BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504419.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP013494//SRP013494.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 = 162,055,620 number of mapped reads = 161,048,624 (99.38%) number of supplementary alignments = 2,672,256 (1.65%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 80,575,200 number of mapped paired reads (second in pair) = 80,473,424 number of mapped paired reads (both in pair) = 160,571,734 number of mapped paired reads (singletons) = 476,890 number of mapped bases = 15,455,945,663 bp number of sequenced bases = 15,450,984,864 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 81,656,836 duplication rate = 34.05% >>>>>>> Insert size mean insert size = 65,321.0756 std insert size = 2,352,314.9312 median insert size = 161 >>>>>>> Mapping quality mean mapping quality = 50.5762 >>>>>>> ACTG content number of A's = 4,632,841,592 bp (29.98%) number of C's = 3,070,286,615 bp (19.87%) number of T's = 4,657,348,488 bp (30.14%) number of G's = 3,078,371,464 bp (19.92%) number of N's = 12,136,705 bp (0.08%) GC percentage = 39.79% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 84,354,461 number of insertions = 1,460,486 mapped reads with insertion percentage = 0.9% number of deletions = 3,069,655 mapped reads with deletion percentage = 1.88% homopolymer indels = 47.8% >>>>>>> Coverage mean coverageData = 4.9927X std coverageData = 112.9768X There is a 27.86% of reference with a coverageData >= 1X There is a 21.86% of reference with a coverageData >= 2X There is a 17.37% of reference with a coverageData >= 3X There is a 14.88% of reference with a coverageData >= 4X There is a 12.88% of reference with a coverageData >= 5X There is a 11.44% of reference with a coverageData >= 6X There is a 10.27% of reference with a coverageData >= 7X There is a 9.33% of reference with a coverageData >= 8X There is a 8.55% of reference with a coverageData >= 9X There is a 7.88% of reference with a coverageData >= 10X There is a 7.31% of reference with a coverageData >= 11X There is a 6.81% of reference with a coverageData >= 12X There is a 6.37% of reference with a coverageData >= 13X There is a 5.98% of reference with a coverageData >= 14X There is a 5.64% of reference with a coverageData >= 15X There is a 5.33% of reference with a coverageData >= 16X There is a 5.05% of reference with a coverageData >= 17X There is a 4.79% of reference with a coverageData >= 18X There is a 4.56% of reference with a coverageData >= 19X There is a 4.35% of reference with a coverageData >= 20X There is a 4.16% of reference with a coverageData >= 21X There is a 3.98% of reference with a coverageData >= 22X There is a 3.81% of reference with a coverageData >= 23X There is a 3.66% of reference with a coverageData >= 24X There is a 3.52% of reference with a coverageData >= 25X There is a 3.38% of reference with a coverageData >= 26X There is a 3.26% of reference with a coverageData >= 27X There is a 3.14% of reference with a coverageData >= 28X There is a 3.03% of reference with a coverageData >= 29X There is a 2.93% of reference with a coverageData >= 30X There is a 2.83% of reference with a coverageData >= 31X There is a 2.74% of reference with a coverageData >= 32X There is a 2.66% of reference with a coverageData >= 33X There is a 2.58% of reference with a coverageData >= 34X There is a 2.5% of reference with a coverageData >= 35X There is a 2.43% of reference with a coverageData >= 36X There is a 2.36% of reference with a coverageData >= 37X There is a 2.29% of reference with a coverageData >= 38X There is a 2.23% of reference with a coverageData >= 39X There is a 2.17% of reference with a coverageData >= 40X There is a 2.11% of reference with a coverageData >= 41X There is a 2.06% of reference with a coverageData >= 42X There is a 2.01% of reference with a coverageData >= 43X There is a 1.96% of reference with a coverageData >= 44X There is a 1.91% of reference with a coverageData >= 45X There is a 1.86% of reference with a coverageData >= 46X There is a 1.82% of reference with a coverageData >= 47X There is a 1.78% of reference with a coverageData >= 48X There is a 1.74% of reference with a coverageData >= 49X There is a 1.7% of reference with a coverageData >= 50X There is a 1.66% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1217084526 4.882974899388516 49.1108366428846 chr2 243199373 1253861560 5.155694048602666 38.5845265956624 chr3 198022430 1083546312 5.471836256125127 45.32367951440082 chr4 191154276 1073150435 5.61405403769257 37.36340927927069 chr5 180915260 1140800512 6.305717450258204 82.9261007741675 chr6 171115067 954510243 5.578177653987653 71.2133995470653 chr7 159138663 853435990 5.362845042879366 63.28718838512782 chr8 146364022 957460709 6.541639782213692 86.56210447938436 chr9 141213431 544780040 3.857848620645723 28.107308511005197 chr10 135534747 729804679 5.384631580859483 71.91297958433147 chr11 135006516 824642620 6.108169030893294 52.77847326982504 chr12 133851895 921967069 6.887964260797354 116.11982911893081 chr13 115169878 503000332 4.367464312152871 40.55892858852972 chr14 107349540 1027642988 9.572868109169354 515.697973647984 chr15 102531392 429163644 4.18568045969765 34.16719801128618 chr16 90354753 331794175 3.672127519401221 55.338530333098475 chr17 81195210 236070497 2.9074436410719304 24.896571519524787 chr18 78077248 396371752 5.0766614110169455 72.78500927480592 chr19 59128983 158067999 2.6732744414021123 43.99936439167738 chr20 63025520 312523240 4.958677691195566 116.68642812682612 chr21 48129895 138324205 2.8739768703006727 19.63554404863462 chr22 51304566 117274473 2.2858486513656504 33.367445117334405 chrMT 16571 1855 0.11194255023836823 0.7592825306409606 chrX 155270560 31690443 0.2040982076705333 4.205523925362358 chrY 59373566 218975365 3.688095220691309 79.72888706957069