Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,880,206	T→C	D339G (GAC→GGC)	recF ←	gap repair protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,880,206	0	T	C	98.2%	194.3 / ‑4.0	54	D339G (GAC→GGC)	recF	gap repair protein
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base C (36/17);  total (37/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.56e-01

GCACCGCATCCAGCCCTTTCAGGACTTTGATACTGGAGGAGTCATAAGAATTCGACATCAACGTTTCTCGCTCATTTATACTTGGGTTAATCCGTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGTCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTCGCTTTTAAGCGGCTGGCAAGCAGCCCGCGACGCTCATCATCAAGCTCAGAGGCAAAATCATCTATCAGGTAGAGACACCGCCGCCCGCTTTCACGG  >  NC_000913/3880062‑3880352                                                                                                                                                 |                                                                                                                                                   gCACCGCATCCAGCCCTTTCAGGACTTTGATACTGGAGGAGTCATAAGAATTCGACATCAACGTTTCTCGCTCATTTATACTTGGGTTAATCCGTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCtata                                                                                                                                               >  1:824921/1‑150 (MQ=255)   aCCGCATCCAGCCCTTTCAGGACTTTGATACTGGAGGAGTCATAAGAATTCGACATCAACGTTTCTCGCTCATTTATACTTGGGTTAATCCGTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACg                                                                                                                                            >  1:203765/1‑151 (MQ=255)            aGCCCTTTCAGGACTTTGATACTGGAGGAGTCATAAGAATTCGACATCAACGTTTCTCGCTCATTTATACTTGGGTTAATCCGTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGc                                                                                                                                    >  1:290932/1‑150 (MQ=255)              cccTTTCAGGACTTTGATACTGGAGGAGTCATAAGAATTCGACATCAACGTTTCTCGCTCATTTATACTTGGGTTAATCCGTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACt                                                                                                                                 <  2:460575/151‑1 (MQ=255)                  ttCAGGACTTTGATACTGGAGGAGTCATAAGAATTCGACATCAACGTTTCTCGCTCATTTATACTTGGGTTAATCCGTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGa                                                                                                                               <  1:537991/149‑1 (MQ=255)                  ttCAGGACTTTGATACTGGAGGAGTCATAAGAATTCGACATCAACGTTTCTCGCTCATTTATACTTGGGTTAATCCGTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATc                                                                                                                             >  2:801590/1‑151 (MQ=255)                       gACTTTGATACTGGAGGAGTCATAAGAATTCGACATCAACGTTTCTCGCTCATTTATACTTGGGTTAATCCGTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCt                                                                                                                        >  1:242135/1‑151 (MQ=255)                            tGATACTGGAGGAGTCATAAGAATTCGACATCAACGTTTCTCGCTCATTTATACTTGGGTTAATCCGTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACa                                                                                                                    >  1:217223/1‑150 (MQ=255)                                  tGGAGGAGTCATAAGAATTCGACATCAACGTTTCTCGCTCATTTATACTTGGGTTAATCCGTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCt                                                                                                             >  1:44858/1‑151 (MQ=255)                                     aggagTCATAAGAATTCGACATCAACGTTTCTCGCTCATTTATACTTGGGTTAATCCGTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCtgtg                                                                                                          <  2:484111/151‑1 (MQ=255)                                     aggagTCATAAGAATTCGACATCAACGTTTCTCGCTCATTTATACTTGGGTTAATCCGTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCtgtg                                                                                                          >  1:461638/1‑151 (MQ=255)                                        agTCATAAGAATTCGACATCAACGTTTCTCGCTCATTTATACTTGGGTTAATCCGTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGAtt                                                                                                       <  1:499468/151‑1 (MQ=255)                                          tCATAAGAATTCGACATCAACGTTTCTCGCTCATTTATACTTGGGTTAATCCGTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGc                                                                                                     >  1:316411/1‑151 (MQ=255)                                           cATAAGAATTCGACATCAACGTTTCTCGCTCATTTATACTTGGGTTAATCCGTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCg                                                                                                    >  1:261057/1‑151 (MQ=255)                                              aaGAATTCGACATCAACGTTTCTCGCTCATTTATACTTGGGTTAATCCGTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTc                                                                                                  <  1:113514/150‑1 (MQ=255)                                              aaGAATTCGACATCAACGTTTCTCGCTCATTTATACTTGGGTTAATCCGTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTCg                                                                                                 >  2:72999/1‑151 (MQ=255)                                                gAATTCGACATCAACGTTTCTCGCTCATTTATACTTGGGTTAATCCGTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTCGCt                                                                                               >  1:127882/1‑151 (MQ=255)                                                  aTTCGACATCAACGTTTCTCGCTCATTTATACTTGGGTTAATCCGTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTCGCttt                                                                                             >  2:709869/1‑151 (MQ=255)                                                      gACATCAACGTTTCTCGCTCATTTATACTTGGGTTAATCCGTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTCGCTTTTa                                                                                           >  1:700973/1‑149 (MQ=255)                                                       aCATCAACGTTTCTCGCTCATTTATACTTGGGTTAATCCGTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTCGCTTTTAAGc                                                                                        >  2:284435/1‑151 (MQ=255)                                                        cATCAACGTTTCTCGCTCATTTATACTTGGGTTAATCCGTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTCGCTTTTAAGCg                                                                                       <  1:544192/151‑1 (MQ=255)                                                        cATCAACGTTTCTCGCTCATTTATACTTGGGTTAATCCGTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTCGCTTTTAAGCg                                                                                       <  2:20135/151‑1 (MQ=255)                                                         aTCAACGTTTCTCGCTCATTTATACTTGGGTTAATCCGTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCtgt                                                                                                           >  1:467715/1‑130 (MQ=255)                                                         aTCAACGTTTCTCGCTCATTTATACTTGGGTTAATCCGTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCtgt                                                                                                           <  2:467751/130‑1 (MQ=255)                                                           cAACGTTTCTCGCTCATTTATACTTGGGTTAATCCGTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGTCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTCGCTTTTAAGCGGCt                                                                                    >  2:797775/1‑151 (MQ=255)                                                           cAACGTTTCTCGCTCATTTATACTTGGGTTAATCCGTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTCGCTTTTAAGCGGCt                                                                                    >  2:456346/1‑151 (MQ=255)                                                             aCGTTTCTCGCTCATTTATACTTGGGTTAATCCGTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTCGCTTTTAAGCGGCTgg                                                                                  <  2:858279/151‑1 (MQ=255)                                                                      gCTCATTTATACTTGGGTTAATCCGTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTCGCTTTTAAGCGGCTGGCAAGCAGcc                                                                         >  2:318150/1‑151 (MQ=255)                                                                      gCTCATTTATACTTGGGTTAATCCGTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTCGCTTTTAAGCGGCTGGCAAGCAGcc                                                                         <  1:436423/151‑1 (MQ=255)                                                                       cTCATTTATACTTGGGTTAATCCGTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTCGCTTTTAAGCGGCTGGCAAGCAGccc                                                                        >  1:766581/1‑151 (MQ=255)                                                                         cATTTATACTTGGGTTAATCCGTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTCGCTTTTAAGCGGCTGGCAAGCAGccc                                                                        <  2:839589/149‑1 (MQ=255)                                                                              ataCTTGGGTTAATCCGTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTCGCTTTTAAGCGGCTGGCAAGCAGCCCGCGACGc                                                                 <  1:210572/151‑1 (MQ=255)                                                                                        tAATCCGTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTCGCTTTTAATCGGCTGGCAAGCAGCCCGCGACGCt                                                                >  2:679963/1‑142 (MQ=255)                                                                                         aaTCCGTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTCGCTTTTAAGCGGCTGGCAAGCAGCCCGCGACGCtcatcatca                                                        >  1:261017/1‑149 (MQ=255)                                                                                         aaTCCGTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTCGCTTTTAAGCGGCTGGCAAGCAGCCCGCGACGCtcatcatca                                                        >  2:667344/1‑149 (MQ=255)                                                                                             cGTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTCGCTTTTAAGCGGCTGGCAAGCAGCCCGCGACGCTCATCATCAAGCTCa                                                  <  2:506409/151‑1 (MQ=255)                                                                                              gTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTCGCTTTTAAGCGGCTGGCAAGCAGCCCGCGACGCTCATCATCAAGCTc                                                   >  2:426904/1‑149 (MQ=255)                                                                                                 aTTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTCGCTTTTAAGCGGCTGGCAAGCAGCCCGCGACGCTCATCATCAAGCTCAGAgg                                              >  1:93052/1‑151 (MQ=255)                                                                                                 aTTTTACCCTTTTCCACGGTAAACATCTTCGAATCTTCGACCGACATGCCTATAACGTGTTCAGCTCTGATCGCGCTGACAAAGACATGTGATTGCGTCGCTTTTAAGCGGCTGGCAAGCAGCCCGCGACGCTCATCATCACGCTCagag                                               >  2:827914/1‑150 (MQ=255)                                                                                                     tACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTCGCTTTTAAGCGGCTGGCAAGCAGCCCGCGACGCTCATCATCAAGCTCAGAGGCaa                                           >  1:700335/1‑150 (MQ=255)                                                                                                       cccTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTCGCTTTTAAGCGGCTGGCAAGCAGCCCGCGACGCTCATCATCAAGCTCAGAGGCAAAat                                        >  2:179062/1‑151 (MQ=255)                                                                                                        ccTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTCGCTTTTAAGCGGCTGGCAAGCAGCCCGCGACGCTCATCATCAAGCTCAGAGGCAAAatc                                       >  1:219441/1‑151 (MQ=255)                                                                                                         cTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTCGCTTTTAAGCGGCTGGCAAGCAGCCCGCGACGCTCATCATCAAGCTCAGAGGCAAAatc                                       >  1:632422/1‑150 (MQ=255)                                                                                                          ttttCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTCGCTTTTAAGCGGCTGGCAAGCAGCCCGCGACGCTCATCATCAAGCTCAGAGGCAAAatcat                                     >  2:666682/1‑151 (MQ=255)                                                                                                             tCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTCGCTTTTAAGCGGCTGGCAAGCAGCCCGCGACGCTCATCATCAAGCTCAGAGGCAAAATCATCt                                   >  1:354978/1‑150 (MQ=255)                                                                                                             tCCACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTCGCTTTTAAGCGGCTGGCAAGCAGCCCGCGACGCTCATCATCAAGCTCAGAGGCAAAATCATCt                                   >  1:602846/1‑150 (MQ=255)                                                                                                              ccACGGTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTCGCTTTTAAGCGGCTGGCAAGCAGCCCGCGACGCTCATCATCAAGCTCAGAGGCAAAATCATCTAt                                 >  2:329120/1‑151 (MQ=255)                                                                                                                   gTAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTCGCTTTTAAGCGGCTGGCAAGCAGCCCGCGACGCTCATCATCAAGCTCAGAGGCAAAATCATCTATCAGGt                            <  2:520816/151‑1 (MQ=255)                                                                                                                    tAAACATCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTCGCTTTTAAGCGGCTGGCAAGCAGCCCGCGACGCTCATCATCAAGCTCAGAGGCAAAATCATCTATCAGGt                            >  2:414476/1‑150 (MQ=255)                                                                                                                         aTCTTCGAATTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTCGCTTTTAAGCGGCTGGCAAGCAGCCCGCGACGCTCATCATCAAGCTCAGAGGCAAAATCATCTATCAGGTAGAGac                      >  2:222604/1‑151 (MQ=255)                                                                                                                                aaTTTTCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTCGCTTTTAAGCGGCTGGCAAGCAGCCCGCGACGCTCATCATCAAGCTCAGAGGCAAAATCATCTATCAGGTAGAGACAccgccg               >  1:354953/1‑151 (MQ=255)                                                                                                                                  ttttCGTCCGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTCGCTTTTAAGCGGCTGGCAAGCAGCCCGCGACGCTCATCATCAAGCTCAGAGGCAAAATCATCTATCAGGTAGAGACACcgccgc              <  1:699099/150‑1 (MQ=255)                                                                                                                                         ccGACATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTCGCTTTTAAGCGGCTGGCAAGCAGCCCGCGACGCTCATCATCAAGCTCAGAGGCAAAATCATCTATCAGGTAGAGACACCGCCGCCCGCTTTc      <  2:809441/151‑1 (MQ=255)                                                                                                                                             cATGCCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTCGCTTTTAAGCGGCTGGCAAGCAGCCCGCGACGCTCATCATCAAGCTCAGAGGCAAAATCATCTATCAGGTAGAGACACCGCCGCCCGCTTTCACgg  <  2:569884/151‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                   GCACCGCATCCAGCCCTTTCAGGACTTTGATACTGGAGGAGTCATAAGAATTCGACATCAACGTTTCTCGCTCATTTATACTTGGGTTAATCCGTTATTTTACCCTTTTCCACGGTAAACATCTTCGAATTTTCGTCCGACATGTCTATAACGTGTTCAGCACTGATCGCGCTGACAAAGACCTGTGATTGCGTCGCTTTTAAGCGGCTGGCAAGCAGCCCGCGACGCTCATCATCAAGCTCAGAGGCAAAATCATCTATCAGGTAGAGACACCGCCGCCCGCTTTCACGG  >  NC_000913/3880062‑3880352

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑