Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913_3_pae_pgi	2,028,160	G→C	11.5%	intergenic (‑143/+28)	yedQ ← / ← yodC	putative membrane‑anchored diguanylate cyclase/uncharacterized protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_pae_pgi	2,028,160	0	G	C	11.5%	127.1 / 7.8	52	intergenic (‑143/+28)	yedQ/yodC	putative membrane‑anchored diguanylate cyclase/uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base G (23/21);  new base C (3/3);  total (26/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.22e-01

ACCCTGACGACTCCCAACCTGCTTTTTTATGATTCTGGCATAACCTGGCGATAGCGTACCGCAAAACAGCGATAATTTTATAATGGTGGCATGATAAGACGCGACTATCATTCATTGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCTCGGTTTCATGAAAAGCTTCCCGCTTGACCCCGTAACCGTCATACCAACGACACTCAACCATACCGCTG  >  NC_000913_3_pae_pgi/2028016‑2028299                                                                                                                                                 |                                                                                                                                            aCCCTGACGACTCCCAACCTGCTTTTTTATGATTCTGGCATAACCTGGCGATAGCGTACCGCAAAACAGCGATAATTTTATAATGGTGGCATGATAAGACGCGACTATCATTCATTGCAGGCATTAGCACACCAGGCCGGATGTGATcc                                                                                                                                         >  1:653313/1‑149 (MQ=255)  cccTGACGACTCCCAACCTGCTTTTTTTTTTTTTTGTCATAACCTGGCGATAGCGTACCGCAAAACAGCGATAATTTTATAATGGTGGCATGATAAGACGCGACTATCATTCATTGCAGCCACTACCACACCATGCCGGATGTCATcag                                                                                                                                        >  2:1000934/1‑147 (MQ=255)   ccTGACGACTCCCAACCTGCTTTTTTATGATTCTGGCATAACCTGGCGATAGCGTACCGCAAATCTGAGATAAATTTATAATAGTGGCATGATAAAACGCGACTATACATCATTGTATGCATTAGCACACCAGGCCGGATGTGGTCAgg                                                                                                                                       >  1:391900/1‑149 (MQ=255)    cTGACGACTCGCAACCTGCTTTTTTATGATTCTGGAATAACCAGGCGATAGCGTAGCGCAAAACGACGATATTTTTATAATGGTGGCATGGTAATACGAGACTATAACAACGTGCAGGCACTAGCACACCAGGCAGGCTGTGATccctg                                                                                                                                      >  2:100123/1‑146 (MQ=255)     tGACGACTCCCAACCTGCTTTTTTATGATTCTGGCATAACCTGGCGATAGCGTACCGCAAAACAGCGATAATTTTATAATGGTGGCATGATAAGACGCGACTATCATTCATTGCAGGCATTAGCACATCAGGCCGGATCACATCCGGcc                                                                                                                                     >  1:436233/1‑149 (MQ=255)           cTCCCAACCTGCTTTTTTATGATTCTGGCATAACCTGGCGATAGCGTACCGCAAAACAGCGATAATTTTATAATGGTGGCATGATAAGACGCGACTATCATTCATTGCAGGCATTAGCACATCAGGCCGGATCACATCCGGCCTGgtgt                                                                                                                               <  2:436233/149‑1 (MQ=255)            tCCCAACCTTCTTTTTTAGTATTCTGGCATAACCTGGCGATAGCGTACCGCAAAACAGCGATAATTTTATAATGGGGGCATGATAAGACGCGACTATCATTCATTGCAGGCATTAGCACACCAGGCCGGATCACATCCGGCCTGgtgtg                                                                                                                              <  2:552019/149‑2 (MQ=255)            tCCCAACCTGCTTTTTTATGATTCTGGCATAACCTGGCGATAGCGTACCGCAAAACAGCGATAATTTTATAATGGTGGCATGATAAGACGCGACTATCATTCATTGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGCCTGAt                                                                                                                                 <  2:637142/146‑1 (MQ=255)            tCCCAACCTGCTTTTTTATGATTCTGGCATAACCTGGCGATAGCGTACCGCAAAACAGCGATAATTTTATAATGGTGGCATGATAAGACGCGACTATCATTCATTGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGCCTGAt                                                                                                                                 >  1:637142/1‑146 (MQ=255)              ccAACCTGCTTTTTTATTATTCTTGCATAACCTGGCGATAGTGTACCGCAAAACAGCGATAATTTTATAATGGTGGCATGATAAGACGCGACTATCATTCATCGAAGTCATGAGCACACCAGGCCGGATGTGATCCGGCCTGATGTTaa                                                                                                                            <  1:239397/149‑1 (MQ=255)              ccAACCTGCTTTTTTATGATTCTGGCATAACCTGGCGATAGCGTACCGCAAAACAGCGATAATTTTATAATGGTGGCATGATAAGACGCGACTATCATTCATTGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGCCTGATGTTaa                                                                                                                            <  1:238703/149‑1 (MQ=255)               cAACCTGCTTTTTTATGATTCTGGCATAACCTGGCGATAGCGTACCGCAAAACAGCGATAATTTTATAATGGTGGCATGATAAGACGCGACTATCATTCATTGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGCCTGATGTTAAt                                                                                                                           >  1:313626/1‑149 (MQ=255)                aaCCTGCTTTTTTATGATTCTGGCATAACCTGGCGATATCGTACCGCAAAACAGCGATAATTTTATAATGGTGGCATGATAAGACTCGACTATCATTCATTGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGCCTGATGTTACTg                                                                                                                          >  1:211590/1‑149 (MQ=255)                       ttttttATGATTCTGGCATAACCTGGCGATAGCGTACCGCAAAACAGCGATAATTTTATAATGGTGGCATGATAAGACGCGACTATCATTCATTGCAGGCATTAGCACACCAGGCCGAATGTGATCCGGCCTGATGTTAATGATACCCt                                                                                                                   >  1:519809/1‑149 (MQ=255)                           ttATGATTCTGGCATAACCTGGCGATAGCGTACCGCCAAACAGCGATAATTTTATAATGGTGGCATGATAAGACGCGACTATCATTCATTGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTca                                                                                                               >  1:993066/1‑149 (MQ=255)                           ttATGATTCTGGCATAACCTGGCGATAGCGTACCGCAAAACAGCGATAATTTTATAATGGTGGCATGATAAGACGCGATTATCATTCATTGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTca                                                                                                               <  2:474379/149‑1 (MQ=255)                           ttATGATTCTGGAATAACCTGGCGATAGCTTACCGCAAAACAGCGATAATTTTATAATGGTGGCATGATAAGACGCGACTATCATTCATTGCAGGCATTATCACACCAGGCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTca                                                                                                               <  2:317900/149‑1 (MQ=255)                                aTTGTGGCATAACCTGGCGAGAGAGTACCGCAAAACAGCGATAATTGTATAATGGGGGCATGATAAGACGCGACTATTATTCTTTGCAGGCATTAGCACACCAGGCCGGCTATGGTACAACTTGATGTTAATGATACCCTTTCACActt                                                                                                          <  2:468795/149‑1 (MQ=255)                                    tGGCATAACCTGGCGATAGCGTACCGCAAAACAGCGATAATTTTATAATGGTGGCATGATAAGACGCGACTATCATTCATTGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTCACACttcttc                                                                                                      <  2:653313/149‑1 (MQ=255)                                       cATAACCTGGCGATAGCGTACCGCAAAACAGCGATAATTTTATAATGGTGGCATGATAAGACGCGACTATCATTCATTGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGc                                                                                                   >  2:538589/1‑149 (MQ=255)                                              tGGCGATAGCGTACCGCAAAACAGCGATAATTTTATAATGGTGGCATGATAAGACGCGACTATCATTCATTGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCCGAACGa                                                                                            >  1:668700/1‑149 (MQ=255)                                              tGGCGATAGCGTACCGCAAAACAGCGATAATTTTATAATGGTGGCATGATAAGACGCGACTATCATTCATTGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGa                                                                                            >  1:667687/1‑149 (MQ=255)                                               ggCTATAGCTTACCGCAAAACATTGATAATTTTATAATGGTGGCATGATAAGACGCGACTATCATTCATTGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGAc                                                                                           <  1:154768/149‑1 (MQ=255)                                                gCGATAGCGTACCGCAAAACAGCGATAATTTTATAATGGTGGCATGATAAGACGCGACTATCATTCATTGCAGGCATTAGCACACCAGGCCGGAGTTGATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGAct                                                                                          >  1:834969/1‑149 (MQ=255)                                                    tAGCGTACCGCAAAACAGCGATAATTTTATAATGGTGGCAAGATAAGACGCGACTATCATTCATTGCAGGCATTGGCACACCAGGCCGGATGTGATCCGGCCTGATGTTAATGCTACCCTTTCACACTTCTTCCGCAGAACGAatcccc                                                                                      >  2:80124/1‑149 (MQ=255)                                                           ccGCAAAACAGCGATAATTTGATAATGGTGGCATGATAAGACGCGACTATCATTCATTGCAGGCATTAGCACACCAGGCCGTATGTGATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGTAGAACGACTCCCCTCCCCCg                                                                               <  2:170372/149‑1 (MQ=255)                                                                    aGCGATAATTTTATAATGGTGGCATGATAAGACGCGACTATCATTCATTGCAGGCATTAGCACACCAGGCCGGATGTGATCAGGCCTGATGTTAATGATACCATTGCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGCAACAAGcg                                                                      >  2:958842/1‑148 (MQ=255)                                                                     gCGATAATTTTATAATGGTGGCATGATAAGACGCGACTATCATTCATTGCAGGCATTAGCACACCAGGCCGGATCACATCCGGCCTggt                                                                                                                                 >  2:317588/1‑87 (MQ=38)                                                                     gCGATAATTTTATAATGGTGGCATGATAAGACGCGACTATCATTCATTGCAGGCATTAGCACACCAGGCCGGATCACATCCGGCCTggt                                                                                                                                 <  1:317588/89‑3 (MQ=38)                                                                      cGATAGTTTTATAACGGGGGCATGATAAGACGCGACTATCATTCATTGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCTCg                                                                    <  2:659634/149‑1 (MQ=255)                                                                      cGATAATTTTATAATGGTGGCATGATAAGACGCGACTATCATTCATTGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGActcc                                                                                        >  2:727839/1‑129 (MQ=255)                                                                      cGATAATTTTATAATGGTGGCATGATAAGACGCGACTATCATTCATTGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGActcc                                                                                        <  1:727839/129‑1 (MQ=255)                                                                            ttttATAATGGTGGCATGATAAGACGCGACTATCATTCATTGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCTCGGTTTCa                                                              >  2:77156/1‑149 (MQ=255)                                                                             tttATAATGGTGGCATGATAAGACGCGACTATCATTCATTGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGTCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCTCGGTTTCAt                                                             <  1:816509/149‑1 (MQ=255)                                                                             tttATAATGGTGGCATGATAAGACGCGACTATCATTCATTGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCTCGGTTTCAt                                                             >  1:49187/1‑149 (MQ=255)                                                                                       tggCATCATAAGACGCGACTATCATTCACTGCAGTCATTAGCACACCAGGCCGGATGTTATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCTCGTCACACTCTCGGTTTCATGAAAAGCTTc                                                   <  2:91481/149‑1 (MQ=255)                                                                                            tGATAAGACGCGACTATCATTCATTGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGa                                                                                            >  2:85611/1‑103 (MQ=255)                                                                                            tGATAAGACGCGACTATCATTCATTGCAGGCATTAGCACACCAGGCCGGATCTGATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGa                                                                                            <  1:85611/103‑1 (MQ=255)                                                                                                 aGACGCGACTATCATTCATTGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCTCGGTTTCATGAAAAGCTTCCCGCTTGAcc                                         <  2:313626/149‑1 (MQ=255)                                                                                                           aTCATTCATTGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCTCGGTTTCATGAAAAGCTTCCCGCTTGACCCCGTAACCGt                               <  1:77156/149‑1 (MQ=255)                                                                                                               ttcattGCAGCCATTAGAACACCACGCCGGAGGTGATACGGCCTGATGTTAATGACACCCTTTCACACTTCTTCTGCAGAACGACTCCCCTCCCCTGGAACAAGCTCGGTTTCATGAAAAGCTTCCCGCTTGACCGCGTAACCGTCATa                           <  2:950840/149‑1 (MQ=255)                                                                                                                        cgCATTAGCATCCCAGTCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCTCGGTTTCATGAAAAGCTTCCCGCTTGACCCCGTAACCGTCATACCAACGaca                  <  2:754049/148‑1 (MQ=255)                                                                                                                         gCATTAGCACACCAGGCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCTCGGTTTCATGAAAAGCTTCCCGCTTGACCCCGTAACCGTCATACCAACGacac                 <  2:49187/149‑1 (MQ=255)                                                                                                                             tAGCACACCAGGCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACCCCCCGCCCCCGGAACAAGCTCGGTTTCATGAAAAGCTTCCCGCTTGACCCCGTAACCGTCATACCAACGACACTCaa             <  1:390602/149‑1 (MQ=255)                                                                                                                                cacaCCAGGCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCTCGGTTTCATGAAAAGCTTCCCGCTTGACCCCGTAACCGTCATACCAACGACACTCAACCa          <  2:992415/149‑1 (MQ=255)                                                                                                                                  cacCAGGCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCTCGGTTTCATGAAAAGCTTCCCGCTTGACCCCGTAACCGTCATACCAACGACACTCAACCATa        >  2:312079/1‑149 (MQ=255)                                                                                                                                   acCAGGCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCTCGGTTTCATGAAAAGCTTCCCGCTTGACCCCGTAACCGTCATACCAACGACACTCAACCATAc       >  2:445254/1‑149 (MQ=255)                                                                                                                                   acCAGGCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCTCGGTTTCATGAAAAGCTTCCCGCTTGACCCCGTAACCGTCATACCAACGACACTCAACCATAc       >  1:515325/1‑149 (MQ=255)                                                                                                                                     cAGGCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACGCCCCTCCCCCGGAACAAGCTCGGTTTCATGAAAAACTTCCCGCTTGACCCCGTAACCGACATACCAACGACACTCAACAATACCg     >  1:446238/1‑149 (MQ=255)                                                                                                                                        ggcGGATGATATCCGGCCTGATGTAAATGATATCCTTTCTCACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCTCGGTTTCATGAAAAGCTTCACGCTTGACCCCGTAACCGTCATACCAACGACACTCAACCATACCGATg  <  2:13572/147‑1 (MQ=255)                                                                                                                                        gCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCTCGGTTTCATGAAAAGCTTCCCGCTTGACCCCGTAACCGTCATACCAACGACACTCAACCATACCGCTg  <  1:445254/149‑1 (MQ=255)                                                                                                                                        gCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCCCGGTTTCATGAAAAGCTTCCCGCTTGACCCCGTAACCATCATACCAACGACACTCAACCATACCACTg  >  1:56301/1‑149 (MQ=255)                                                                                                                                                 |                                                                                                                                            ACCCTGACGACTCCCAACCTGCTTTTTTATGATTCTGGCATAACCTGGCGATAGCGTACCGCAAAACAGCGATAATTTTATAATGGTGGCATGATAAGACGCGACTATCATTCATTGCAGGCATTAGCACACCAGGCCGGATGTGATCCGGCCTGATGTTAATGATACCCTTTCACACTTCTTCCGCAGAACGACTCCCCTCCCCCGGAACAAGCTCGGTTTCATGAAAAGCTTCCCGCTTGACCCCGTAACCGTCATACCAACGACACTCAACCATACCGCTG  >  NC_000913_3_pae_pgi/2028016‑2028299

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑