Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP009273	3,370,787	T→G	intergenic (‑8/+387)	sspA ← / ← rpsI	stringent starvation protein A, phage P1 late gene activator, RNAP‑associated acid‑resistance protein, inactive glutathione S‑transferase homolog/30S ribosomal subunit protein S9

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	3,370,787	0	T	G	98.1%	178.9 / NA	53	intergenic (‑8/+387)	sspA/rpsI	stringent starvation protein A, phage P1 late gene activator, RNAP‑associated acid‑resistance protein, inactive glutathione S‑transferase homolog/30S ribosomal subunit protein S9
Reads supporting (aligned to +/- strand):  ref base T (0/0);  major base G (27/25);  minor base C (0/1);  total (27/26)
Fisher's exact test for biased strand distribution p-value = 4.91e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

CGGATTGTCCTTTTCCACGTGTTCGATCTCGAAACTTACACCTTTCTCAGCCAGCACAATGCGGACCTGATGGCTATAGATGTCAGTAGGACCGGAAAACAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCTCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAAAATCAAACAAAAAATGAGCAATACCCGACATTTGGGCAGAAAATTGGATGAT  >  CP009273/3370642‑3370931                                                                                                                                                  |                                                                                                                                                 cGGATTGTCCTTTTCCACGTGTTCGATCTCGAAACTTACACCTTTCTCAGCCAGCACAATGCGGACCTGATGGCTATAGATGTCAGTAGGACCGGAAAACAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCGCCa                                                                                                                                               <  1:587373/149‑1 (MQ=255)      tGTCCTTTTCCACGTGTTCGATCTCGAAACTTACACCTTTCTCAGCCAGCAAAATGCGGACCTGATGGCTATAGATGTCAGTAGGACCGGAAAACAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCGCCAGGtac                                                                                                                                          <  1:473578/149‑2 (MQ=255)           ttttCCACGTGTTCGATCTCGAAACTTACACCTTTCTCAGCCAGCACAATGCGGACCTGATGGCTATAGATGTCAGTAGGACCGGACAACAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCGCCAGGTATAGTCa                                                                                                                                     >  1:629224/1‑149 (MQ=255)                cACGTGTTCGATCTCGAAACTTACACCTTTCTCAGCCAGCACAATGCGGACCTGATGGCTATAGATGTCAGTAGGACCGGAAAACAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCGCCAGGTATAGTCAGAAtt                                                                                                                                <  1:344694/149‑1 (MQ=255)                    tgtTCGATCTCGAGACTTACACCTTTCTCAGCCAGCACAATGCGGACCTGATGGCTATAGATGTCAGTAGGACCGGAAAACAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCGCCAGGTATAGTCAGAATTTTTa                                                                                                                            >  1:633270/1‑149 (MQ=255)                        cGATCTCGAAACTTACACCTTTCTCAGCCAGCACAATGCGGACCTGATGGCTATAGATGTCAGTAGGACCGGAAAACAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCGCCAGGTATAGTCAGAATTTTTACTGc                                                                                                                        <  1:875187/149‑1 (MQ=255)                         gATCTCGAAACTTACACCTTTCTCAGCCAGCACAATGCGGACCTGATGGCTATAGATGTCAGTAGGACCGGAAAACAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCGCCAGGTATAGTCAGAATTTTTa                                                                                                                            >  2:308845/1‑144 (MQ=255)                          aTCTCGAAACTGACCCCTTTCTCAGCCAGCACAATGCGGACCTGATGGCTATAGATGTCAGTAGGACCGGAAAACAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCGCCAGGTATAGTCAGAATTTTTAc                                                                                                                           <  2:560145/144‑1 (MQ=255)                             tcGAAACTTACACCTTTCTCAGCCAGCACAATGCGGACCTGATGGCTATAGATGTCAGTAGGACCGGAAAACAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCGCCAGGTATAGTCAGAATTTTTACTGc                                                                                                                        >  2:297661/1‑144 (MQ=255)                             tcGAAACTTACACCTTTCTCAGCCAGCACAATGCGGACCTGATGGCTATAGATGTCAGTAGGACCGGAAAACAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCGCCAGGTATAGTCAGAATTTTTACTGCTACCa                                                                                                                   >  1:342098/1‑149 (MQ=255)                                       cacCTTTCTCAGCCAGCACAATGCGGACCTGATGGCTATAGATGTCAGTAGGACCGGAAAACAGCGTCATTACCGAACGTTTTGTGGCAGCGACTGCCATGAAAACCGCCAGGTAAAGTCAGAATTTTTACTGCTACCAGccac                                                                                                              <  2:380992/144‑1 (MQ=255)                                        acCTTTCTCAGCCAGCACAATGCGGCCCTGATGGCTATAGATGTCAGTAGGACCGGAAAACAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCGCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTg                                                                                                        >  1:920660/1‑149 (MQ=255)                                        acCTTTCTCAGCCAGCACAATGCGGACCTGATGGCTATAGATGTCAGTAGGACCGGAAAACAGCGTCATTACCGAACGTTGGTTGGCAGCGACAGCCATGAAAACCGCCAGGTATAGTCAGAATCTTTACAGCTACAAGccacc                                                                                                             >  2:267277/1‑144 (MQ=255)                                               tcAGCCAGCACAATGCGGACCTGATGGCTATAGATGTCAGTAGGACCGGAAAACAGCGTCATTACCGAACGTTTGTTGGCCGCGACAGCCATGAAAACCGCCAGGAATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGc                                                                                                      >  2:754315/1‑144 (MQ=255)                                                cagccagcACAATGCGGACCTGATGGCTATAGATGTCAGTAGGACCGGAAAACACCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCGCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGcc                                                                                                     <  2:607859/144‑1 (MQ=255)                                                 ggcccgcACACTGCGGCGCTTATGTCTATAGATGTCAGTAGGACCGGAAAACAGCGTCAGTACCGAACGTTTGTCGGCAGCGACAGCCATGAACACCGCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCa                                                                                                    <  2:396299/143‑1 (MQ=255)                                                 cgccagcACAATGCGTACCTGATGGCTATAGATGTCAGTAGGACCGGAAAACAGCGTCATTACCGAACGTTTGTTGGCAGCTACAGCCATGAAAACCGCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAg                                                                                               <  1:741538/148‑1 (MQ=255)                                                     agcACAAGGCGGACCTGATGGCTATAGATGTCAGTAGGACCGGAAAACAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCGCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCa                                                                                                <  2:584980/144‑1 (MQ=255)                                                      gcACAATGCGGACCTGAGCGCTATAGATGTCAGTAGGACCGGAAAACAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCGCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGtt                                                                                          <  1:13424/149‑1 (MQ=255)                                                        acaATGCGGACCTGATGGCTATAGATGTCAGTAAGACCGGAAAACAGCGTCATTACCGCACGTTTGTTGGCAGCGGCAGCCATGAAAACCGCCAGGTTTAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGCAGTtgt                                                                                        >  1:695521/1‑149 (MQ=255)                                                         caATGCGGACCTGATGGCTATAGATGTCAGTAGGACCGGAAAACAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCGCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTtgtg                                                                                       <  1:240193/149‑1 (MQ=255)                                                          aaTGCGGACCTGATGGCTATAGATGTCAGTAGGACCGGAAAACAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCGCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTTAGAAGgtgtgt                                                                                      >  1:342717/1‑149 (MQ=255)                                                              cGGATCTGCTGGCTATAGATGTCAGTAGGACCGGAAAACAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAACCCGCCAGGTATAGTCAGAATTTTTCCTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTAcc                                                                                  <  1:241582/149‑1 (MQ=255)                                                               ggACCTGATGGCTATAGATGTCAGTAGGACCGGAAAACAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCGCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTgtgt                                                                                      >  2:561204/1‑144 (MQ=255)                                                                 aCCGGATGGCTGTAAGTGCCAGAAGGACCGGACAACCGCGCCAGTCCCCAACGTTGGTAGGCAGCGGCAGCCATGAAAACCGCGAGGTATAGGCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTACCCaa                                                                               <  1:816468/149‑1 (MQ=255)                                                                  ccTGATGGCTATAGATGTCAGTAGGACCGGAAAACAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCGCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAAt                                                                              <  1:850792/149‑1 (MQ=255)                                                                    tGATGGCTATAGATGTCAGTAGGACCGGAAAACAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCGCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTAccc                                                                                 >  2:750460/1‑144 (MQ=255)                                                                      aTGGCTATAGATGTCAGTAGGACCGGAAAACAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCGCCAGGTATAGTCAGAATTTTTACTGCTACCAGACACAATGTGGCCGGTCAGAAGTTGTGTTCCCCAATAAgg                                                                          >  1:716495/1‑149 (MQ=255)                                                                        ggCTATAGATGTCAGTAGGACCGGAAAACAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCGCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGaa                                                                        <  1:330014/149‑1 (MQ=255)                                                                                aTGTCAGTAGGACCGGAAAACAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCGCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGActctc                                                                >  1:243224/1‑149 (MQ=255)                                                                                 tGTCAGTAGGACCGGAAAACAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCGCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGActctct                                                               >  1:143575/1‑149 (MQ=255)                                                                                    cAGTAGGCCCGGAAAACACCGTCATTACCGTACGTTTGGTGGCAGCGACAGCCATGAAAACCGCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGActct                                                                 <  2:614612/144‑1 (MQ=255)                                                                                            ccGGAAAACAGCGTCATTACCGAACGTTTGTTGGCTGCGACAGCCATGAAAACCGCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATGAGGAACGACTCTCTTTGTTCGaaaa                                                    <  1:518511/149‑1 (MQ=255)                                                                                            ccGGAAAACAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCGCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTc                                                         >  2:837321/1‑144 (MQ=255)                                                                                            ccGGAAAACAGCGTCATTACCGAACGTTTGCTGGCAGCGACAGCCATGAAAACCGCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGaaaa                                                    <  1:659788/149‑1 (MQ=255)                                                                                                    cAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCGCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAAAATca                                                 >  2:154872/1‑144 (MQ=255)                                                                                                    cAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCGCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAAAATca                                                 >  2:594267/1‑144 (MQ=255)                                                                                                      gCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCGCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAAAATcaaa                                               <  2:664518/144‑1 (MQ=255)                                                                                                         tCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCGCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAAAATCAAACAAAAAAt                                       >  1:292079/1‑149 (MQ=255)                                                                                                           aTTACCGAACGTTTGTTGGTAGCGACAGCCATGAAAACCGCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAAAATCAAACAAAAAATGa                                     <  1:239644/149‑1 (MQ=255)                                                                                                             tACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCGCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAAAATCAAACAAAAAATGAGc                                   >  1:432407/1‑149 (MQ=255)                                                                                                                 gagcgcatgtggGAAGCGACAGCCATAAAAACCGCCACGAAAAGTCAGAATTTCTACAGCTACCAGCCACCAGGTCGCCAGTCAGAAGGTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAAAATCAAACAAAAAATGAGCAATa                               <  1:95359/142‑1 (MQ=255)                                                                                                                       ttgttgGCAGCGACAGCCATGAAAATCGCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAAAATCAAACAAAAAATGAGCAATGACCGAc                         >  1:466659/1‑149 (MQ=255)                                                                                                                             gCAGCGACAGCCATGAAAACCGCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAAAAGCAAACAAAAAATGAGCAATACCCGACa                        >  2:470835/1‑144 (MQ=255)                                                                                                                                 cGACAGCCATGAAAACCGCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAAAATCAAACAAAAAATGAGCAATACCCGACATTTGGGCAg               >  1:207119/1‑149 (MQ=255)                                                                                                                                        cATGAAAACCGCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAAAATCAAACAAAAAATGAGCAATACCCGACATTTGGGCAGAAAAtgg        >  1:786105/1‑147 (MQ=255)                                                                                                                                          tGAAAACCGCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAAAATCAAACAAAAAATGAGCAATACCCGACATTTGGGCAGAAAATTGga      <  1:853497/149‑1 (MQ=255)                                                                                                                                          cgtaaaCCCCCAGGGATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAAAATCAAACAAAAAATGAGCAATACCCGACATTTGGGCAGAAAATTGga      <  1:397767/146‑1 (MQ=255)                                                                                                                                           gAAAACCGCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGACGATGTGTTAACCAATCAGCAACGCCTCCCCTTGTTCGAAAATCCAACAAAAAATGAGAAATACCCGACATCTGGGAAGCAACTTggct     >  1:191323/1‑147 (MQ=255)                                                                                                                                           gAAAACCGCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAAAATCAAACAAAAAATGAGCAATACCCGACATTTGGGCAGAAAATTGgat     >  1:432067/1‑149 (MQ=255)                                                                                                                                            aacaCCGCCAGGTATAGTCAGAATTTTGACTGCTACCAGCAATCAGGTGGTGAGGCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAAAATCAAACTAATAATGTGCAATACCCGACATTTGGGCAGAAAAtt         <  2:634969/141‑1 (MQ=255)                                                                                                                                            aaaaCCGCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAAAATCAAACAAAAAATGAGCAATACCCGACATTTGGGCAGAAAAtt         <  2:575032/144‑1 (MQ=255)                                                                                                                                              aaCCGCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAAAATCAGACAAAAAATGAGCAATACCCGACATTTGGGCAGAAAATTGgatgat  >  1:94062/1‑149 (MQ=255)                                                                                                                                                  |                                                                                                                                                 CGGATTGTCCTTTTCCACGTGTTCGATCTCGAAACTTACACCTTTCTCAGCCAGCACAATGCGGACCTGATGGCTATAGATGTCAGTAGGACCGGAAAACAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCTCCAGGTATAGTCAGAATTTTTACTGCTACCAGCCACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAAAATCAAACAAAAAATGAGCAATACCCGACATTTGGGCAGAAAATTGGATGAT  >  CP009273/3370642‑3370931

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑