Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,679,145	G→T	12.4%	R4R (CGC→CGA)	recO ←	recombination protein RecO

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,679,145	0	G	T	12.4%	137.5 / 3.3	52	R4R (CGC→CGA)	recO	recombination protein RecO
Reads supporting (aligned to +/- strand):  ref base G (15/30);  new base T (5/2);  total (20/32)
Fisher's exact test for biased strand distribution p-value = 9.25e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTGTAAACCCGTCTTAACTTTTTTAGCACGCCTTGCCATAAGTGGTACTTTTGCACCATGCTCATTTAAAATCGTGATAATTTTATCAGATTCACCATAATCAACTGCTTTGATGATAATCCCTTTTTGGCGCATTAACAATTATCTTCACCACTTTTAAGATTAATCTTGGTCTTCAACATAACCAATTTGGCG‑AATAAAGTTAACTTTGTTTCGCCAGTCTCTTTGAACTTTGACCCATAATTCTAAGTAAACTTTAGAGCCTAGAAG  >  CP000730/1679016‑1679285                                                                                                                                  |                                                                                                                                              ttGTAAACCCGTCTTAACTTTTTTAGCACGCCTTGCCATAAGTGGTACTTTTGCACCATGCTCATTTAAAATCGTGATAATTTTATCAGATTCACCATAATCAACTGCTTTGATGATAATCCCTTTTTGGCGCATTAACaa                                                                                                                                    <  1:434841/141‑1 (MQ=255) ttGTAAACCCGTCTTAACTTTTTTAGCACGCCTTGCCATAAGTGGTACTTTTGCACCATGCTCATTTAAAATCGTGATAATTTTATCAGATTCACCATAATCAACTGCTTTGATGATAATCCCTTTTTGGCGCATTAACaa                                                                                                                                    <  1:698869/141‑1 (MQ=255)      aaCCCGTCTTAACTTTTTTAGCACGCCTTGCCATAAGTGGTACTTTTGCACCATGCTCATTTAAAATCGTGATAATTTTATCAGATTCACCATAATCAACTGCTTTGATGATAATCCCTTTTTGGCGCATTAACAATTATc                                                                                                                               >  1:41119/1‑141 (MQ=255)       aCCCGTCTTAACTTTTTTAGCACGCCTTGCCATAAGTGGTACTTTTGCACCATGCTCATTTAAAATCGTGATAATTTTATCAGATTCACCATAATCAACTGCTTTGATGATAATCCCTTTTTGGCGCATTAACAATTATCt                                                                                                                              >  1:179519/1‑141 (MQ=255)        cccGTCTTAACTTTTTTAGCACGCCTTGCCATAAGTGGTACTTTTGCACCATGCTCATTTAAAATCGTGATAATTTTATCAGATTCACCATAATCAACTGCTTTGATGATAATCCCTTTTTGGCGCATTAACAATTATCtt                                                                                                                             >  1:828367/1‑141 (MQ=255)                   tttttgAGCACGCCTTGCCATAAGTGGTACTTTTGCACCATGCTCATTTAAAATCGTGATAATTTTATCAGATTCACCATAATCAACTGCTTTGATGATAATCCCTTTTTGGCGCATTAACAATTATCTTCACCACTTTTa                                                                                                                  <  2:34170/141‑1 (MQ=255)                      tttactccGCCTTGCCATAATGGGTCCTTTGGGACCATGCTCATTTAAAATCGTGATAATTTTATCAGATTCACCATAATCAACTGCTTTGATGATAATCCCTTTTTGGCGCATTAACAATTATCTTCACCACTTTTAAGa                                                                                                               <  2:691528/134‑1 (MQ=255)                      ttgaGCACGCCTTGCCATAAGTGGTACTTTTGCACCATGCTCATTTAAAATCGTGATAATTTTATCAGATTCACCATAATCAACTGCTTTGAGGATAATCCCTTTTTGGCGCATTAACAATTATCTTCACCACTTTTAAGa                                                                                                               <  2:670500/138‑1 (MQ=255)                               ccTTGCCATAAGTGGTACTTTTGCACCATGCTCATTTAAAATCGTGATAATTTTATCAGATTCACCATAATCAACTTCTTTGATGATAATCCCTTTTTGGCGCATTAACAATTATCTTCACCACTTTTAAGATTAATCTTg                                                                                                      >  1:598452/1‑141 (MQ=255)                               ccTTGCCATAAGTGGTACTTTTGCACCATGCTCATTTAAAATCGTGATAATTTTATCAGATTCACCATAATCAACTGCTTTGATGATAATCCCTTTTTGGCGCATTAACAATTATCTTCACCACTTTTAAGATTAATCTTg                                                                                                      <  2:83664/141‑1 (MQ=255)                                   gCCATAAGTGGTACTTTTGCACCATGCTCATTTAAAATCGTGATAATTTTATCAGATTCACCATAATCAACTGCTTTGATGATAATCCCTTTTTGGCGCATTAACAATTATCTTCACCACTTTTAAGATTAATCTTGGTCt                                                                                                  >  1:185995/1‑141 (MQ=255)                                   gCCATAAGTGGTACTTTTGCACCATGCTCATTTAAAATCGTGATAATTTTATCAGATTCACCATAATCAACTGCTTTGATGATAATCCCTTTTTGGCGCATTAACAATTATCTTCACCACTTTTAAGATTAATCTTGGTCt                                                                                                  >  1:720459/1‑141 (MQ=255)                                         aGTGGTACTTTTGCACCATGCTCATTTAAAATCGTGATAATTTTATCAGATTCACCATAATCAACTGCTTTGATGATAATCCCTTTTTGGCGCATTAACAATTATCTTCACCACTTTTAAGATTAATCTTGGTCTTCAACa                                                                                            <  1:733650/141‑1 (MQ=255)                                          gTGGTACTTTTGCACCATGCTCATTTAAAATCGTGATAATTTTATCAGATTCACCATAATCAACTGCTTTGATGATAATCCCTTTTTGGCGCATTAACAATTATCTTCACCACTTTTAAGATTAATCTTGGTCTTCaccca                                                                                           >  1:181138/1‑137 (MQ=255)                                            ggTACTTTTGCACCATGCTCATTTAAAATCGTGATAATTTTATCAGATTCACCATAATCAACTGCTTTGATGATAATCCCTTTTTGGCGCATTAACAATTATCTTCACCACTTTTAAGATTAATCTTGGTCTTCAACATaa                                                                                         <  2:179519/141‑1 (MQ=255)                                              tACTTTTGCACCATGCTCATTTAAAATCGTGATAATTTTATCAGATTCACCATAATCAACTGCTTTGATGATAATCCCTTTTTGGCGCATTAACAATTATCTTCACCACTTTTAAGATTAATCTTGGTCTTCAACATAAcc                                                                                       <  2:828367/141‑1 (MQ=255)                                              gatgcttGCACCATGGTCATTTCAATTCGTGATAATTTTATCAAATTCAGCGTTAGCGACTTCGTGGAGGATAACCCCTTTTTGGCGCATGAACAATTATCTTCACCACTTTTAAGAGTAATCTTGGTCTTCAACATAAcc                                                                                       <  1:387792/136‑1 (MQ=255)                                                       aCCATGCTCATTTAAAATCGTGATAATTTTATCAGATTCACCATAATCAACTGCTTTGATGATAATCCCTTTTTGGCGCATTAACAATTATCTTCACCACTTTTAAGATTAATCTTGGTCTTCAACATAACCAATTTGGCg                                                                              >  2:663367/1‑141 (MQ=255)                                                                aTTTAAAATCGTGATAATTTTATCAGATTCACCATAATCAACTGCTTTGATGATAATCCCTTTTTTTTGTTTTTTTAATTATCTTCACCACTTTTAAGATTTATCTTGTTCTTCAAGATAACCAATTTGGCG‑AATTAGGtt                                                                    >  2:411597/1‑141 (MQ=255)                                                                   tAAAAGCGTGATAATTTTATCAGATTCACCATAATCAACTGCTTTGATGATAATCCCTATTTGGCGCATTAACAATTATCTTCACCACATTCAAGATTAATCTTGGTCTTCAACATAACCAATTTGGCG‑AATAAAGTTAAc                                                                 <  2:3461/141‑1 (MQ=255)                                                                    aaaaTCGTGATAATTTTATCAGATTCACCATAATCAACTGCTTTGATGATAATCCCTTTTTGGCGCATTAACAATTATCTTCACCACTTTTAAGATTAATCTTGGTCTTCAACATAACCAATTTGGCG‑AATAAAGTTAACt                                                                <  1:765649/141‑1 (MQ=255)                                                                    aaaaTCGTGATAATTTTATCAGATTCACCATAATCAACTGCTTTGATGATAATCCCCTTTTGGCGCATTAACAATTATCTTCACCACTTTTAAGATTAATCTTGGTCTTCAACATAACCAATTTGGCG‑AATAAAGTTAACt                                                                <  1:94205/141‑1 (MQ=255)                                                                    aaaaTCGTGATAATTTTATCAGATTCACCATAATCAACTGCTTGGATGATAATCCCTTTTTGGCGCATTAACAATTATCTTCACCACTTTTAAGATTAATCTTGGTCTTCAACATAACCAATTTGGCG‑AATAAAGTTAACt                                                                <  2:293823/141‑1 (MQ=255)                                                                     aaaTCGTGATAATTTTATCAGATTCACCATAATCAACTGCTTTGATGATAATCCCTTTTTGGCGCATTAACAATTATCTTCACCACTTTTAAGATTAATCTTGGTCTTCAACATAACCAATTTGGCGAAACAAAGTTAACt                                                                <  1:584061/141‑1 (MQ=255)                                                                     aaaTCGTGATAATTTTATCAGATTCACCATAATCAACTGCTTTGATGATAATCCCTTTTTGGCGCATTAACAATTATCTTCACCACTTTTAAGATTAATCTTGGTCTTCAACATAACCAATTTGGCGAAACAAAGTTAACt                                                                <  1:583933/141‑1 (MQ=255)                                                                      aaTAGTGATAATTTTATCAGATTCACCATAATCAACTGCTTTGATGATAATCCCTTTTTGGCGCATTAACAATTATCTTCACCACTTTTAAGATTAATCTTGGTCTTCAACATAACCAATTTGGCG‑AATAAAGTTAACttt                                                              <  1:690452/141‑1 (MQ=255)                                                                        tCGAGATAATTTTATCAGATTCACCATAATCAACTGCTTTGATGATAATCCCTTTTTGGCGCATTAACAATTATCTTCACCACTTTTAAGATTAATCTTGGTCTTCAACATAACCAATTTGGCG‑AATAAAGTTAACTTTGt                                                            <  2:581604/141‑1 (MQ=255)                                                                            gATAATTTTATCAGATTCACCATAATCAACTGCTTTGATGATAATCCCTTTTTGGCGCATTAACAATTATCTTCACCACTTTTAAGATTAATCTTGGTCTTCAACATAACCAATTTGGCG‑AATAAAGTTAACTTTGTTTCg                                                        <  1:491400/141‑1 (MQ=255)                                                                            gATAATTTTATCAGATTCACCATAATCAACTGCTTTGATGATAATCCCTTTTTGGCGCATTAACAATTATCTTCACCACTTTTAAGATTAATCTTGGTCTTCAACATAACCAATTTGGCG‑AATAAAGTTAACTTTGTTTCg                                                        <  1:734220/141‑1 (MQ=255)                                                                              tAATTTTATCAGATTCACCATAATCAACTGCTTTGATGATAATCCCTTTTTGGCGCATTAACAATTATCTTCACCACTTTTAAGATTAATCTTGGTCTTCAACATAACCAATTTGGCG‑AATAAAGTTAACTTTGTTTCGcc                                                      <  2:616876/141‑1 (MQ=255)                                                                              tAATTTTATCAGATTCAACATTATCAACTGCTTTGATGACAATCCCTTTTAGTCGCACGAACAATTATCTTCACCACTTTTCACATTAATCTTGGTCCTCAACATAACCAATTTGGCG‑AATAAAGTTAACTTTGTTTCGcc                                                      <  2:648031/141‑1 (MQ=255)                                                                                aTTTTATCAGATTCACCATAATCAACTGCTTTGATGATAATCCCTTTTTGGCGCATTAACAATTATCTTCACCACTTTTAAGATTAATCTTGGTCTTCAACATAACCAATTTGGCG‑AATAAAGTTAACTTTGTTTCGCCAg                                                    >  2:454200/1‑141 (MQ=255)                                                                                     aTCAGATTCACCATAATCAACTGCTTTGATGATAATCCCTTTTTTTTTTTTTTTCAATTATCTTCACCACTTTTAAGATTAATCTTGGTCTTCAACATAACCAATTTGGCG‑AATAAAGTTAACTTTGtttttctagtgttt                                               >  2:495634/1‑130 (MQ=255)                                                                                     aTCAGATTCACCATAATCAACTGCTTTGATGATAATCCCTTTTTGGCGCATTAACAATTATCTTCACCACTTTTAAGATTAATCTTGGTCTTCAACATAACCAATTTGGCG‑AATAAAGTTAACTTTGTTTCGCCAGTctct                                               >  2:495651/1‑141 (MQ=255)                                                                                        aGATTCACCATAATCAACTGCTTTGATGATAATCCCTTTTTGGCGCATTAACAATTATCTTCACCACTTTTAAGATTAATCTTGGTCTTCAACATAACCAATTTGGCG‑AATAAAGTTAACTTTGTTTCGCCAGTCTCTTTg                                            <  2:598452/141‑1 (MQ=255)                                                                                           ttCACCATAATCAACTGCTTTGATGATAATCCCTTTTTGGCGCATTAACAATTATCTTCACCACTTTTAAGATTAATCTTGGTCTTCAACATAACCAATTTGGCG‑AATAAAGTTAACTTTGTTTCGCCAGTCTCTTTGAAc                                         <  2:425555/141‑1 (MQ=255)                                                                                               ccATAATCAACTGCTTTGATGATAATCCCTTTTTGGCGCATTAACAATTATCTTCACCACTTTTAAGATTAATCTTGGTCTTCAACATAACCAATTTGGCG‑AATAAAGTTAACTTTGTTTCGCCAGt                                                   >  2:143990/1‑127 (MQ=255)                                                                                               ccATAATCAACTGCTTTGATGATAATCCCTTTTTGGCGCATTAACAATTATCTTCACCACTTTTAAGATTAATCTTGGTCTTCAACATAACCAATTTGGCG‑AATAAAGTTAACTTTGTTTCGCCAGt                                                   <  1:143990/127‑1 (MQ=255)                                                                                                cATAATCAACTGCTTTGATGATAATCCCTTTTTGGCGCATTAACAATTATCTTCACCACTTTTAAGATTAATCTTGGTCTTCAACATAACCAATTTGGCG‑AATAAAGTTAACTTTGTTTCGCCAGTCTCTTTGAACTTTGa                                    <  1:376779/141‑1 (MQ=255)                                                                                                 aTAATCAACTGCTTTGATGATAATCCCTTTTTGGCGCATTAACAATTATCTTCACCACTTTTAAGATTAATCTTGGTCTTCAACATTACCAATTTGGCG‑AATAAAGTTAACTTTGTTTCGCCAGTCTCTTTGAACTTTGAc                                   <  1:767423/141‑1 (MQ=255)                                                                                                  tAATCAACTGCTTTGATGATAATCCCTTTTTGGCGCATTAACAATTATCTTCACCACTTTTAAGATTAATCTTGGTCTTCAACATAACCAATTTGGCG‑AATAAAGTTAACTTTGTTTCGCCAGTCTCTTTGAACTTTGAcc                                  >  1:787972/1‑141 (MQ=255)                                                                                                   aaTCAACTGCTTTGATGATAATCCCTTTTTTTTTTTTTTTCAATTATCTTCACCACTTTTAAGATTAATCTTGGTCTTCAACATAACCAATTTGGCG‑AATAAAGTTAACTTTGTTTCGCCAGTCTCTTTGAACTTTGAccc                                 >  2:746228/1‑141 (MQ=255)                                                                                                   aaTCAACTGCTTTGATGATAATCCCTTTTTTTTTTTTTTTCAATTATCTTCAACACTCTTAAAATTAATCTTGGTCTTCAACATAACCAATTTGGCG‑AATAAAGTTAACTTTGTTTCGCCAGACCCTTTGAACTTTAAccc                                 >  2:799910/1‑141 (MQ=255)                                                                                                   aaTCAACTGCTTTGATGATAATCCCTTTTTGGCGCATTAACAATTATCTTCACCACTTTTAAGATTAATCTTGGTCTTCAACATAACCAATTTGGCG‑AATAAAGTTAACTTTGTTTCGCCAGTCTCTTTGAACTTTGAccc                                 >  2:57737/1‑141 (MQ=255)                                                                                                    aTCAACTGCTTTTATGATAATCCCTTTTTGTCGCATTAACAATTATCTTCACCACTTTTAAGATTAATCTTGGTCTTCAACATAACCAATTTGGCG‑AATAAAGTTAACTTTGTTTCGCCAGTCTCTTTGAACTTTGGCCCa                                <  1:604866/141‑1 (MQ=255)                                                                                                    aTCAACTGATTTGATTATAATCCCTTTTTGGCGCAGTAACAATTATCTTCACCACTTTTAAGATTAATCTTGGTCTTCAACATAACCAATTTGGCG‑AATAAAGTTAACTTTGTTTCGCCAGTCTCTTTGAACTTTGGCCCa                                <  1:790216/141‑1 (MQ=255)                                                                                                         cTGCTTTGATGATAATCCCTTTTTGGCGCATTAACAATTATCTTCACCACTTTTAAGATTAATCTTGGTCTTCAACATAACCAATTTGGCG‑AATAAAGTTAACTTTGTTTCGCCAGTCTCTTTGAACTTTGACCCATAAtt                           >  1:79906/1‑141 (MQ=255)                                                                                                           gCTTTGATGATAATCCCTTTTTTTTTTTTTTACAATTATCTTCACCACTTTTAAGATTAATCTGGGTCTTCAACATAACCAATTTGGCG‑ATTAAAGTTAATTTTGTTTCGCTAGTCTATTTGACCTTTGTCCCATAATTCt                         >  2:419000/1‑141 (MQ=255)                                                                                                                    atAATCCCTTTTTGGCGCATTAACAATTATCTTCACCACTTTTAAGATTAATCTTGGTCTTCAACATAACCAATTTGGCG‑AATAAAGTTAACTTTGTTTCGCCAGTCTCTTTGAACTTTGACCCATAATTCTAAGTAAACt                <  1:454200/141‑1 (MQ=255)                                                                                                                      aaTTCCTTTTTGGCGCATGAACAATTATCTTCACAACTTTTAAGATTAATCTTGGTCTTCAACGTAACCAATTTGGCG‑AATAAAGTTAACTTTGTTTCGCCAGTCCCTTTGACATTTGAGCCATAATTCTAAGTATACttt              >  2:573400/1‑141 (MQ=255)                                                                                                                            ttgttGGCGCATTAAAAATTATATTCACCACTTTTAAGATTAATCTTGGTCTTCAACATAACCAATTTGGCG‑AATAAAGTTAACTTTGTTTCGCCAGTCTCTTTGAACTTTGACCCATAATTCTAAGTAAACTTTAGAGcc        <  2:379617/138‑1 (MQ=255)                                                                                                                                tGGCGCATTACCAATTATCTTCACCACTTTTAAGATTAATCTTGGTCTTCTACATAATCAATTTGGCG‑GATAATGTCAAGTTTGTTTCGCCATTCTCTGTGAACTCTGACCCATAATTCTATGTAGACTTTAGAGCCTAGa    <  1:647284/141‑1 (MQ=255)                                                                                                                                 ggCGCATTAACAATTATCTTCACCACTTTTAAGATTAATCTTGGTCTTCAACATAACCAATTTGGCG‑AATAAAGTTAACTTTGTTTCGCCAGTCTCTTTGAACTTTGACCCATTTTTGAAAATAAGCTTTAGAGCCTAGaa   <  2:185995/141‑1 (MQ=255)                                                                                                                                 ggCGCATTAACAATTATCTTCACCACTTTTAAGATTAATCTTGGTCTTCAACATAACCAATTTGGCG‑AATAAAGTTAACTTTGTTTCGCCAGTCTCTTTGAACTTTGACCCATAATTCTAAGTAAACTTTAGAGCCTAGaa   <  2:720459/141‑1 (MQ=255)                                                                                                                                  gcgcATTAACAATTATCTTCACCACTTTTAAGATTAATCTTGGTCTTCAACATAACCAATTTGGCG‑AATAAAGTTAACTTTGTTTCGCCAGTCTCTTTGAATTTTGGACCATAATTCTAAGTAAACTTTAGAGCCTAGAAg  >  1:109247/1‑141 (MQ=255)                                                                                                                                  gcgcATTAACAATTATCTTCACCACTTTTAAGATTAATCTTGGTCTTCAACATAACCAATTTGGCG‑AATAAAGTTAACTTTGTTTCGCCAGTCTCTTTGAACTTTGACCCATAATTCTAAGTAAACTTTAGAGCCTAGAAg  >  2:294947/1‑141 (MQ=255)                                                                                                                                  gcgcATTAACAATTATCTTCACCACTTTTAAGATTAATCTTGATCTTCCAGCTAACCAATTTGGCG‑AATAAAGTTAACTTTGTTTCGCTAGGCTCTTTGAACTTTAACCCCTAATTCTAAGTAAACTTTAGAGCCTAGAAg  >  1:721567/1‑141 (MQ=255)                                                                                                                                  |                                                                                                                                              TTGTAAACCCGTCTTAACTTTTTTAGCACGCCTTGCCATAAGTGGTACTTTTGCACCATGCTCATTTAAAATCGTGATAATTTTATCAGATTCACCATAATCAACTGCTTTGATGATAATCCCTTTTTGGCGCATTAACAATTATCTTCACCACTTTTAAGATTAATCTTGGTCTTCAACATAACCAATTTGGCG‑AATAAAGTTAACTTTGTTTCGCCAGTCTCTTTGAACTTTGACCCATAATTCTAAGTAAACTTTAGAGCCTAGAAG  >  CP000730/1679016‑1679285

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: ‑