BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472688.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 13,882,150 number of mapped reads = 13,757,578 (99.1%) number of supplementary alignments = 21,935 (0.16%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,919,370 number of mapped paired reads (second in pair) = 6,838,208 number of mapped paired reads (both in pair) = 13,669,108 number of mapped paired reads (singletons) = 88,470 number of mapped bases = 1,357,645,767 bp number of sequenced bases = 1,357,451,406 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,120,364 duplication rate = 45.63% >>>>>>> Insert size mean insert size = 20,651.9125 std insert size = 1,474,470.018 median insert size = 234 >>>>>>> Mapping quality mean mapping quality = 54.7698 >>>>>>> ACTG content number of A's = 369,850,893 bp (27.25%) number of C's = 308,756,533 bp (22.75%) number of T's = 376,552,329 bp (27.74%) number of G's = 301,990,703 bp (22.25%) number of N's = 300,948 bp (0.02%) GC percentage = 44.99% >>>>>>> Mismatches and indels general error rate = 0.0046 number of mismatches = 6,159,373 number of insertions = 63,065 mapped reads with insertion percentage = 0.45% number of deletions = 77,279 mapped reads with deletion percentage = 0.55% homopolymer indels = 44.47% >>>>>>> Coverage mean coverageData = 0.4386X std coverageData = 9.1522X There is a 3.14% of reference with a coverageData >= 1X There is a 1.39% of reference with a coverageData >= 2X There is a 0.77% of reference with a coverageData >= 3X There is a 0.67% of reference with a coverageData >= 4X There is a 0.58% of reference with a coverageData >= 5X There is a 0.56% of reference with a coverageData >= 6X There is a 0.53% of reference with a coverageData >= 7X There is a 0.51% of reference with a coverageData >= 8X There is a 0.49% of reference with a coverageData >= 9X There is a 0.48% of reference with a coverageData >= 10X There is a 0.46% of reference with a coverageData >= 11X There is a 0.45% of reference with a coverageData >= 12X There is a 0.44% of reference with a coverageData >= 13X There is a 0.43% of reference with a coverageData >= 14X There is a 0.42% of reference with a coverageData >= 15X There is a 0.41% of reference with a coverageData >= 16X There is a 0.4% of reference with a coverageData >= 17X There is a 0.39% of reference with a coverageData >= 18X There is a 0.38% of reference with a coverageData >= 19X There is a 0.38% of reference with a coverageData >= 20X There is a 0.37% of reference with a coverageData >= 21X There is a 0.36% of reference with a coverageData >= 22X There is a 0.35% of reference with a coverageData >= 23X There is a 0.35% of reference with a coverageData >= 24X There is a 0.34% of reference with a coverageData >= 25X There is a 0.34% of reference with a coverageData >= 26X There is a 0.33% of reference with a coverageData >= 27X There is a 0.32% of reference with a coverageData >= 28X There is a 0.32% of reference with a coverageData >= 29X There is a 0.31% of reference with a coverageData >= 30X There is a 0.31% of reference with a coverageData >= 31X There is a 0.3% of reference with a coverageData >= 32X There is a 0.3% of reference with a coverageData >= 33X There is a 0.29% of reference with a coverageData >= 34X There is a 0.29% of reference with a coverageData >= 35X There is a 0.28% of reference with a coverageData >= 36X There is a 0.28% of reference with a coverageData >= 37X There is a 0.28% of reference with a coverageData >= 38X There is a 0.27% of reference with a coverageData >= 39X There is a 0.27% of reference with a coverageData >= 40X There is a 0.26% of reference with a coverageData >= 41X There is a 0.26% of reference with a coverageData >= 42X There is a 0.26% of reference with a coverageData >= 43X There is a 0.25% of reference with a coverageData >= 44X There is a 0.25% of reference with a coverageData >= 45X There is a 0.24% of reference with a coverageData >= 46X There is a 0.24% of reference with a coverageData >= 47X There is a 0.24% of reference with a coverageData >= 48X There is a 0.23% of reference with a coverageData >= 49X There is a 0.23% of reference with a coverageData >= 50X There is a 0.23% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 144826234 0.5810466325778983 10.819744026201883 chr2 243199373 101373554 0.416833122345262 9.2415466910423 chr3 198022430 125555156 0.6340451230701492 10.276378250874469 chr4 191154276 39135652 0.20473333277671488 5.595638352174048 chr5 180915260 52610451 0.290801621709523 6.501869670606701 chr6 171115067 100595915 0.5878846133403319 10.01402895030289 chr7 159138663 86155149 0.5413841449704777 11.202624092992167 chr8 146364022 79035294 0.539991269165861 9.975189552752203 chr9 141213431 92067437 0.6519736568117235 11.217992473260333 chr10 135534747 28551349 0.21065704280246306 5.0871422224688505 chr11 135006516 33883364 0.25097576771775965 5.298323175667293 chr12 133851895 51304122 0.3832902178934411 6.63485341721399 chr13 115169878 44953342 0.3903220423659735 10.74400145659783 chr14 107349540 20898766 0.19467960458889716 4.423259765130294 chr15 102531392 16648610 0.16237573366798727 3.6699802808210884 chr16 90354753 79933601 0.884664041967997 16.89280688262307 chr17 81195210 54857852 0.6756291658091653 10.477529255120121 chr18 78077248 11790953 0.1510165035529941 3.325931610501698 chr19 59128983 41760390 0.7062592299279018 9.72511807300891 chr20 63025520 57287353 0.9089548646326123 17.53826996129891 chr21 48129895 10796207 0.22431395289767408 9.180224499549487 chr22 51304566 23144905 0.45112758579811396 9.612775366382156 chrMT 16571 49763 3.0030173194134333 2.1514648474656357 chrX 155270560 58584084 0.3773032312113771 6.1417117053890395 chrY 59373566 1846264 0.03109572364240342 0.9828488945897632