BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124838.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 143,354,098 number of mapped reads = 139,722,382 (97.47%) number of supplementary alignments = 1,155,513 (0.81%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 70,519,017 number of mapped paired reads (second in pair) = 69,203,365 number of mapped paired reads (both in pair) = 137,959,944 number of mapped paired reads (singletons) = 1,762,438 number of mapped bases = 19,321,578,668 bp number of sequenced bases = 19,309,559,801 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,859,364 duplication rate = 27.63% >>>>>>> Insert size mean insert size = 40,454.0386 std insert size = 1,925,218.914 median insert size = 262 >>>>>>> Mapping quality mean mapping quality = 54.0273 >>>>>>> ACTG content number of A's = 5,499,523,594 bp (28.48%) number of C's = 3,901,281,685 bp (20.2%) number of T's = 5,582,167,952 bp (28.91%) number of G's = 4,326,540,036 bp (22.41%) number of N's = 46,534 bp (0%) GC percentage = 42.61% >>>>>>> Mismatches and indels general error rate = 0.0119 number of mismatches = 223,392,505 number of insertions = 2,872,418 mapped reads with insertion percentage = 1.94% number of deletions = 6,349,542 mapped reads with deletion percentage = 4.38% homopolymer indels = 46.79% >>>>>>> Coverage mean coverageData = 6.2414X std coverageData = 51.5667X There is a 59.95% of reference with a coverageData >= 1X There is a 51.61% of reference with a coverageData >= 2X There is a 44.63% of reference with a coverageData >= 3X There is a 39.34% of reference with a coverageData >= 4X There is a 34.77% of reference with a coverageData >= 5X There is a 30.98% of reference with a coverageData >= 6X There is a 27.7% of reference with a coverageData >= 7X There is a 24.89% of reference with a coverageData >= 8X There is a 22.42% of reference with a coverageData >= 9X There is a 20.26% of reference with a coverageData >= 10X There is a 18.36% of reference with a coverageData >= 11X There is a 16.68% of reference with a coverageData >= 12X There is a 15.18% of reference with a coverageData >= 13X There is a 13.85% of reference with a coverageData >= 14X There is a 12.65% of reference with a coverageData >= 15X There is a 11.58% of reference with a coverageData >= 16X There is a 10.62% of reference with a coverageData >= 17X There is a 9.75% of reference with a coverageData >= 18X There is a 8.96% of reference with a coverageData >= 19X There is a 8.25% of reference with a coverageData >= 20X There is a 7.61% of reference with a coverageData >= 21X There is a 7.02% of reference with a coverageData >= 22X There is a 6.49% of reference with a coverageData >= 23X There is a 6.01% of reference with a coverageData >= 24X There is a 5.56% of reference with a coverageData >= 25X There is a 5.16% of reference with a coverageData >= 26X There is a 4.79% of reference with a coverageData >= 27X There is a 4.44% of reference with a coverageData >= 28X There is a 4.13% of reference with a coverageData >= 29X There is a 3.84% of reference with a coverageData >= 30X There is a 3.58% of reference with a coverageData >= 31X There is a 3.34% of reference with a coverageData >= 32X There is a 3.11% of reference with a coverageData >= 33X There is a 2.91% of reference with a coverageData >= 34X There is a 2.72% of reference with a coverageData >= 35X There is a 2.54% of reference with a coverageData >= 36X There is a 2.38% of reference with a coverageData >= 37X There is a 2.22% of reference with a coverageData >= 38X There is a 2.08% of reference with a coverageData >= 39X There is a 1.95% of reference with a coverageData >= 40X There is a 1.83% of reference with a coverageData >= 41X There is a 1.72% of reference with a coverageData >= 42X There is a 1.62% of reference with a coverageData >= 43X There is a 1.52% of reference with a coverageData >= 44X There is a 1.43% of reference with a coverageData >= 45X There is a 1.35% of reference with a coverageData >= 46X There is a 1.27% of reference with a coverageData >= 47X There is a 1.19% of reference with a coverageData >= 48X There is a 1.13% of reference with a coverageData >= 49X There is a 1.06% of reference with a coverageData >= 50X There is a 1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1706918365 6.848201052225262 63.64915252176977 chr2 243199373 1457304902 5.992223104950193 52.82488294308239 chr3 198022430 1251602751 6.320510009901404 10.71573159010123 chr4 191154276 997136429 5.216396147999326 37.372242514263576 chr5 180915260 1108287419 6.126002964039628 10.700775949825875 chr6 171115067 879064446 5.137270851783028 26.296357236449058 chr7 159138663 1658706392 10.423025811144335 86.34257139641613 chr8 146364022 1489377066 10.175841341665235 29.798151348628863 chr9 141213431 896186285 6.346324699100329 90.41044411614143 chr10 135534747 877314097 6.472982880176107 115.51550624790552 chr11 135006516 925681145 6.8565664267641715 33.47131335150963 chr12 133851895 951651179 7.109732581671705 11.794596226920797 chr13 115169878 575136979 4.99381425931527 9.243117502386424 chr14 107349540 500611615 4.663379228266837 9.781756840636115 chr15 102531392 389065693 3.794600711165611 7.580503372790667 chr16 90354753 664710086 7.356669836726796 49.73985680979207 chr17 81195210 576972837 7.105995994098667 100.20395854127685 chr18 78077248 358253569 4.588450261464134 61.740933143827135 chr19 59128983 259788172 4.393584310421845 34.64621946971842 chr20 63025520 393544379 6.244206775287217 14.860882025866381 chr21 48129895 158861502 3.3006824968140904 18.0658271793148 chr22 51304566 179081460 3.490555986771236 8.391509124278752 chrMT 16571 5867732 354.0964335284533 172.6535279035027 chrX 155270560 921622295 5.935589431763497 19.033079587336786 chrY 59373566 138831873 2.3382774920408185 46.99346686225865