Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,210,063	C→T	L127L (CTG→TTG)	pinE →	site‑specific DNA recombinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,210,063	0	C	T	89.7%	66.8 / ‑2.4	29	L127L (CTG→TTG)	pinE	site‑specific DNA recombinase
Reads supporting (aligned to +/- strand):  ref base C (1/2);  new base T (15/11);  total (16/13)
Fisher's exact test for biased strand distribution p-value = 5.73e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTCAGGACATTATCGGCAGGTGACACTCTGGTTGTCTGGAAGCTGGATCGGCTGGGGCGTAGTATGCGGCATCTTGTCGTGCTGGTGGAGGAGTTGCGCGAACGAGGCATCAACTTTCGTAGTCTGACGGATTCAATTGATACCAGCACACCAATGGGACGCTTTTTCTTTCATGTGATGGGTGCCCTGGCTGAAATGGAGCGTGAACTGATTGTTGAACGAACAAAAGCTGGACTGGAAACTGCTCGTGCACAGGGACGAATTGGTGGACGTCGTCCCAAACTTACACCAGAACAATGGGCACAAGCTGGACGATTAATTGCAGCAGGAACTCCTCGCCAGAAGGTGGCGATTATCTATGATGTTGGTGTGTCAACTTTGTATAAGAGGTTTCCTGCAGGGGATAAATAAAGTTAAAGACACTTTGTGTACAAAAGAAAGTAAAACAACAGCAACTTGTTGCAATTTTATCAATAA  >  NC_000913/1209829‑1210305                                                                                                                                                                                                                                           |                                                                                                                                                                                                                                                   cgcAGGACATTATCGGCAGGTGACACTCGGGTTGTCTGGAAGCTGGATCGGCTGGGGCGTAGTATGCGGCATCTTGTCGTGCTGGTGGAGGAGTTGCGCGAACGAGGCATCAACTTTCGTAGTCTGACGGATTCAATTGATACCAGCACACCAATGGGACGCTTTTTCTTTCATGTGATGGGTGCCCTGGCTGAAATGGAGCGTGAACTGATTGTTAAACGAACAAAAGCTGGATTGGAAACTGCTCGTGc                                                                                                                                                                                                                                    <  2:137110/249‑1 (MQ=255)              cGGCAGGTGACACTCTGGTTGTCTGGAAGCTGGATCGGCTGGGGCGTAGTATGCGGCATCTTGTCGTGCTGGTGGAGGAGTTGCGCGAACGAGGCATCAACTTTCGTAGTCTGACGGATTCAATTGATACCAGCACACCAATGGGACGCTTTTTCTTTCATGTGATGGGTGCCCTGGCTGAAATGGAGCGTGAACTGATTGTTGAACGAACAAAAGCTGGATTGGAAACTGCTCGTGCACAGGGACGAAt                                                                                                                                                                                                                        <  1:8894/250‑1 (MQ=255)                 cAGGTGACACTCTGGTTGTCTGGAAGCTGGATCGGCTGGGGCGTAGTATGCGGCATCTTGTCGTGCTGGTGGAGGAGTTGCGCGAACGAGGCATCAACTTTCGTAGTCTGACGGATTCAATTGATACCAGCACACCAATGGGACGCTTTTTCTTTCATGTGATGGGTGCCCTGGCTGAAATGGAGCGTGAACTGATTGTTGAACGAACAAAAGCTGGATTGGAAACTGCTCGTGCACAGGGACGAATtggt                                                                                                                                                                                                                    >  1:604216/1‑251 (MQ=255)                                 tGTCTGGAAGCTGGATCGGCTGGGGCGTAGTATGCGGCATCTTGTCGTGCTGGTGGAGGAGTTGCGCGAACGAGGCATCAACTTTCGTAGTCTGACGGATTCAATTGATACCAGCACACCAATGGGACGCTTTTTCTTTCATGTGATGGGTGCCCTGGCTGAAATGGAGCGTGAACTGATTGTTGAACGAACAAAAGCTGGATTGGAAACTGCTCGTGCACTGGGACGAATTGGTGGACGTCGTCCCAAAc                                                                                                                                                                                                    >  2:129525/1‑251 (MQ=255)                                                               gaTGCGGCATCTGGTCGTTCTTGTGGAGGAGTGGCGAGAACGATGCATCAACTTTCGTAGTCTGACGGATTCAATTGATCCCAGCACGCCAATGGGTCGCTTTTTCTTTCATGTGATGGGTGCCCTGGCTGAAATGGAGCGTGCACTTATTGTTGAACGAACAAAATCTGTACTGGAAACTGCTCGTGCACAGGGACTAATTGCGGGACGTCGTCTTACACTCACACCAGAACAATGGTCACACGCTGGat                                                                                                                                                                      <  2:355132/250‑2 (MQ=255)                                                                          ttGTCGTGCTGGTGGAGGAGTTGCGCGAACGAGGCATCAACTTTCGTAGTCTGACGGATTCAATTGATACCAGCACACCAATGGGACGCTTTTTCTTTCATGTGATGGGTGCCCTGGCTGAAATGGAGCGTGAACTGATTGTTGAACGAACAAAAGCTGGATTGGAAACTGCTCGTGCACAGGGACGAATTGGTGGACGTCGTCCCAAACTTACACCAGAACAATGGGCACAAGCTGGACGATTAATTgc                                                                                                                                                            >  1:609398/1‑250 (MQ=255)                                                                            gTCGTGCTGGTGGAGGAGTTGCGCGAACGAGGCATCAACTTTCGTAGTCTGACGGATTCAATTGATACCAGCACACCAATGGGACGCTTTTTCTTTCATGTGATGGGTGCCCTGGCTGAAATGGAGCGTGAACTGATTGTTGAACGAACAAAAGCTGGATTGGAAACTGCTCGTGCACAGGGACGAATTGGTGGACGTCGTCCCAAACTTACACCAGAACAATGGGCACAAGCTGGACGATTAATTgc                                                                                                                                                            >  1:33240/1‑248 (MQ=255)                                                                                                  gcgAACGAGGCATCAACTTTCGTAGTCTGACGGATTCAATTGATACCAGCACACCAATGGGACGCTTTTTCTTTCATGTGATGGGTGCCCTGGCTGAAATGGAGCGTGAACTGATTGTTGAACGAACAAAAGCTGGATTGGAAACTGCTCGTGCACAGGGACGAATTGGTGGACGTCGTCCCAAACTTACACCAGAACAATGGGCACAAGCTGGACGATTAATTGCAGCAGGAACTCCTCGCCAGAAGGTg                                                                                                                                   <  1:625858/251‑1 (MQ=255)                                                                                                        gAGGCATCAACTTTCGTAGTCTGACGGATTCAATTGATACCAGCACACCAATGGGACGCTTTTTCTTTCATGTGATGGGTGCCCTGGCTGAAATGGAGCGTGAACTGATTGTTGAACGAACAAAAGCTGGATTGGAAACTGCTCGTGCACAGGGACGAATTGGTGGACGTCGTCCCAAACTTACACCAGAACAATGGGCACAAGCTGGACGATTAATTGCAGCAGGAACTCCTCGCCAGAAGGTGGCGAtt                                                                                                                             >  2:232550/1‑251 (MQ=255)                                                                                                           gCATCAACTTTCGTAGTCTGACGGATTCAATTGATACCAGCACACCAATGGGACGCTTTTTCTTTCATGTGATGGGTGCCCAGGCTGAAATGGAGCGTGAACTGATTGTTGAACGAACAAAAGCTGGATTGGAAACTGCTCGTGCACAGGGACGAATTGGTGGACGTCGTCCCAAACTTACACCAGAACAATGGGCACAAGCTGGACGATTAATTGCAGCAGGAACTCCTCGCCAGAAGGAGGCGAttctc                                                                                                                          >  1:327238/1‑248 (MQ=255)                                                                                                                            cTGACGGATTCAATTGATACCAGCACACCAATGGGACGCTTTTTCTTTCATGTGATGGGTGCCCTGGCTGAAATGGAGCGTGAACTGATTGTTGAACGAACAAAAGCTGGATTGGAAACTGCTCGTGCACAGGGACGAATTGGTGGACGTCGTCCCAAACTTACACCAGAACAATGGGCACAAGCTGGACGATTAATTGCAGCAGGAACTCCTCGCCAGAAGGTGGCGATTATCTATGATGTTGGTGTGTc                                                                                                         >  1:84423/1‑251 (MQ=255)                                                                                                                              gACGGATTCAATTGATACCAGCACACCAATGGGACGCTTTTTCTTTCATGTGATGGGTGCCCTGGCTGAAATGGATCGTGAACTGATTGTTGAACGAACAAAAGCTGGATTGGAAACTGCTCGTGCACAGGGACGAATTGGTGGACGTCGTCCCAAACTTACACCAGAACAATGGGCACAAGCTGGACGATTAATTGCAGCAGGAACTCCTCGCCAGAAGGTGGCGATTATCTATGATGTTGGTGTGTc                                                                                                         <  1:103672/249‑1 (MQ=255)                                                                                                                                  gATTCAATTGATACAAGCACACCAATGGGACGCTTTTTCTTTCATGAGATGGGTGCCCTGGCTGAAATGGAGCGTGAACTGATTGTTGAACGCACAAACGCTGGACTGGAACCTGCTCGTGCACAGGGACGAATTGGTGGACGTCGTCCCAAACTTACACCAGAACAATGGGCACAAGCTGGACGATTAATTGCAGCAGGAACTCCTCGCCAGAAGGTGGCGATTATCTATGATGTTGGTGTGTCAACttt                                                                                                   >  2:412904/1‑251 (MQ=255)                                                                                                                                      cAATTGATACCAGCACACCAATGGGACGCTTTTTCTTTCATGTGATGGGTGCCCTGGCTGAAATGGAGCGTGAACTGATTGTTGAACGAACAAAAGCTGGATTGGAAACTGCTCGTGCACAGGGACGAATTGGTGGACGTCGTCCCAAACTTACACCAGAACAATGGGCACAAGCTGGACGATTAATTGCAGCAGGAACTCCTCGCCAGAAGGTGGCGATTATCTATGATGTTGGTGTGTCAACTTTGtat                                                                                               >  2:13437/1‑251 (MQ=255)                                                                                                                                                                cGCTTTTTCTTTCATGTGATGGTTGCCCTGGCTGAAATTGAGCGTGAACTGATTGTTGAACGAACAAAAGCTGGATTGGAAACTGCTCGTGCACAGGGACGAATTGGTGGACGTCGTCCCAAACTTACACCAGAACAATGGGCACAAGCTGGACGATTAATTGCAGCAGGAACTCCTCGCCAGAAGGTGGCGATTATCTATGATGTTGGTGTGTCAACTTTGTATAAGAGGTTTCCTGCAGGGGataaata                                                                     <  1:82866/251‑1 (MQ=255)                                                                                                                                                                        ctttcATGTGATGGGTGCACTGGCTGAAATGGAGAGTGAACTGATTGTTGAACGAACAAAAGCTGGATTGGAAACTGCTCGTGCACAGGGACGAATTGGTGGACGTCGTCCCAAACTTACACCAGAACAATGGGCACAAGCTGGACGATTAATTGCAGCAGGAACTCCTCGCCAGAAGGTGGCGATTATCTATGATGTTGGTGTGTCAACTTTGTCTAAGAGGTTTCCTGCAGGGGATAAATAAAGTTaa                                                              >  1:478295/1‑250 (MQ=255)                                                                                                                                                                          ttcATGTGATGGGTGCCCTGGCTGAAATGGAGCGTGAACTGATTGTTGAACGAACAAAAGCTGGATTGGAAACTGCTCGTGCACAGGGACGAATTGGTGGACGTCGTCCCAAACTTACACCAGAACAATGGGCACAAGCTGGACGATTAATTGCAGCAGGAACTCCTCGCCAGAAGGTGGCGATTATCTATGATGTTGGTGTGTCAACTTTGTATAAGAGGTTTCCTGCAGGGGATAAATAAAGTTaaa                                                             <  1:433779/249‑1 (MQ=255)                                                                                                                                                                             aTGTGATGGGTGCCCTGGCTGAAATGGAGCGTGAACTGATTGTTGAACGAACAAAAGCTGGATTGGAAACTGCTCGTGCACAGGGACGAATTGGTGGACGTCGTCCCAAACTTACACCAGAACAATGGGCACAAGCTGGACGATTAATTGCAGCAGGAACTCCTCGCCAGAAGGTGGCGATTATCTATGATGTTGGTGTGTCAACTTTGTATAAGAGGTTTCCTGCAGGGGATAAATAAAGTTAAAGacac                                                        >  2:152452/1‑251 (MQ=255)                                                                                                                                                                                          ccTGGCTGAAATGGAGCGTGAACTGATTGTTGAACGAACAAAAGCTGGATTGGAAACTGCTCGTGCACAGGGACGAATTGGTGGACGTCGTCCCAAACTTACACCAGAACAATGGGCACAAGCTGGACGATTAATTGCAGCAGGAACTCCTCGCCAGAAGGTGGCGATTATCTATGATGTTGGTGTGTCAACTTTGTATAAGAGGTTTCCTGCAGGGGat                                                                          <  1:68316/220‑1 (MQ=255)                                                                                                                                                                                          ccTGGCTGAAATGGAGCGTGAACTGATTGTTGAACGAACAAAAGCTGGATTGGAAACTGCTCGTGCACAGGGACGAATTGGTGGACGTCGTCCCAAACTTACACCAGAACAATGGGCACAAGCTGGACGATTAATTGCAGCAGGAACTCCTCGCCAGAAGGTGGCGATTATCTATGATGTTGGTGTGTCAACTTTGTATAAGAGGTTTCCTGCAGGGGat                                                                          >  2:68316/1‑220 (MQ=255)                                                                                                                                                                                                    aTGGAGCGTGAACTGATTGTTGAACGAACAAAAGCTGGATTGGAAACTGCTCGTGCACAGGGACGAATTGGTGGACGTCGTCCCAAACTTACACCAGAACAATGGGCACAAGCTGGACGATTAATTgcagc                                                                                                                                                         <  1:469126/131‑1 (MQ=255)                                                                                                                                                                                                    aTGGAGCGTGAACTGATTGTTGAACGAACAAAAGCTGGATTGGAAACTGCTCGTGCACAGGGACGAATTGGTGGACGTCGTCCCAAACTTACACCAGAACAATGGGCACAAGCTGGACGATTAATTgcagc                                                                                                                                                         >  2:469126/1‑131 (MQ=255)                                                                                                                                                                                                        ggCGTGAACTGATTGTGGAAAGAACAAAAGCTGGATGGGAAACTGCTCGTGCACAGGGACGAATTGGTGGACGGCGTCCCAAACTTACACCAGAACAATGGGCACAAGCTGGACGATTAATTGCAGCAGGAACTCCTCGCCAGAAGGTGGCGATTATGGATGATGGTGGGGTGTCAACTTTGTATAAGAGGTTGGCTGCAGGGGATAAATAAGGTTAAAGACGCTTTGTTTACAAAAGAAAGTAAaacaac                             <  2:604216/250‑1 (MQ=255)                                                                                                                                                                                                          cGTGAACTGATTGTTGAACGAACAAAAGCTGGACTGGAAACTGCTCGTGCACAGGGACGAATTGGTGGACGTCGTCCCAAACTTACACCAGAACAATGGGCACAAGCTGGACGATTAATTGCAGCAGGAACTCCTCGCCAGAAGGTGTCGATTATCTATGATGTTGGGGTGTCAACTTTGTATAAGAGGGTTCCTGCAGGGGATAAATAAAGTTAAAGACACTTGGTGTACAAAAGAAAGTAAAACAACAg                           <  2:578497/251‑1 (MQ=255)                                                                                                                                                                                                                 tGATTGTTGACCGAACCAAAACTGGATCGGAAACTGCTCGTGCACAGGGACGAAATGGTGGACGTCGTGCCAACCTTACCCCAGAACAATGGACACAAGCAGGACGCTTAATTGCAGCAGGAACTCCTCGCCAGAAGGTGGCGATTATCTATGATGGTGGTGTGTCAACTTTGTATAAGAGGATTCTTGCAGGTGATAAATATAGTTCAAGGCACTTTTTGTACAAAAGAAAGTAAAACAACAACAACttg                    >  2:70764/1‑251 (MQ=255)                                                                                                                                                                                                                 tGATTGTTGAACGAACAAAAGCTGGATTGGAAACTGCTCGTGCACAGGGACGAATTGGTGGACGTCGTCCCAAACTTACACCAGAACAATGGGCACAAGCTGGACGATTAATTGCAGCAGGAACTCCTCGCCAGAAGGTGGCGATTATCTATGATGTTGGTGTGTCAACTTTGTATAAGAGGTTTCCTGCAGGGGATAAATAAAGTTAAAGACACTTTGTGTACAAAAGAAAGTAAAACAACAGCAACttg                    >  1:185045/1‑251 (MQ=255)                                                                                                                                                                                                                        tgAACGAACAAAAGCTGGATTGGAAACTGCTCGTGCACAGGGACGAATTGGTGGACGTCGTCCCAAACTTACACCAGAACAATGGGCACAAGCTGGACGATTAATTGCAGCAGGAACTCCTCGCCAGAAGGTGGCGATTATCTATGATGTTGgtgt                                                                                                            <  2:490944/156‑1 (MQ=255)                                                                                                                                                                                                                        tgAACGAACAAAAGCTGGATTGGAAACTGCTCGTGCACAGGGACGAATTGGTGGACGTCGTCCCAAACTTACACCAGAACAATGGGCACAAGCTGGACGATTAATTGCAGCAGGAACTCCTCGCCAGAAGGTGGCGATTATCTATGATGTTGgtgt                                                                                                            >  1:490944/1‑156 (MQ=255)                                                                                                                                                                                                                                   aaGCTGGATTGGAAACTGCTCGTGCACAGGGACGAATTGGTGGACGTCGTCCCAAACTTACACCAGAACAATGGGCACAAGCTGGACGATTAATTGCAGCAGGAACTCCTCGCCAGAAGGTGGCGATTATCTATGATGTTGGTGTGTCAACTTTGTATAAGAGGTTTCCTGCAGGGGATAAATAAAGTTAAAGACACTTTGTGTACAAAAGAAAGTAAAACAACAGCAACTTGTTGCAATTTTATCAATaa  <  1:850/251‑1 (MQ=255)                                                                                                                                                                                                                                           |                                                                                                                                                                                                                                                   CTCAGGACATTATCGGCAGGTGACACTCTGGTTGTCTGGAAGCTGGATCGGCTGGGGCGTAGTATGCGGCATCTTGTCGTGCTGGTGGAGGAGTTGCGCGAACGAGGCATCAACTTTCGTAGTCTGACGGATTCAATTGATACCAGCACACCAATGGGACGCTTTTTCTTTCATGTGATGGGTGCCCTGGCTGAAATGGAGCGTGAACTGATTGTTGAACGAACAAAAGCTGGACTGGAAACTGCTCGTGCACAGGGACGAATTGGTGGACGTCGTCCCAAACTTACACCAGAACAATGGGCACAAGCTGGACGATTAATTGCAGCAGGAACTCCTCGCCAGAAGGTGGCGATTATCTATGATGTTGGTGTGTCAACTTTGTATAAGAGGTTTCCTGCAGGGGATAAATAAAGTTAAAGACACTTTGTGTACAAAAGAAAGTAAAACAACAGCAACTTGTTGCAATTTTATCAATAA  >  NC_000913/1209829‑1210305

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑