Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,898,419	T→C	intergenic (+123/‑8)	sdaA → / → pdeD	L‑serine deaminase I/putative c‑di‑GMP phosphodiesterase PdeD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,898,419	0	T	C	97.8%	157.0 / NA	46	intergenic (+123/‑8)	sdaA/pdeD	L‑serine deaminase I/putative c‑di‑GMP phosphodiesterase PdeD
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base C (26/19);  total (26/20)
Fisher's exact test for biased strand distribution p-value = 4.35e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGACTAATACTTCTTACTCGCCCATCTGCAACGGATGGGCGAATTTATACCCGCTTTCTCGTCTGCTGTAATATTCCCCACTACACTTCCACTGTTGCGTCAGGCGTTTGTCGCCATACGCTTACAGGGTGGCCCGCATGCAAAAAGCACAACGGATCATTAAAACCTATCGTCGTAATCGAATGATTGTTTGTACGATTTGCGCACTCGTTACGCTCGCTTCGACCCTGAGCGTGCGATTTATTTCACA  >  NC_000913/1898290‑1898539                                                                                                                                  |                                                                                                                         tgACTAATACTTCTTACTCGCCCATCTGCAACGGATGGGCGAATTTATACCCGCTTTCTCGTCTGCTGTAATATTCCCCACTACACTTCCACTGTTGCGTCAGGCGTTTGTCGCCATACGCTTACAGggcggc                                                                                                                       <  2:349581/133‑1 (MQ=255)        tACTTCTTACTCGCCCATCTGCAACGGATGGGCGAATTTATACCCGCTTTCTCGTCTGCTGTAATATTCCCCACTACACTTCCACTGTTGCGTCAGGCGTTTGTCGCCATACGCTTACAGGGCGGCCCGCATg                                                                                                                >  2:593977/1‑133 (MQ=255)             cttACTCGCCCATCTGCAACGGATGGGCGAATTTATACCCGCTTTCTCGTCTGCTGTAATATTCCCCACTACACTTCCACTGTTGCGTCAGGCGTTTGTCGCCATACGCTTACAGGGCGGCCCGCATGCaaaa                                                                                                           >  1:142218/1‑133 (MQ=255)               tACTCGCCCATCTGCAACGGATGGGCGAATTTATACCCGCTTTCTCGTCTGCTGTAATATTCCCCACTACACTTCCACTGTTGCGTCAGGCGTTTGTCGCCATACGCTTACAGGGCGGCCCGCATGCAAAAAg                                                                                                         >  1:453561/1‑133 (MQ=255)                     cccATCTGCAACGGATGGGCGAATTTATACCCGCTTTCTCGTCTGCTGTAATATTCCCCACTACACTTCCACTGTTGCGTCAGGCGTTTGTCGCCATACGCTTACAGGGCGGCCCGCATGCAAAAAGCACAAc                                                                                                   >  2:568643/1‑133 (MQ=255)                     cccATCTGCAACGGATGGGCGAATTTATACCCGCTTTCTCGTCTGCTGTAATATTCCCCACTACACTTCCACTGTTGCGTCAGGCGTTTGTCGCCATACGCTTACAGGGCGGCCCGCATGCAAAAAGCACAAc                                                                                                   >  2:456742/1‑133 (MQ=255)                     cccATCTGCAACGGATGGGCGAATTTATACCCGCTTTCTCGTCTGCTGTAATATTCCCCACTACACTTCCACTGTTGCGTCAGGCGTTTGTCGCCATACGCTTACAGGGCGGCCCGCATGCAAAAAGCACAAc                                                                                                   >  1:86785/1‑133 (MQ=255)                        aTCTGCAACGGATGGGCGAATTTATACCCGCTTTCTCGTCTGCTGTAATATTCCCCACTACACTTCCACTGTTGCGTCAGGCGTTTGTCGCCATACGCTTACAGGGCGGCCCGCATGCAAAAAGCACAACGGa                                                                                                <  2:642990/133‑1 (MQ=255)                             cAACGGATGGGCGAATTTATACCCGCTTTCTCGTCTGCTGTAATATTCCCCACTACACTTCCACTGTTGCGTCAGGCGTTTGTCGCCATACGCTTACAGGGCGGCCCGCATGCAAAAAGCACAACGGATCAtt                                                                                           <  1:22046/133‑1 (MQ=255)                              aaCGGATGGGCGAATTTATACCCGCTTTATCGTCTGCTGTAATATTCCCCACTACACTTCCACTGTTGCGTCAGGCGTTTGTCGCCATACGCTTACAGGGCGGCCCGCATGCAAAAAGCACAACGGATCATTa                                                                                          <  2:262835/133‑1 (MQ=255)                                  gATGGGCGAATTTATACCCGCTTTCTCGTCTGCTGTAATATTCCCCACTACACTTCCACTGTTGCGTCAGGCGTTTGTCGCCATACGCTTACAGGGCGGCCCGCTTGCAAAAAGCACGACGGATCATTAAAAc                                                                                      >  2:229358/1‑133 (MQ=255)                                  gATGGGCGAATTTATACCCGCTTTCTCGTCTGCTGTAATATTCCCCACTACACTTCCACTGTTGCGTCAGGCGTTTGTCGCCATACGCTTACAGGGCGGCCCGCATGCAAAAAGCACAACGGATCATTAAAAc                                                                                      >  1:622876/1‑133 (MQ=255)                                  gATGGGCGAATTTATACCCGCTTTCTCGTCTGCTGTAATATTCCCCACTACACTTCCACTGTTGCGTCAGGCGTTTGTCGCCATACGCTTACAGGGCGGCCCGCATGCAAAAAGCACAACGGATCATTAAAAc                                                                                      >  2:373565/1‑133 (MQ=255)                                  gATGGGCGAATTTATACCCGCTTTCTCGTCTGCTGTAATATTCCCCACTACACTTCCACTGTTGCGTCAGGCGTTTGTCGCCATACGCTTACAGGGCGGCCCGCATGCAAAAAGCACAACGGATCATTAAAAc                                                                                      >  1:480227/1‑133 (MQ=255)                                    tGGGCGAATTTATACCCGCTTTCTCGTCTGCTGTAATATTCCCCACTACACTTCCACTGTTGCGTCAGGCGTTTGTCGCCATACGCTTACAGGGCGGCCCGCGTGCAAAAGGCAAAATGGATCAATAAAACCt                                                                                    >  1:189560/1‑133 (MQ=255)                                    tGGGCGAATTTATACCCGCTTTCTCGTCTGCTGTAATATTCCCCACTACACTTCCACTGTTGCGTCAGGCGTTTGTCGCCATACGCTTACAGGGCGGCCCGCATGCAAAAAGCACAACGGATCATTAAAACCt                                                                                    >  1:44753/1‑133 (MQ=255)                                          aaTTTATACCCGCTTTCTCGTCTGCTGTAATATTCCCCACTACACTTCCACTGTTGCGTCAGGCGTTTGTCGCCATACGCTTACAGGGCGGCCCGCATGCAAAAAGCACAACGGATCATTAAAACCTAtcgtc                                                                              >  1:565678/1‑133 (MQ=255)                                              tataCCCGCTTTCTCGTCTGCTGTAATATTCCCCACTACACTTCCACTGTTGCGTCAGGCGTTTGTCGCCATACGCTTACAGGGCGGCCCGCATGCAAAAAGCACAACGGATCATTAAAACCTATCGTCGTaa                                                                          <  2:86785/133‑1 (MQ=255)                                              tataCCCGCTTTCTCGTCTGCTGTAATATTCCCCACTACACTTCCACTGTTGCGTCAGGCGTTTGTCGCCATACGCTTACAGGGCGGCCCGCATGCAAAAAGCACAACGGATCATTAAAACCTATCGTCGTaa                                                                          <  2:142218/133‑1 (MQ=255)                                                      cTTTCTCGTCTGCTGTAATATTCCCCACTACACTTCCACTGTTGCGTCAGGCGTTTGTCGCCATACGCTTACAGGGCGGCCCGCATGCAAAAAGCACAACGGAACATTAAAACCTATCGTCGTAATCGAATGa                                                                  >  1:534603/1‑133 (MQ=255)                                                                        tatTCCCCACTACACTTCCACTGTTGCGTCAGGCGTTTGTCGCCATACGCTTACAGGGCGGCCCGCATGCAAAAAGCACAACGGATCATTAAAACCTATCGTCGTAATCGAATGATTGTTTGTACGATTTgcg                                                <  1:593977/133‑1 (MQ=255)                                                                          ttCCCCACTACACTTCCACTGTTGCGTCAGGCGTTTGTCGCCATACGCTTACAGGGCGGCCCGCATGCAAAAAGCACAACGGATCATTAAAACCTATCGTCGTAATCGAATGATTGTTTGTACGATTTGCGCa                                              <  1:373565/133‑1 (MQ=255)                                                                               cACTACACTTCCACTGTTGCGTCAGGCGTTTGTCGCCATACGCTTACAGGGCGGCCCGCATGCAAAAAGCACAACGGATCATTAAAACCTATCGTCGTAATCGAATGATTGTTTGTACGATTTGCGCa                                              <  2:609185/128‑1 (MQ=255)                                                                               cACTACACTTCCACTGTTGCGTCAGGCGTTTGTCGCCATACGCTTACAGGGCGGCCCGCATGCAAAAAGCACAACGGATCATTAAAACCTATCGTCGTAATCGAATGATTGTTTGTACGATTTGCGCa                                              >  1:609185/1‑128 (MQ=255)                                                                               cACTACACTTCCACTGTTGCGTCAGGCGTTTGTCGCCATACGCTTACAGGGCGGCCCGCATGCAAAAAGCACAACGGATCATTAAAACCTATCGTCGTAATCGAATGATTGTTTGTACGATTTGCGCACTCGt                                         >  1:451579/1‑133 (MQ=255)                                                                               cACTACACTTCCACTGTTGCGTCAGGCGTTTGTCGCCATACGCTTACAGGGCGGCCCGCATGCAAAAAGCACAACGGATCATTAAAACCTATCGTCGTAATCGAATGATTGTTTGTACGATTTGCGCACTCGt                                         <  1:596986/133‑1 (MQ=255)                                                                                    cacTTCCACTGTTGCGTCAGGCGTTTGTCGCCATACGCTTACAGGGCGGCCCGCATGCAAAAAGCACAACGGATCATTAAAACCTATCGTCGTAATCGAATGATTGTTTGTACGATTTGCGCACTCGTTAcgc                                    >  1:491441/1‑133 (MQ=255)                                                                                       ttCCACTGTTGCGTCAGGCGTTTGTCGCCATACGCTTACAGGGCGGCCCGCATGCAAAAAGCACAACGGATCATTAAAACCTATCGTCGTAATCGAATGATTGTTTGTACGATTTGCGCACTCGTTAcgctcg                                 >  2:447868/1‑133 (MQ=255)                                                                                         ccACTGTTGCTTCAGGCGTTTGTCTCCATACGCTTACAGGGTGGCCCGCATGCAAAAAGCACAACGGATCATTAAAACCTATCGTCGTAATCGAATGATTGTTTGTACGATTTGCGCACTCGTTAcgctcgct                               <  2:263391/133‑1 (MQ=255)                                                                                         ccACTGTTGCGTCAGGCGTTTGTCGCCATACGCTTACAGGGCGGCCCGCATGCAAAAAGCACAACGGATCATTAAAACCTATCGTCGTAATCGAATGATTGTTTGTACGATTTGCGCACTCGTTAcgctcgct                               <  2:480227/133‑1 (MQ=255)                                                                                         ccACTGTTGCGTCAGGCGTTTGTCGCCATACGCTTACAGGGCGGCCCGCATGCAAAAAGCACAACGGATCATTAAAACCTATCGTCGTAATCGAATGATTGTTTGTACGATTTGCGCACTCGTTAcgctcgct                               <  2:453561/133‑1 (MQ=255)                                                                                         ccACTGTTGCGTCAGGCGTTTGTCGCCATACGCTTACAGCGCGGCCCGCATGCAAAAAGCACAACGGATCATTAAAACCTATCGTCGTAATCGAATGATTGTTTGTACGATTTGCGCACTCGTTAcgctcgct                               >  2:494890/1‑133 (MQ=255)                                                                                           aCTGTTGCGTCAGGCCTTCGTCACCATACGTTTACAGGGCGGCCCGCATGCAAAAAGCACAACGGATCATTAAAACCTATCGTCGTAATCGAATGATTGTTTGTACGATTTGCGCACTCGTTACGCTCGCTTc                             <  1:204274/133‑1 (MQ=255)                                                                                              gTTGCGTCAGGCGTTTGTCGCCATACGCTTACAGGGCGGCCCGCATGCAAAAAGCACAACGGATCATTAAAACCTATCGTCGTAATCGAATGATTGTTTGTACGATTTGCGCACTCGTTACGCTCGCTTCGAc                          >  1:327886/1‑133 (MQ=255)                                                                                               ttGCGTCAGGCGTTTGTCGCCATACGCTTACAGGGCGGCCCGCATGCAAAAAGCACAACGGATCATTAAAACCTATCGTCGTAATCGAATGATTGTTTGTACGATTTGCGCACTCGTTACGCTCGCTTCGAcc                         >  1:323090/1‑133 (MQ=255)                                                                                               ttGCGTCAGGCGTTTGTCGCCATACGCTTACAGGGCGGCCCGCATGCAAAAAGCACAACGGATCATTAAAACCTATCGTCGTAATCGAATGATTGTTTGTACAATTTGCGCACTGGTTACGCTCGCTTCGAcc                         >  1:213401/1‑133 (MQ=255)                                                                                                tGCGTCAGGCGTTTGTCGCCATACGCTTACAGGGCGGCCCGCATGCAAAAAGCACAACGGATCATTAAAACCTATCGTCGTAATCGAATGATTGTTTGTACGATTTGCGCACTCGTTACGCTCGCTTCGAccc                        <  2:44753/133‑1 (MQ=255)                                                                                                tGCGTCAGGCGTTTGTCGCCATACGCTTACAGGGCGGCCCGCATGCAAAAAGCACAACGGATCATTAAAACCTATCGTCGTAATCGAATGAATGTTTGTAGGATATGCCCACTCGTTCCGCTCGCTTCGAccc                        >  2:256085/1‑133 (MQ=255)                                                                                                 gCGTCAGGCGTTTGTCGCCATACGCTTACAGGGCGGCCCGCATGCAAAAAGCACAACGGATCATTAAAACCTATCGTCGTAATCGAATGATTGTTTGTACGATTTGCGCACTCGATACGCTCGCATCGACCCt                       >  1:263391/1‑133 (MQ=255)                                                                                                        gCGTTTGTCGCCATACGCTTACAGGGCGGCCCGCATGCAAAAAGCACAACGGATCATTAAAACCTATCGTCGTAATCGAATGATTGTTTGTACGATTTGCGCACTCGTTACGCTCGCTTCGACCCTGAGCGTg                <  1:456742/133‑1 (MQ=255)                                                                                                        gCGTTTGTCGCCATACGCTTACAGGGCGGCCCGCATGCAAAAAGCACAACGGATCATTAAAACCTATCGTCGTAATCGAATGATTGTTTGTACGATTTGCGCACTCGTTACGCTCGCTTCGACCCTGAGCGTg                <  1:568643/133‑1 (MQ=255)                                                                                                        gCGTTTGTCGCCATACGCGTACAGGGCGGCCCGCATGCAAAAAGCACAACGGATCATTAAAACCTATCGTCGTAATCGAATGATTGTTTGTACGATTTGCGCCCTCGTTACGCTCGCTTCGACCCTGAGCGTg                <  1:494890/133‑1 (MQ=255)                                                                                                          gTTTGTCGCCCTACGCTTACAGGGCGGCTCGCTTGCAAAAACCACAACGGATCATTAAAACCTATCGTCGTAATCGAATGATTGTTTGTACGATTTGCGCACTCGTTACGCTCGCTTCGACCCTGAGCGTGCg              <  2:213401/133‑1 (MQ=255)                                                                                                          gTTTGTCGCCATACGCTTACAGGGCGGCCCGCATGCAAAAAGCACAACGGATCATTAAAACCTATCGTCGTAATCGAATGATTGTTTGTACGATTTGCGCACTCGTTACGCTCGCTTCGACCCTGAGCGTGCg              <  2:323090/133‑1 (MQ=255)                                                                                                          gTTTGTCGCCATACGCTTACAGGGCGGCCCGCATGCAAAAAGCACAACGGATCATTAAAACCTATCGTCGTAATCGAATGATTGTTTGTACGATTTGCGCACTCGTTACGCTCGCTTCGACCCTGAGCGTGCg              <  1:139205/133‑1 (MQ=255)                                                                                                             tGTCGCCATACGCTTACAGGGCGGCCCGCATGCAAAAAGCACAACGGATCATTAAAACCTATCGTCGTAATCGAATGATTGTTTGTACGATTTGCGCACTCGTTACGCTCGCTTCGACCCTGAGCGTGCg              <  1:325699/130‑1 (MQ=255)                                                                                                             tGTCGCCATACGCTTACAGGGCGGCCCGCATGCAAAAAGCACAACGGATCATTAAAACCTATCGTCGTAATCGAATGATTGTTTGTACGATTTGCGCACTCGTTACGCTCGCTTCGACCCTGAGCGTGCg              >  2:325699/1‑130 (MQ=255)                                                                                                                      aCGCTTACAGGGCGGCCCGCATGCAAAAAGCACAACGGATCATTAAAACTTATCGTCGTAATCGAATGATTGTTTGTACGATTTGCGCACTCGTTACGCTCGCTTCGACCCTGAGCGTGCGATTTATTTcaca  >  2:130451/1‑133 (MQ=255)                                                                                                                                  |                                                                                                                         TGACTAATACTTCTTACTCGCCCATCTGCAACGGATGGGCGAATTTATACCCGCTTTCTCGTCTGCTGTAATATTCCCCACTACACTTCCACTGTTGCGTCAGGCGTTTGTCGCCATACGCTTACAGGGTGGCCCGCATGCAAAAAGCACAACGGATCATTAAAACCTATCGTCGTAATCGAATGATTGTTTGTACGATTTGCGCACTCGTTACGCTCGCTTCGACCCTGAGCGTGCGATTTATTTCACA  >  NC_000913/1898290‑1898539

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑