Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,318,344	G→A	intergenic (‑55/‑293)	metY ← / → argG	tRNA‑Met/argininosuccinate synthetase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,318,344	0	G	A	98.7%	257.0 / ‑4.5	76	intergenic (‑55/‑293)	metY/argG	tRNA‑Met/argininosuccinate synthetase
Reads supporting (aligned to +/- strand):  ref base G (0/1);  new base A (38/37);  total (38/38)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.34e-01

GGGTTATGAGCCCGACGAGCTACCAGGCTGCTCCACCCCGCGCCTGAAACGTGGCAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGGATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATCCACGCCACATTTTGTCAACGTTTATTGCTAATCATGTGAATGAATA  >  NC_000913/3318248‑3318439                                                                                                 |                                                                                                gggTTATGAGCCCGACGAGCTACCAGGCTGCTCCACCCCGCGCCTGAAACGTGGCAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAAtt                                                                                              >  1:2028772/1‑100 (MQ=255) gggTTATGAGCCCGACGAGCTACCAGGCTGCTCCACCCCGCGCCTGAAACGTGGCAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAAtt                                                                                              >  1:1606011/1‑100 (MQ=255) gggTTATGAGCCCGACGAGCTACCAGGCTGCTCCACCCCGCGCCTGAAACGTGGCAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAAtt                                                                                              <  2:1606002/100‑1 (MQ=255)  ggTTATGAGCCCGACGAGCTACCAGGCTGCTCCACCCCGCGCCTGAAACGTGGCAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAAttt                                                                                             <  1:1747455/100‑1 (MQ=255)  ggTTATGAGCCCGACGAGCTACCAGGCTGCTCCACCCCGCGCCTGAAACGTGGCAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAAttt                                                                                             <  2:1400602/100‑1 (MQ=255)   gTTATGAGCCCGACGAGCTACCAGGCTGCTCCACCCCGCGCCTGAAACGTGGCAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTg                                                                                            >  1:1619804/1‑100 (MQ=255)    ttATGAGCCCGACGAGCTACCAGGCTGCTCCACCCCGCGCCTGAAACGTGGCAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTgg                                                                                           <  2:486580/100‑1 (MQ=255)      aTGAGCCCGACGAGCTACCAGGCTGCTCCACCCCGCGCCTGAAACGTGGCAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTGgtg                                                                                         <  1:1814363/100‑1 (MQ=255)       tGAGCCCGACGAACTACCAGGCTGCTCCACCCCGCGCCTGAAACGTGGCAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTGgtgt                                                                                        >  1:1477748/1‑100 (MQ=255)        gAGCCCGACGAGCTACCAGGCTGCTCCACCCCGCGCCTGAAACGTGGCAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTGGTGTa                                                                                       >  2:1852346/1‑100 (MQ=255)        gAGCCCGACGAGCTACCAGGCTGCTCCACCCCGCGCCTGAAACGTGGCAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTGGTGTa                                                                                       >  1:504291/1‑100 (MQ=255)        gAGCCCGACGAGCTACCAGGCTGCTCCACCCCGCGCCTGAAACGTGGCAAATTCTACTCGTTGTGGGTTAAAAATGCGAATACCGCTGGAATTTGGTGTa                                                                                       >  2:1524630/1‑100 (MQ=37)          gCCCGACGAGCTACCAGGCTGCTCCACCCCGCGCCTGAAACGTGGCAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGGATTTGGTGTAcc                                                                                     <  2:793099/100‑1 (MQ=255)          gCCCGACGAGCTACCAGGCTGCTCCACCCCGCGCCTGAAACGTGGCAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTGGTGTAcc                                                                                     <  1:507309/100‑1 (MQ=255)           cccGACGAGCTACCAGGCTGCTCCACCCCGCGCCTGAAACGTGGCAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTGGTGTACCg                                                                                    <  1:2218729/100‑1 (MQ=255)            ccGACGAGCTACCAGGCTGCTCCACCCCGCGCCTGAAACGTGGCAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTGGTGTACCga                                                                                   >  1:1827108/1‑100 (MQ=255)                  aGCTACCAGGCTGCTCCACCCCGCGCCTGAAACGTGGCAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTGGTGTACCGAGACggg                                                                             >  1:367477/1‑100 (MQ=255)                  aGCTACCAGGCTGCTCCACCCCGCGCCTGAAACGTGGCAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTGGTGTACCGAGACggg                                                                             >  2:1413155/1‑100 (MQ=255)                     tACCAGGCTGCTCCACCCCGCGCCTGAAACGTGGCAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACg                                                                          >  2:157413/1‑100 (MQ=255)                      aCCAGGCTGCTCCACCCCGCGCCTGAAACGTGGCAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGt                                                                         >  1:326/1‑100 (MQ=255)                       ccAGGCTGCTCCACCCCGCGCCTGAAACGTGGCAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTa                                                                        <  1:177314/100‑1 (MQ=255)                             tgctCCACCCCGCGCCTGAAACGTGGCAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCt                                                                  <  1:907532/100‑1 (MQ=255)                                tCCACCCCGCGCCTGAAACGTGGCAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCa                                                               >  2:715263/1‑100 (MQ=255)                                tCCACCCCGCGCCTGAAACGTGGCAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCa                                                               <  1:838701/100‑1 (MQ=255)                                 ccACCCCGCGCCTGAAACGTGGCAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTGGTGTACCGAGACGTGACATATAATCttaag                                                              >  2:561139/1‑96 (MQ=255)                                 ccACCCCGCGCCTGAAACGTGGCAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAg                                                              >  2:1973986/1‑100 (MQ=255)                                 ccACCCCGCGCCTGAAACGTGGCAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAg                                                              >  2:1656785/1‑100 (MQ=255)                                  cACCCCGCGCCTGAAACGTGGCAAACTCTACTCGTTTTGGGTAAAAAATGCAAATCCTGCTGGAATTTGCTGTAAAGAGCAGGGACGTAAACTCTGCAgg                                                             >  2:1577635/1‑100 (MQ=255)                                    ccccGCGCCTGAAACGTGGCAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAGTTTGGTTTACCGAGACGGGTCGCAAAATCta                                                                 >  2:2069383/1‑93 (MQ=255)                                    ccccGCGCCTGAAACGTGGCAAATTCTACTCGTTTTGAGTAAAAAATGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCa                                                           >  2:1216470/1‑100 (MQ=255)                                           ccTGAAACGTGGCAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAg                                                     <  2:317124/99‑1 (MQ=255)                                           ccTGAAACGTGGCAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGt                                                    <  1:2072266/100‑1 (MQ=255)                                           ccTGAAACGTGGCAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGt                                                    <  1:1656794/100‑1 (MQ=255)                                           ccTGAAACGTGGCAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGt                                                    >  2:492730/1‑100 (MQ=255)                                              gAAACGTGGCAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGATGTAAAATCTGCAGGCATTATAGTg                                                   <  2:937487/98‑1 (MQ=255)                                               aaaCGTGGCAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATc                                                <  1:1142199/100‑1 (MQ=255)                                                   gTGGCAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATCCACg                                            <  1:2017066/100‑1 (MQ=255)                                                    tGGCAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATCCACGc                                           <  2:2239591/100‑1 (MQ=255)                                                    tGGCAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACCGCTGGAATTTGGTGTACTGAGACGGGACTTAAAATCTGCAGGCATTATAGTGATCCAccc                                           <  1:1524639/100‑3 (MQ=255)                                                       cacaTTCTACTCGTTTTGGGTACAAAATGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATCCACGcc                                          <  1:1577644/95‑1 (MQ=255)                                                       cAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATCCACGCcac                                        >  1:2131709/1‑100 (MQ=255)                                                         aaTTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATATGCAGGCATTATAGTGATCCACGCCACAt                                      >  2:222994/1‑100 (MQ=255)                                                             cTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATCCACGCCACATTTTg                                  <  1:342679/100‑1 (MQ=255)                                                              tACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATCCACGCCACATTTTGt                                 >  1:1001458/1‑100 (MQ=255)                                                              tACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATCCACGCCACATTTTGt                                 <  1:1413164/100‑1 (MQ=255)                                                               aCTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATCCACGCCACATTTTGTc                                <  1:719854/100‑1 (MQ=255)                                                               aCTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATCCACGCCACATTTTGTc                                >  1:1203097/1‑100 (MQ=255)                                                               aCTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATCCACGCCACATTTTGTc                                <  2:510632/100‑1 (MQ=255)                                                                cTCGTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATCCACGCCACATTTTGTCa                               <  2:1619795/100‑1 (MQ=255)                                                                  cGTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACATAAAATCTGCAGGCATTATAGTGATCCACGCCACATTTTGTCAAc                             >  2:2228027/1‑100 (MQ=255)                                                                   gTTTTGGGTAAAAAATGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATCCACGCCACATTTTGTCAAcn                            <  1:1336783/100‑2 (MQ=255)                                                                     tttGGGTAAAAAATGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATTCACGCCACATTTTGTCAACg                            >  2:636034/1‑98 (MQ=255)                                                                     tttGGGTAAAAAATGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATCCACGCCACATTTTGTCAACGtt                          <  1:469861/100‑1 (MQ=255)                                                                        gggTAAAAAATGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATCCACGCCACATTTTGTCAACGTTTAt                       >  1:1944880/1‑100 (MQ=255)                                                                         ggTAAAAAATGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATCCACGCCACATTTTGTCAACGattatt                      >  2:2191884/1‑100 (MQ=255)                                                                           tAAAAAATGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATCCACGCCACATTTTGTTAACGttt                         >  2:1758355/1‑95 (MQ=255)                                                                           tAAAAAATGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATCCACGCCACATTTTGTCAACGTTTATTGc                    <  2:2131694/100‑1 (MQ=255)                                                                            aaaaaaTGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATCCACGCCACATTTTGTCAACGTTTATTGCt                   >  1:803830/1‑100 (MQ=255)                                                                            aaaaaaTGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATCCACGCCACATTTTATCAACGTTTATTGCt                   >  1:2221303/1‑100 (MQ=255)                                                                              aaaaTGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATCCACGCCACATTTTGTCAACGTTTATTGCTaa                 >  1:602718/1‑100 (MQ=255)                                                                               aaaTGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATCCACGCCACATTTTGTCAACGTTTATTGCTAAt                <  2:1613958/100‑1 (MQ=255)                                                                               aaaTGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATCCACGCCACATTTTGTCAACGTTTATTGCTAAt                <  2:1614005/100‑1 (MQ=255)                                                                                aaTGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATCCACGCCACATTTTGTCAACGTTTATTGCTAATc               <  2:2116916/100‑1 (MQ=255)                                                                                  tGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATCCACGCCACATTTTGTCAACGTTTATTGCTAATCAt             <  2:504288/100‑1 (MQ=255)                                                                                  tGCAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATCCACGCCACATTTTGTCAACGTTTATTGCTAATCAt             >  1:2255167/1‑100 (MQ=255)                                                                                    cAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATCCACGCCACATTTTGTCAACGTTTATTGCTAATCAtgt           <  2:546648/100‑1 (MQ=255)                                                                                    cAAATACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATCCACGCCACATTTTGTCAACGTTTATTGCTAATCAtgt           >  2:554557/1‑100 (MQ=255)                                                                                     cttccgatctgGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATCCACGCCACATTTTGTCAACGTTTATTGCTAATCAtgtg          <  1:1495128/92‑1 (MQ=255)                                                                                     aaaTACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATCCACGCCACATTTTGTCAACGTTTATTGCTAATCAtgtg          <  2:998108/100‑1 (MQ=255)                                                                                     aaaTACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATCCACGCCACATTTTGTCAACGTTTATTGCTAATCAtgtg          <  1:715269/100‑1 (MQ=255)                                                                                      aaTACTGCTGGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATCCACGCCACATTTTGTCAACGTTTATTGCTAATCATGtga         >  1:893983/1‑100 (MQ=255)                                                                                            gctgGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATCCACGCCACATTTTGTCAACGTTTATTGCTAATCATGTgaatgaat   >  1:703654/1‑100 (MQ=255)                                                                                            gctgGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATCCACGCCACATTTTGTCAACGTTTATTGCTAATCATGTgaatgaat   >  1:1645369/1‑100 (MQ=255)                                                                                            gctgGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATCCACGCCACATTTTGTCAACGTTTATTGCTAATCATGTgaatgaat   <  2:902484/100‑1 (MQ=255)                                                                                            gctgGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATCCACGCCACATTTTGTCAACGTTTATTGCTAATCATGTgaatgaat   >  1:1095979/1‑100 (MQ=255)                                                                                             ctgGAATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATCCACGCCACATTTTGTCAACGTTTATTGCTAATCATGTGAATGAata  <  1:157416/100‑1 (MQ=255)                                                                                                 |                                                                                                GGGTTATGAGCCCGACGAGCTACCAGGCTGCTCCACCCCGCGCCTGAAACGTGGCAAATTCTACTCGTTTTGGGTAAAAAATGCAAATACTGCTGGGATTTGGTGTACCGAGACGGGACGTAAAATCTGCAGGCATTATAGTGATCCACGCCACATTTTGTCAACGTTTATTGCTAATCATGTGAATGAATA  >  NC_000913/3318248‑3318439

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑