Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	AE015451	2,087,690	G→A	14.7%	intergenic (+503/+415)	PP_1865 → / ← aroH	transposase/Phospho‑2‑dehydro‑3‑deoxyheptonate aldolase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AE015451	2,087,690	0	G	A	14.7%	74.6 / 9.4	34	intergenic (+503/+415)	PP_1865/aroH	transposase/Phospho‑2‑dehydro‑3‑deoxyheptonate aldolase
Reads supporting (aligned to +/- strand):  ref base G (19/10);  new base A (3/2);  total (22/12)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.73e-02

GAGGTTCTGCCCGGTCATCTGGATAAGGATATCGCCGGCATGGCTGCCCTCGGCCTGGTGTACCTGGAAGAACGCCGTTGCTCTTGCTCTTGCTCTTGCTTTGGCTTTTGCTTCTAAGCGCGCGGTAGTTCAGGCGACGCAGATTGCGACTTCAGGAGGCCGAGCGCAGGGCTTGCGGA‑GGGAGGTGACGGGCATGGATGCCCGTCAAGCGCTG‑GGCCCCA‑GGATGGGGCCTGCAGCGCGGTCCTCCCGGGAGCAAGCCCGGAGTGAGGGGACCCCGGAGCGTAGCGTAGGGGCCGGATGATGGGAGCCGACGGTTTTGGTTACTTTGGCCACGACCAAAGTAACCCGCCGGAAGGGCGGAAAGGTGAATAGGCGCCTACATCGTGAATGAATGTCTACTTGATGCGAAAGC  >  AE015451/2087506‑2087917                                                                                                                                                                                          |                                                                                                                                                                                                                                      gAGGTTCTGCCCGGTCATCTGGATAAGGATATCGCCGGCATGGCTGCCCTCGGCCTGGTGTACCTGGAAGAACGCCGTTGCTCTTGCTCTTGCTCTTGCTTTGGCTTTTGCTTCTAAGCGCGCGGTAGTTCAGGCGACGCAGATTGCGACTTCAGGAGGCCGAGCGCAGGGCTTGCGGA‑GGGAGGTGACGGGCATGGATGCCCGTCAAGCGCTG‑GGCCCCA‑GGATGGGGCCTGCAg                                                                                                                                                                                  >  1:214844/1‑236 (MQ=255) gAGGTTCTGCCCGGTCATCTGGATAAGGATATCGCCGGCATGGCTGCCCTCGGCCTGGTGTACCTGGAAGAACGCCGTTGCTCTTGCTCTTGCTCTTGCTTTGGCTTTTGCTTCTAAGCGCGCGGTAGTCCAGGCGACGCAGATTGCGACTTCAGGAGGCCGAGTGGAGGCATTGCGGA‑GGGAGATGACGGGCATGGATGCCCGTCAAGCGCTGAGGCCCCATGGATGGGGcc                                                                                                                                                                                       >  2:560856/1‑233 (MQ=21)                     ggATAAGGATATCGCCGGCATGGCTGCCCTCGGCCTGGTGTACCTGGAAGAACGCCGTTGCTCTTGCTCTTGCTCTTGCTTTGGCTTTTGCTTCTAAGCGCGCGGTAGTCCAGGCGACGCAGATTGCGACTTCAGGAGGCCGAGTGGAGGCATTGCGGA‑GGGAGATGACGGGCATGGATGCCCGTCAAgcg                                                                                                                                                                                                             <  1:644626/191‑1 (MQ=21)                     ggATAAGGATATCGCCGGCATGGCTGCCCTCGGCCTGGTGTACCTGGAAGAACGCCGTTGCTCTTGCTCTTGCTCTTGCTTTGGCTTTTGCTTCTAAGCGCGCGGTAGTCCAGGCGACGCAGATTGCGACTTCAGGAGGCCGAGTGGAGGCATTGCGGA‑GGGAGATGACGGGCATGGATGCCCGTCAAgcg                                                                                                                                                                                                             >  2:644623/1‑191 (MQ=21)                          aGGATATCGCCGGCATGGCTGCCCTCGGCCTGGTGTACCTGGAAGAACGCCGTTGCTCTTGCTCTTGCTCTTGCTTTGGCTTTTGCTTCTAAGCGCGCGGTAGTTCAGGCGACGCAGATTGCGACTTCAGGAGGCCGAGCGCAGGGCTTGCGGA‑GGGAGGTGACGGGCATGGATGCCCGTCAAGCGCTG‑GGCCCCA‑GGATGGGGCCTGCAGCGCGGTCCTCCCGGGAGCAAGcc                                                                                                                                                           >  2:423558/1‑234 (MQ=255)                                   ccGGCATGGCTGCCCTCGGCCTGGTGTACCTGGAAGAACGCCGTTGCTCTTGCTCTTGCTCTTGCTTTGGCTTTTGCTTCTAAGCGCGCGGTAGTTCAGGCGACGCAGATTGCGACTTCAGGAGGCCGAGCGCAGGGCTTGCGGA‑GGGAGGTGACGGGCATGGATGCCCGTCAAGCGCTG‑GGCCCCA‑GGATggg                                                                                                                                                                                          >  1:447854/1‑194 (MQ=255)                                    cGGCATGGCTGCCCTCGGCCTGGTGTACCTGGAAGAACGCCGTTGCTCTTGCTCTTGCTCTTGCTTTGGCTTTTGCTTCTAAGCGCGCGGTAGTTCAGGCGACGCAGATTGCGACTTCAGGAGGCCGAGCGCAGGGCTTGCGGA‑GGGAGGTGACGGGCATGGATGCCCGTCAAGCGCTG‑GGc                                                                                                                                                                                                      >  2:755771/1‑182 (MQ=255)                                    cGGCATGGCTGCCCTCGGCCTGGTGTACCTGGAAGAACGCCGTTGCTCTTGCTCTTGCTCTTGCTTTGGCTTTTGCTTCTAAGCGCGCGGTAGTTCAGGCGACGCAGATTGCGACTTCAGGAGGCCGAGCGCAGGGCTTGCGGA‑GGGAGGTGACGGGCATGGATGCCCGTCAAGCGCTG‑GGc                                                                                                                                                                                                      <  1:755774/182‑1 (MQ=255)                                      gCATGGCTGCCCTCGGCCTGGTGTACCTGGAAGAACGCCGTTGCTCTTGCTCTTGCTCTTGCTTTGGCTTTTGCTTCTAAGCGCGCGGTAGTTCAGGCGACGCAGATTGCGACTTCAGGAGGCCGAGCGCAGGGCTTGCGGA‑GGGAGGTGACGGGCATGGAAGCCCGTCAAGCGCTG‑CGCCCCA‑g                                                                                                                                                                                                >  1:822229/1‑185 (MQ=255)                                         tGGCTGCCCTCGGCCTGGTGTACCTGGAAGAACGCCGTTGCTCTTGCTCTTGCTCTTGCTTTGGCTTTTGCTTCTAAGCGCGCGGTAGTTCAGGCGACGCAGATTGCGACTTCAGGAGGCCGAGCGCAGGGCTTGCGGA‑GGGAGGTGACGGGCATGGATGCCCGTCAAGCGCTG‑GGCCCCA‑GGATGGGGc                                                                                                                                                                                        >  1:685424/1‑190 (MQ=255)                                          ggCTGCCCTCGGCCTGGTGTACCTGGAAGAACGCCGTTGCTCTTGCTCTTGCTCTTGCTTTGGCTTTTGCTTCTAAGCGCGCGGTAGTTCAGGCGACGCAGATTGCGACTTCAGGAGGCCGAGCGCAGGGCTTGCGGA‑GGGAGGTGACGGGCATGGATGCCCGTCAAGCGCTG‑GGc                                                                                                                                                                                                      >  1:652408/1‑176 (MQ=255)                                            cTGCCCTCGGCCTGGTGTACCTGGAAGAACGCCGTTGCTCTTGCTCTTGCTCTTGCTTTGGCTTTTGCTTCTAAGCGCGCGGTAGTTCAGGCGACGCAGATTGCGACTTCAGGAGGCCGAGCGCAGGGCTTGCGGA‑GGGAGGTGACGGGCATGGATGCCCGTCAAGCGCTG‑GGCCCCA‑GGATGGGGCCTGCAGCGCGGTCCTCCCGGGAGCAAGCCCGGAGTGAGGGGACCCCGGa                                                                                                                                       <  1:423561/236‑1 (MQ=255)                                               cccTCGGCCTGGTGTACCTGGAAGAACGCCGTTGCTCTTGCTCTTGCTCTTGCTTTGGCTTTTGCTTCTAAGCGCGCGGTAGTTCAGGCGACGCAGATTGCGACTTCAGGAGGCCGAGCGCAGGGCTTGCGGA‑GGGAGGTGACGGGCATGGGTGCCCGTCAAGCGCTG‑GGCCCCA‑g                                                                                                                                                                                                >  1:351577/1‑176 (MQ=255)                                                        tGGTGTACCTGGAAGAACGCCGTTGCTCTTGCTCTTGCTCTTGCTTTGGCTTTTGCTTCTAAGCGCGCGGTAGTTCAGGCGACGCAGATTGCGACTTCAGGAGGCCGAGCGCAGGGCTTGCGGA‑GGGAGGTGACGGGCATGGATGCCCGTCAAGCGCTG‑GGCCCCA‑GGATGGGGCCTg                                                                                                                                                                                     >  1:229964/1‑178 (MQ=255)                                                           tgtACCGGGAAGCACGCCGTTGCTCTTGCTCTTGCTCGTGCTTTGGCTTTGGCTTCTGGGCGCGCGGTAGTTCAGGCGACGCAGATTGCGACTTCAGGAGGCCGAGCGCAGGGCTTGCGGA‑GGGAGGTGACGGGCATGGATGccc                                                                                                                                                                                                                     <  2:21831/145‑1 (MQ=17)                                                                 tGGAAGAACGCCGTTGCTCTTGCTCTTGCTCTTGCTTTGGCTTTTGCTTCTAAGCGCGCGGTAGTTCAGGCGACGCAGATTGCGACTTCAGGAGGCCGAGCGCAGGGCTTGCGGA‑GGGAGGTGACGGGCATGGATGCCCGTCAAGCGCTG‑GGCCCCA‑GGATGGGGCCTGCAGCGCGGTCCTCCCGGGAGCAAGCCCGGAGTGAGGGGACCCCGGAGCGTAGCGGAGGGGCCGgat                                                                                                                   >  1:248774/1‑235 (MQ=255)                                                                   gaagaaCGCCGTTGCTCTTGCTCTTGCTCTTGCTTTGGCTTTTGCTTCTAAGCGCGCGGTAGTTCAGGCGACGCAGATTGCGACTTCAGGAGGCCGAGCGCAGGGCTTGCGGA‑GGGAGGTGACGGGCATGGATGCCCGTCAAGCGCTG‑GGCCCCA‑GGATGGGGCCTGCAGCGCGGTCCTCCCGGGAGCAAGCCCGGAGTg                                                                                                                                                    <  2:773131/200‑1 (MQ=255)                                                                                    ttgctcttgctcttgctTTGGCTTTTGCTTCTAGGCGCGCGGTAGTTCAGGCGACGAAGATTGCGACTTCAGGAGGCCGAGCGCAGGGCTTGCGGA‑GGGAGGTGACGGGCATGGATGCCCGTCAAGCGCTG‑GGCCCCA‑GGAt                                                                                                                                                                                             <  1:307536/142‑1 (MQ=255)                                                                                    ttgctcttgctcttgctTTGGCTTTTGCTTCTAAGCGCGCGGTAGTTCAGGCGACGCAGATTGCGACTTCAGGAGGCCGAGCGCAGGGCTTGCGGAGGGGAGGTGACGGGCATGGATGCCCGTCAAGCGCTG‑GGCCCCA‑GGATGGGGCCTGCAGCGCGGTCCTCCCGGGa                                                                                                                                                                  <  1:388688/170‑1 (MQ=37)                                                                                         cttgctcttgctTTGGCTTTTGCTTCTAAGCGCGCGGTAGTTCAGGCGACGCAGATTGCGACTTCAGGAGGCCGAGCGCAGGGCTTGCGGAGGGGAGGTGACGGGCATGGATGCCCGTCAAGCGCTG‑GGCCCCA‑GGATGGGGc                                                                                                                                                                                        >  2:388685/1‑143 (MQ=18)                                                                                              tcttgctTTGGCTTTTGCTTCTAAGCGTGCGGTAGTTCAGGCGACGCAGATTGCGACTTCAGGAGGCCGAGCGCAGGGCTTGCGGA‑GGGAGGTGACGGGCATGGATGCCCGTc                                                                                                                                                                                                                  >  1:574848/1‑113 (MQ=17)                                                                                              tcttgctTTGGCTTTTGCTTCTAAGCGCGCGGTAGTTCAGGCGACGCAGATTGCGACTTCAGGAGGCCGAGCGCAGGGCTTGCGGA‑GGGAGGTGACGGGCATGGATGCCCGTCAAGCGCTG‑GGCCCCA‑GGATGGGGCCTGCAGCGCGGTCCTCCCGGGAGCAAGCCCGGAGTGAGGGGACCCCGGAGCGTAGCGTAGGGGCCGGATGATGGGAGCCGACGGTTTTGGTTACTTTg                                                                                      >  1:603821/1‑235 (MQ=34)                                                                                               cttgctTTGGCTTTTGCTTCTAAGCGCGCGGTAGTTCAGGCGACGCAGATTGCGACTTCAGGAGGCCGAGCGCAGGGCTTGCGGA‑GGGAGGTGACGGGCATGGATGCCCGTCAAGCGCTG‑GGCCCCA‑GGATGGGGCCTGCAGCGCGGTCCTCCCGGGAGCAAGCCCGGCGt                                                                                                                                                     >  1:870569/1‑171 (MQ=14)                                                                                               cttgctTTGGCTTTTGCTTCTAAGCGCGCGGTAGTTCAGGCGACGCAGATTGCGACTTCAGGAGGCCGAGCGCAGGGCTTGCGGA‑GGGAGGTGACGGGCATGGATGCCCGTCAAGCGCTG‑GGCCCCA‑GGATGGGGCCTGCAGCACGGTCCTCCCGGGAGCAAGCCCGGAGTGAGGGGACCCCGGAGCGTAGCGTAGGGGCCGGATGATGGGAGCCGACGGTTTTGGTTACTTTGGc                                                                                    >  1:573484/1‑236 (MQ=21)                                                                                                         cTTTTGCTTCTAGGCGCGCGGTAGTTCTGGCGACGCAGATTGCGACTGCAGGAGGCCGAGCGCAGGGCGTGCGGA‑GGGAGGTGACGGGCATGGATGCCCGTCAAgcg                                                                                                                                                                                                             <  2:176473/107‑1 (MQ=11)                                                                                                                ttCTAAGCGCGCGGTAGTTCAGGCGACGCAGATTGCGACTTCAGGAGGCCGAGCGCAGGGCTTGCGGA‑GGGAGGTGACGGGCATGGATGCCCGTCAAGCGCTG‑GGCCCCA‑GGATGGGGCCTg                                                                                                                                                                                     <  2:927401/122‑1 (MQ=32)                                                                                                                 tCTAAGCGCGCGGTAGTTCAGGCGACGCAGATTGCGACTTCAGGAGGCCGAGCGCAGGGCTTGCGGA‑GGGAGGTGACGGGCAt                                                                                                                                                                                                                             >  2:663180/1‑83 (MQ=33)                                                                                                                                             aGATTGCGACTTCAGGAGGCCGAGTGGAGGCATTGCGGA‑GGGAGATGACGGGCATCCATGCCCGTCAAGCGCTG‑GGCCCCA‑GGATGGGGCCTGCAGCGCGGTCCTCCCGGGAGCAAGCCCGGAGTGAGGGGACCCCGGAGCGTAGCGTAGGGGCCGGATGATGGGAGCCGACGGtt                                                                                                  >  2:529768/1‑176 (MQ=11)                                                                                                                                             aGATTGCGACTTCAGGAGGCCGAGTGGAGGCATTGCGGA‑GGGAGATGACGGGCATCCATGCCCGTCAAGCGCTG‑GGCCCCA‑GGATGGGGCCTGCAGCGCGGTCCTCCCGGGAGCAAGCCCGGAGTGAGGGGACCCCGGAGCGTAGCGTAGGGGCCGGATGATGGGAGCCGACGGtt                                                                                                  <  1:529771/176‑1 (MQ=11)                                                                                                                                             aGATTGCGACTTCAGGAGGCCGAGCGCAGGGCTTGCGGA‑GGGAGGTGACGGGCATGGATGCCCGTCAAGCGCTG‑GGCCCCA‑GGATGGGGCCTGCAGCGCGGTCCTCCCGGGAGCAAGCCCGGAGTGAGGGGACCCCGGAGCGTAGCGTAGGGGCCGGATGATGGGAGCCGACGGTTTTGGTTACTTTGGCCACGACCAAAGTAACCCGCCGGAAGGGCGGAAAGGTGAATAGgc                                        >  1:555602/1‑234 (MQ=32)                                                                                                                                                                   aGCGCAGGGCTGGCGGA‑GGGAGGTGACGGGCATGGATGCCCGGCAAGCGCTG‑GGCCCCA‑GGAGGGGGCCTGCAGCGCGGTCCTCCCGGGAGCAAGCCCGGAGTGAGGGGACCCCGGAGCGTAGCGTAGGGGCCGGATGATGGGAGCCGACGGTTTTGGTTACTTTGGCCACGACCAAAGt                                                                        <  1:25740/180‑1 (MQ=16)                                                                                                                                                                      gcAGGGCTTGCGGA‑GGGAGGTGACGGGCATGGATGCCCGTCAAGCGCTG‑GGCCCCA‑GGATGGGGCCTGCAGCGCGGTCCTCCCGGGAGCAAGCCCGGAGTGAGGGGACCCCGGAGCGTAGCGTAGGGGCCGGATGATGGGAg                                                                                                           >  2:477912/1‑142 (MQ=32)                                                                                                                                                                      gcAGGGCTTGCGGA‑GGGAGGTGACGGGCATGGATGCCCGTCAAGCGCTG‑GGCCCCA‑GGATGGGGCCTGCAGCGCGGTCCTCCCGGGAGCAAGCCCGGAGTGAGGGGACCCCGGAGCGTAGCGTAGGGGCCGGATGATGGGAGCCGACGGTTTTGGTTACTTTGGCCACGACCAAAGTAACCCGCCGGAAGGGCGGAAAGGTGAATAGGCGCCTACATCGTGAATGAATGTCTAc               >  2:492523/1‑234 (MQ=34)                                                                                                                                                                             ttGCGGA‑GGGAGGTGACGGGCATGGATGCCCGTCAAGCGCTG‑GGCCCCA‑GGATGGGGCCTGCAGCGCGGTCCTCCCGGGAGCAAGCCCGGAGTGAGGGGACCCCGGAGCGTAGCGTAGGGGCCGGATGATGGGAGCCGACGGTTTTGGTTACTTTGGCCACGACCAAAGTAACCCGCCGGAAgg                                                          <  2:567557/184‑1 (MQ=33)                                                                                                                                                                                        aggTGACGGGCATGGATGCCCGTCAAGCGCTG‑GGCCCCA‑GGATGGGGCCTGCAGCGCGGTCCTCCCGGGAGCAAGCCCGGAGTGAGGGGACCCCGGAGCGTAGCGTAGGGGCCGGATGATGGGAGCCGACGGTTTTGGTTACTTTGGCCACGACCAAAGTAACCCGCCGGAAGGGCGGAAAGGTGAATAGGCGCCTACATCGTGAATGAATGTCTACTTGATGCGAAAgc  >  1:372439/1‑230 (MQ=35)                                                                                                                                                                                        aggTGACGGGCATGGATGCCCGTCAAGCGCTG‑GGCCCCA‑GGATGGGGCCTGCAGCGCGGTCCTCCCGGGAGCAAGCCCGGAGTGAGGGGACCCCGGAGCGTAGCGAAGGGGCCGGATGATGGGAGCCGACGGTTTTg                                                                                               >  1:218320/1‑137 (MQ=18)                                                                                                                                                                                          |                                                                                                                                                                                                                                      GAGGTTCTGCCCGGTCATCTGGATAAGGATATCGCCGGCATGGCTGCCCTCGGCCTGGTGTACCTGGAAGAACGCCGTTGCTCTTGCTCTTGCTCTTGCTTTGGCTTTTGCTTCTAAGCGCGCGGTAGTTCAGGCGACGCAGATTGCGACTTCAGGAGGCCGAGCGCAGGGCTTGCGGA‑GGGAGGTGACGGGCATGGATGCCCGTCAAGCGCTG‑GGCCCCA‑GGATGGGGCCTGCAGCGCGGTCCTCCCGGGAGCAAGCCCGGAGTGAGGGGACCCCGGAGCGTAGCGTAGGGGCCGGATGATGGGAGCCGACGGTTTTGGTTACTTTGGCCACGACCAAAGTAACCCGCCGGAAGGGCGGAAAGGTGAATAGGCGCCTACATCGTGAATGAATGTCTACTTGATGCGAAAGC  >  AE015451/2087506‑2087917

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑