Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,188,787	A→T	E1146D (GAA→GAT)	rpoC →	RNA polymerase, beta prime subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,188,787	0	A	T	84.3%	181.3 / 25.4	71	E1146D (GAA→GAT)	rpoC	RNA polymerase, beta prime subunit
Reads supporting (aligned to +/- strand):  ref base A (5/6);  new base T (27/32);  total (33/38)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

GATCAGCTCTGGTGACACCCTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGAAGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGAAACCAAAGGTAAACGTCGTCTGGTTATCACCCCG  >  NC_000913/4188691‑4188886                                                                                                 |                                                                                                    gATCAGCTCTGGTGACACCCTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCa                                                                                                  <  1:1637533/100‑1 (MQ=255) gATCAGCTCTGGTGACACCCTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCa                                                                                                  <  1:1637456/100‑1 (MQ=255) gATCAGCTCTGGTGACACCCTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGAAGCa                                                                                                  <  2:256383/100‑1 (MQ=255) gATCAGCTCTGGTGACACCCTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGAAGCa                                                                                                  >  1:1222294/1‑100 (MQ=255)   tCAGCTCTGGTGACACCCTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGCCCTGTTCGATGCAcg                                                                                                <  1:361738/100‑1 (MQ=255)   tCAGCTCTGGTGACACCCTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGAAGCAcg                                                                                                >  2:1744258/1‑100 (MQ=255)    cAGCTCTGGTGACACCCTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCAcgt                                                                                               >  2:157573/1‑100 (MQ=255)    cAGCTCTGGTGACACCCTGGCGCGTATTCCGCAGGAAACCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCAcgt                                                                                               >  1:1042064/1‑100 (MQ=255)     aGCTCTGGTGACACCCTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCAcgtc                                                                                              >  2:427175/1‑100 (MQ=255)      gCTCTGGTGACACCCTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCAcgtcg                                                                                             <  2:303545/100‑1 (MQ=255)        tctGGTGACACCCTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACgtcgtc                                                                                           <  2:894913/100‑1 (MQ=255)         ctGGTGACACCCTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTcc                                                                                          <  1:53122/100‑1 (MQ=255)          tGGTGACACCCTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCg                                                                                         >  1:111027/1‑100 (MQ=255)           ggTGACACCCTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCg                                                                                         >  2:1656546/1‑99 (MQ=255)            gTGACACCCTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCTTTGCGGACCTGTTCGATTCACGTCGTCCgca                                                                                       <  2:1309683/100‑3 (MQ=255)              gACACCCTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAag                                                                                     >  1:964614/1‑100 (MQ=255)                cacCCTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAagag                                                                                   >  2:1525968/1‑100 (MQ=255)                  cccTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGcc                                                                                 <  2:1089682/100‑1 (MQ=255)                  cccTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGcc                                                                                 <  1:743564/100‑1 (MQ=255)                   ccTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCg                                                                                >  2:713950/1‑100 (MQ=255)                      ggCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGAAGCACGTCGTCCGAAAGAGCCGGCa                                                                             <  2:1861189/100‑1 (MQ=255)                       gcgcGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCaa                                                                            >  2:166672/1‑100 (MQ=255)                        cgcgTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAAt                                                                           >  1:1702357/1‑100 (MQ=255)                        cgcgTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAAt                                                                           <  1:156780/100‑1 (MQ=255)                        cgcgTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGACGCACGTCGTCCGAAAGAGCCGGCAAt                                                                           >  2:733483/1‑100 (MQ=255)                          cgTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATcc                                                                         <  2:1825958/100‑1 (MQ=255)                             aTTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTgg                                                                      <  2:1042065/100‑1 (MQ=255)                              ttCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGc                                                                     >  2:254452/1‑100 (MQ=255)                               tCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCt                                                                    <  2:955902/100‑1 (MQ=255)                               tCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCt                                                                    >  2:415552/1‑100 (MQ=255)                                ccGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTg                                                                   >  2:298440/1‑100 (MQ=255)                                ccGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTg                                                                   >  2:96932/1‑100 (MQ=255)                                 cGCAGTAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCGGTTCGAAGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGa                                                                  <  2:882853/100‑1 (MQ=255)                                   cAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGaaa                                                                >  1:127327/1‑100 (MQ=255)                                   cAGGAAGCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTg                                                                   <  1:340284/97‑1 (MQ=255)                                   cAGGAACCCGGCGGTACCAAGGACCTCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGaa                                                                 <  1:599497/99‑1 (MQ=255)                                       aaTCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAg                                                            >  2:181161/1‑100 (MQ=255)                                        aTCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCGCGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGc                                                           >  1:574724/1‑100 (MQ=255)                                           cggcggTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGt                                                        <  2:722745/100‑1 (MQ=255)                                               ggTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCg                                                    <  1:427173/100‑1 (MQ=255)                                                   ccAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTc                                                <  1:275503/100‑1 (MQ=255)                                                    cAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGAAGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTcc                                               <  2:1694034/100‑1 (MQ=255)                                                       ggACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTc                                            <  2:667791/100‑1 (MQ=255)                                                       ggACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTc                                            <  1:233763/100‑1 (MQ=255)                                                         aCATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCgg                                          <  2:381113/100‑1 (MQ=255)                                                         aCATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCgg                                          <  1:1577541/100‑1 (MQ=255)                                                         aCATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCgg                                          <  2:475690/100‑1 (MQ=255)                                                          cATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGt                                         >  2:1503627/1‑100 (MQ=255)                                                          cATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGt                                         <  1:1722000/100‑1 (MQ=255)                                                           aTCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTa                                        <  2:944791/100‑1 (MQ=255)                                                             cACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTaaa                                      <  1:1866163/100‑1 (MQ=255)                                                              cgatctggtCTGCCGCGCGTTGCGGACCTGTTCGAAGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTaaan                                     <  1:107051/95‑2 (MQ=255)                                                              aCCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGAAGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAg                                     <  1:1744247/100‑1 (MQ=255)                                                               ccGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGa                                    >  1:1638222/1‑100 (MQ=255)                                                                cGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGan                                   <  1:1656536/100‑2 (MQ=255)                                                                  gtggtCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCCGCGGTATCGTTTCCTTCGGTAAAGAAAc                                 >  2:961604/1‑100 (MQ=255)                                                                  gtggtCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGAAAc                                 <  2:321119/100‑1 (MQ=255)                                                                  gtggtCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGAAAc                                 >  2:424529/1‑100 (MQ=255)                                                                    ngtCTGCCGCGCGTTGCGGACCTGTTCGAAGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGagatcg                               >  2:107051/2‑95 (MQ=255)                                                                     gtCTGCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGAAACCaa                              >  1:1681083/1‑100 (MQ=255)                                                                         gCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGAAACCAAAgg                           <  1:331397/99‑1 (MQ=255)                                                                         gCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGAAACCAAAGGt                          >  1:628652/1‑100 (MQ=255)                                                                         gCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGAAACCAAAGGt                          >  1:17245/1‑100 (MQ=255)                                                                         gCCGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGAAACCAAAGGt                          >  2:394113/1‑100 (MQ=255)                                                                          ccGCGCGTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGAAACCAAAGGTa                         >  2:1292209/1‑100 (MQ=255)                                                                           cgcgcgTTGCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGAAACCAAAGGTaa                        >  1:434592/1‑100 (MQ=255)                                                                                   gCGGACCTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGAAACCAAAGGTAAACgtcgtc                <  1:713949/100‑1 (MQ=255)                                                                                        ccTGTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGAAACCAAAGGTAAACGTCGTCTGGtt           <  1:756328/100‑1 (MQ=255)                                                                                        ccTGTTCGAAGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGAAACCAAAGGTAAACGTCGTCTGGtt           >  2:535940/1‑100 (MQ=255)                                                                                           gTTCGATGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGAAACCAAAGGTAAACGTCGTCTGGTTATc        <  1:691751/100‑1 (MQ=255)                                                                                               gAAGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGAAACCAAAGGTAAACGTCGTCTGGTTATCAccc    >  1:1716279/1‑100 (MQ=255)                                                                                                 aGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGAAACCAAAGGTAAACGTCGTCTGGTTATCACCCCg  <  1:1764884/100‑1 (MQ=255)                                                                                                 |                                                                                                    GATCAGCTCTGGTGACACCCTGGCGCGTATTCCGCAGGAATCCGGCGGTACCAAGGACATCACCGGTGGTCTGCCGCGCGTTGCGGACCTGTTCGAAGCACGTCGTCCGAAAGAGCCGGCAATCCTGGCTGAAATCAGCGGTATCGTTTCCTTCGGTAAAGAAACCAAAGGTAAACGTCGTCTGGTTATCACCCCG  >  NC_000913/4188691‑4188886

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑