.04% of reference with a coverageData >= 6X There is a 7.85% of reference with a coverageData >= 7X There is a 6.89% of reference with a coverageData >= 8X There is a 6.08% of reference with a coverageData >= 9X There is a 5.41% of reference with a coverageData >= 10X There is a 4.83% of reference with a coverageData >= 11X There is a 4.33% of reference with a coverageData >= 12X There is a 3.91% of reference with a coverageData >= 13X There is a 3.53% of reference with a coverageData >= 14X There is a 3.2% of reference with a coverageData >= 15X There is a 2.91% of reference with a coverageData >= 16X There is a 2.66% of reference with a coverageData >= 17X There is a 2.43% of reference with a coverageData >= 18X There is a 2.23% of reference with a coverageData >= 19X There is a 2.05% of reference with a coverageData >= 20X There is a 1.88% of reference with a coverageData >= 21X There is a 1.74% of reference with a coverageData >= 22X There is a 1.61% of reference with a coverageData >= 23X There is a 1.49% of reference with a coverageData >= 24X There is a 1.38% of reference with a coverageData >= 25X There is a 1.28% of reference with a coverageData >= 26X There is a 1.19% of reference with a coverageData >= 27X There is a 1.11% of reference with a coverageData >= 28X There is a 1.04% of reference with a coverageData >= 29X There is a 0.97% of reference with a coverageData >= 30X There is a 0.91% of reference with a coverageData >= 31X There is a 0.85% of reference with a coverageData >= 32X There is a 0.8% of reference with a coverageData >= 33X There is a 0.75% of reference with a coverageData >= 34X There is a 0.7% of reference with a coverageData >= 35X There is a 0.66% of reference with a coverageData >= 36X There is a 0.62% of reference with a coverageData >= 37X There is a 0.59% of reference with a coverageData >= 38X There is a 0.55% of reference with a coverageData >= 39X There is a 0.52% of reference with a coverageData >= 40X There is a 0.49% of reference with a coverageData >= 41X There is a 0.47% of reference with a coverageData >= 42X There is a 0.44% of reference with a coverageData >= 43X There is a 0.42% of reference with a coverageData >= 44X There is a 0.39% of reference with a coverageData >= 45X There is a 0.37% of reference with a coverageData >= 46X There is a 0.35% of reference with a coverageData >= 47X There is a 0.34% of reference with a coverageData >= 48X There is a 0.32% of reference with a coverageData >= 49X There is a 0.3% of reference with a coverageData >= 50X There is a 0.29% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 524820289 2.1055927038191813 9.817103882320524 chr2 243199373 487546296 2.0047185565729233 8.921345862486412 chr3 198022430 383043574 1.9343443770486 6.639539896269541 chr4 191154276 289426734 1.514100233886476 6.227743721836838 chr5 180915260 331949877 1.834836248749829 6.998265928384974 chr6 171115067 320713204 1.8742546148785366 6.754468903016746 chr7 159138663 288718941 1.814260190183953 6.729597281990065 chr8 146364022 292592517 1.999074041570134 7.033126505787606 chr9 141213431 256208911 1.814338120571548 8.294570711548722 chr10 135534747 303234550 2.2373196299248637 7.477660564860669 chr11 135006516 301060129 2.2299673965366233 8.329771501704236 chr12 133851895 271355859 2.0272844026601193 7.668912391765774 chr13 115169878 150476196 1.306558612487199 5.400302785740785 chr14 107349540 183351489 1.7079857910895566 6.594655093774744 chr15 102531392 194145822 1.8935256628526023 7.484100173796078 chr16 90354753 215628691 2.386467605085479 14.369520144556787 chr17 81195210 199400910 2.455821100776758 9.339139849453924 chr18 78077248 155770941 1.9950874933501754 8.50357139698196 chr19 59128983 129099969 2.1833619056157283 8.826270548924859 chr20 63025520 166524923 2.642182452441487 8.30086102029633 chr21 48129895 76989609 1.5996213787709281 9.912435512623112 chr22 51304566 107850512 2.102162057076947 8.378220542752333 chrMT 16571 41968 2.532617222859212 11.038239687901772 chrX 155270560 10984486 0.07074416425109821 1.7403130299754181 chrY 59373566 46627402 0.7853225794118548 6.116864979656885