BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777275.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 = 64,891,842 number of mapped reads = 64,764,106 (99.8%) number of supplementary alignments = 227,006 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 32,386,622 number of mapped paired reads (second in pair) = 32,377,484 number of mapped paired reads (both in pair) = 64,734,908 number of mapped paired reads (singletons) = 29,198 number of mapped bases = 6,450,251,171 bp number of sequenced bases = 6,446,849,847 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,880,050 duplication rate = 48.25% >>>>>>> Insert size mean insert size = 131,839.6677 std insert size = 3,710,285.9882 median insert size = 226 >>>>>>> Mapping quality mean mapping quality = 55.022 >>>>>>> ACTG content number of A's = 1,563,215,540 bp (24.25%) number of C's = 1,632,357,537 bp (25.32%) number of T's = 1,567,230,507 bp (24.31%) number of G's = 1,653,959,525 bp (25.66%) number of N's = 30,086,738 bp (0.47%) GC percentage = 50.98% >>>>>>> Mismatches and indels general error rate = 0.0111 number of mismatches = 70,780,817 number of insertions = 705,828 mapped reads with insertion percentage = 1.08% number of deletions = 2,673,484 mapped reads with deletion percentage = 4.04% homopolymer indels = 54.64% >>>>>>> Coverage mean coverageData = 2.0836X std coverageData = 28.8881X There is a 13.03% of reference with a coverageData >= 1X There is a 7.65% of reference with a coverageData >= 2X There is a 5.06% of reference with a coverageData >= 3X There is a 3.91% of reference with a coverageData >= 4X There is a 3.21% of reference with a coverageData >= 5X There is a 2.8% of reference with a coverageData >= 6X There is a 2.5% of reference with a coverageData >= 7X There is a 2.29% of reference with a coverageData >= 8X There is a 2.13% of reference with a coverageData >= 9X There is a 2% of reference with a coverageData >= 10X There is a 1.89% of reference with a coverageData >= 11X There is a 1.8% of reference with a coverageData >= 12X There is a 1.72% of reference with a coverageData >= 13X There is a 1.65% of reference with a coverageData >= 14X There is a 1.59% of reference with a coverageData >= 15X There is a 1.54% of reference with a coverageData >= 16X There is a 1.49% of reference with a coverageData >= 17X There is a 1.44% of reference with a coverageData >= 18X There is a 1.4% of reference with a coverageData >= 19X There is a 1.36% of reference with a coverageData >= 20X There is a 1.32% of reference with a coverageData >= 21X There is a 1.29% of reference with a coverageData >= 22X There is a 1.26% of reference with a coverageData >= 23X There is a 1.23% of reference with a coverageData >= 24X There is a 1.2% of reference with a coverageData >= 25X There is a 1.17% of reference with a coverageData >= 26X There is a 1.15% of reference with a coverageData >= 27X There is a 1.13% of reference with a coverageData >= 28X There is a 1.1% of reference with a coverageData >= 29X There is a 1.08% of reference with a coverageData >= 30X There is a 1.06% of reference with a coverageData >= 31X There is a 1.04% of reference with a coverageData >= 32X There is a 1.02% of reference with a coverageData >= 33X There is a 1% of reference with a coverageData >= 34X There is a 0.98% of reference with a coverageData >= 35X There is a 0.97% of reference with a coverageData >= 36X There is a 0.95% of reference with a coverageData >= 37X There is a 0.94% of reference with a coverageData >= 38X There is a 0.92% of reference with a coverageData >= 39X There is a 0.91% of reference with a coverageData >= 40X There is a 0.89% of reference with a coverageData >= 41X There is a 0.88% of reference with a coverageData >= 42X There is a 0.86% of reference with a coverageData >= 43X There is a 0.85% of reference with a coverageData >= 44X There is a 0.84% of reference with a coverageData >= 45X There is a 0.83% of reference with a coverageData >= 46X There is a 0.81% of reference with a coverageData >= 47X There is a 0.8% of reference with a coverageData >= 48X There is a 0.79% of reference with a coverageData >= 49X There is a 0.78% of reference with a coverageData >= 50X There is a 0.77% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 703138991 2.8210119925839625 33.19170487885467 chr2 243199373 461781247 1.8987764701186134 26.206655733430303 chr3 198022430 342192976 1.7280515949632576 25.574244724384094 chr4 191154276 177468317 0.9284035948010915 19.033230811438695 chr5 180915260 261475910 1.4452949408468916 20.51527253734989 chr6 171115067 303262460 1.7722721050624957 26.607969930959904 chr7 159138663 391845465 2.46228953802383 33.64293606561293 chr8 146364022 160943759 1.09961284747969 18.824414884724295 chr9 141213431 259698754 1.839051371820291 26.020984153555954 chr10 135534747 258715123 1.9088472050639531 27.06568521129122 chr11 135006516 476713600 3.531041420252634 39.564092623643084 chr12 133851895 365863253 2.7333438424611023 36.29459270579435 chr13 115169878 120260018 1.0441967994443826 20.1258289940646 chr14 107349540 146188298 1.3617971534857065 20.423987222383555 chr15 102531392 312082865 3.043778679996854 37.20264419214371 chr16 90354753 278587445 3.083262758739432 34.98811841922028 chr17 81195210 385161929 4.743653338663697 44.88526035471896 chr18 78077248 67607828 0.865909464431943 13.821197022614651 chr19 59128983 341738710 5.77954655502869 48.17345866469644 chr20 63025520 257531564 4.086147389184571 47.13196362621463 chr21 48129895 44808776 0.9309967536808463 15.11260669799966 chr22 51304566 145537828 2.8367422112098173 32.18094902731798 chrMT 16571 50404 3.0416993542936455 3.7405593376433757 chrX 155270560 185923816 1.19741833867283 20.25823055266458 chrY 59373566 1671835 0.028157901110403238 1.1478779627015792