BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1299077.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 = 802,305,020 number of mapped reads = 706,307,743 (88.03%) number of supplementary alignments = 630,350 (0.08%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 361,156,846 number of mapped paired reads (second in pair) = 345,150,897 number of mapped paired reads (both in pair) = 686,616,278 number of mapped paired reads (singletons) = 19,691,465 number of mapped bases = 59,331,712,471 bp number of sequenced bases = 59,320,384,512 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 687,543,521 duplication rate = 75.69% >>>>>>> Insert size mean insert size = 513,019.6827 std insert size = 7,034,847.508 median insert size = 234 >>>>>>> Mapping quality mean mapping quality = 54.3568 >>>>>>> ACTG content number of A's = 15,882,686,152 bp (26.77%) number of C's = 14,082,306,612 bp (23.74%) number of T's = 15,351,765,817 bp (25.88%) number of G's = 13,992,120,634 bp (23.59%) number of N's = 11,505,297 bp (0.02%) GC percentage = 47.33% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 305,576,740 number of insertions = 2,637,666 mapped reads with insertion percentage = 0.37% number of deletions = 5,490,842 mapped reads with deletion percentage = 0.77% homopolymer indels = 47.82% >>>>>>> Coverage mean coverageData = 19.1659X std coverageData = 1,296.7104X There is a 29.1% of reference with a coverageData >= 1X There is a 25.68% of reference with a coverageData >= 2X There is a 22.88% of reference with a coverageData >= 3X There is a 20.29% of reference with a coverageData >= 4X There is a 17.82% of reference with a coverageData >= 5X There is a 15.53% of reference with a coverageData >= 6X There is a 13.4% of reference with a coverageData >= 7X There is a 11.53% of reference with a coverageData >= 8X There is a 9.86% of reference with a coverageData >= 9X There is a 8.47% of reference with a coverageData >= 10X There is a 7.27% of reference with a coverageData >= 11X There is a 6.32% of reference with a coverageData >= 12X There is a 5.48% of reference with a coverageData >= 13X There is a 4.83% of reference with a coverageData >= 14X There is a 4.24% of reference with a coverageData >= 15X There is a 3.78% of reference with a coverageData >= 16X There is a 3.35% of reference with a coverageData >= 17X There is a 3.01% of reference with a coverageData >= 18X There is a 2.68% of reference with a coverageData >= 19X There is a 2.43% of reference with a coverageData >= 20X There is a 2.18% of reference with a coverageData >= 21X There is a 1.98% of reference with a coverageData >= 22X There is a 1.79% of reference with a coverageData >= 23X There is a 1.63% of reference with a coverageData >= 24X There is a 1.48% of reference with a coverageData >= 25X There is a 1.36% of reference with a coverageData >= 26X There is a 1.24% of reference with a coverageData >= 27X There is a 1.14% of reference with a coverageData >= 28X There is a 1.05% of reference with a coverageData >= 29X There is a 0.97% of reference with a coverageData >= 30X There is a 0.89% of reference with a coverageData >= 31X There is a 0.83% of reference with a coverageData >= 32X There is a 0.77% of reference with a coverageData >= 33X There is a 0.72% of reference with a coverageData >= 34X There is a 0.67% of reference with a coverageData >= 35X There is a 0.63% of reference with a coverageData >= 36X There is a 0.58% of reference with a coverageData >= 37X There is a 0.55% of reference with a coverageData >= 38X There is a 0.52% of reference with a coverageData >= 39X There is a 0.49% of reference with a coverageData >= 40X There is a 0.46% of reference with a coverageData >= 41X There is a 0.43% of reference with a coverageData >= 42X There is a 0.41% of reference with a coverageData >= 43X There is a 0.39% of reference with a coverageData >= 44X There is a 0.37% of reference with a coverageData >= 45X There is a 0.35% of reference with a coverageData >= 46X There is a 0.34% of reference with a coverageData >= 47X There is a 0.32% of reference with a coverageData >= 48X There is a 0.31% of reference with a coverageData >= 49X There is a 0.29% of reference with a coverageData >= 50X There is a 0.28% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7921783408 31.782401890184257 1881.0348904985215 chr2 243199373 2821775489 11.602725180545592 899.8732969583486 chr3 198022430 3327306726 16.80267596958587 1220.328552119642 chr4 191154276 1348827094 7.056222451440218 600.9050851925143 chr5 180915260 3009460021 16.634638896685665 1190.9067268709814 chr6 171115067 3809108108 22.26050677349178 1420.4053353793925 chr7 159138663 3316462970 20.840083154399757 1408.9826370994099 chr8 146364022 1985900553 13.568228898492555 1010.411506535486 chr9 141213431 2148465183 15.214311895020808 1039.3636542581398 chr10 135534747 1390108875 10.256475964794474 711.5486287840006 chr11 135006516 5090729125 37.707284624691745 1996.1600995228716 chr12 133851895 1849851122 13.82013397718426 860.3962230424291 chr13 115169878 1016520618 8.826271553400447 819.8121391411214 chr14 107349540 2402720773 22.382217688124236 1456.3957550668104 chr15 102531392 1866825464 18.207355109350313 1195.1307491465254 chr16 90354753 2360873117 26.128931114448402 1502.836913178293 chr17 81195210 1464408801 18.03565507127822 1023.5829526357281 chr18 78077248 1356200158 17.369978998235183 1267.5121064645807 chr19 59128983 3819357837 64.59366698392225 2409.3250008226573 chr20 63025520 1964869786 31.175780636161353 1685.908793244988 chr21 48129895 1169086930 24.290244763675467 1579.7741822320409 chr22 51304566 265755740 5.179962734700845 394.9628468378122 chrMT 16571 9920943 598.6930782692656 192.05305972170962 chrX 155270560 3586693676 23.09963766473181 1435.886862317293 chrY 59373566 28699954 0.48337932068961464 18.758591287861705