Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP002094	1,319,382	(A)7→6	coding (34/348 nt)	LLNZ_06950 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP002094	1,319,376	0	A	.	98.6%	338.6 / ‑2.7	73	coding (28/348 nt)	LLNZ_06950	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base . (41/31);  total (41/32)
Fisher's exact test for biased strand distribution p-value = 4.38e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

CAGGATATGAAAGCAAAATTAGGAAATACAATTATAGATTTTTGGAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTGAAAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTGCAAGCAAGCAGCAACTAATAGCTAGTGGAATGACCCAAAAATATTCAG  >  CP002094/1319279‑1319469                                                                                                  |                                                                                              cAGGATATGAAAGCAAAATTAGGAAATACAATTATAGATTTTTGGAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTGaa                                                                                              <  1:686694/99‑1 (MQ=255) cAGGATATGAAAGCAAAATTAGGAAATACAATTATAGATTTTTGGAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTGaa                                                                                              >  1:1408720/1‑99 (MQ=255)   ggATATGAAAGCAAAATTAGGAAATACAATTATAGATTTTTGGAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTGaaaa                                                                                            >  2:1150906/1‑99 (MQ=255)     atatGAAAGCAAAATTAGGAAATACAATTATAGATTTTTGGAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTGaaaaaa                                                                                          >  1:1410101/1‑99 (MQ=255)       atGAAAGCAAAATTAGGAAATACAATTATAGATTTTTGGAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTGaaaaaagg                                                                                        >  1:962794/1‑97 (MQ=255)       atGAAAGCAAAATTAGGAAATACAATTATAGATTTTTGGAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTGaaaaaagg                                                                                        <  1:1622956/99‑3 (MQ=255)       atGAAAGCAAAATTAGGAAATACAATTATAGATTTTTGGAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTGaaaaaagg                                                                                        <  1:355413/99‑3 (MQ=255)          aaaGCAAAATTAGGAAATACAATTATAGATTTTTGGAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAg                                                                                    >  1:929814/1‑99 (MQ=255)           aaGCAAAATTAGGAAATACAATTATAGATTTTTGGAAAATCAGCACCAGTAATCCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGa                                                                                   <  1:505221/99‑1 (MQ=255)            aGCAAAATTAGGAAATACAATTATAGATTTTTGGAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGAt                                                                                  >  2:1159656/1‑99 (MQ=255)            aGCAAAATTAGGAAATACAATTATAGATTTTTGGAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGAt                                                                                  >  2:1268295/1‑99 (MQ=255)             gCAAAATTAGGAAATACAATTATAGATTTTTGGAAAATCAGCACCAGTAAACCCGAAAATGAACCATGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGAtt                                                                                 >  2:915668/1‑99 (MQ=255)                aaaTTAGGAAATACAATTATAGATTTTTGGAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTcc                                                                              <  1:239684/99‑1 (MQ=255)                aaaTTAGGAAATACAATTATAGATTTTTGGAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTcc                                                                              >  2:1426302/1‑99 (MQ=255)                 aaTTAGGAAATACAATTATAGATTTTTGGAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCt                                                                             <  2:850293/99‑1 (MQ=255)                 aaTTAGGAAATACAATTATAGATTTTTGGAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCt                                                                             >  1:93561/1‑99 (MQ=255)                  aTTAGGAAATACAATTATAGATTTTTGGAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTg                                                                            >  1:25158/1‑99 (MQ=255)                  aTTAGGAAATACAATTATAGATTTTTGGAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTg                                                                            >  2:185215/1‑99 (MQ=255)                    tAGGAAATACAATTATAGATTTTTGGAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGt                                                                          <  2:190084/99‑1 (MQ=255)                    tAGGAAATACAATTATAGATTTTTGGAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGt                                                                          >  1:867237/1‑99 (MQ=255)                      ggAAATGCAATTATAGATTTTTGGAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCa                                                                        >  1:1219132/1‑99 (MQ=255)                      ggAAATACAATTATAGATTTTTGGAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCa                                                                        >  2:707921/1‑99 (MQ=255)                       gAAATACAATTATAGATTTTTGGAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAg                                                                       >  1:1276730/1‑99 (MQ=255)                         aaTACAATTATAGATTTTTGGAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGc                                                                     >  2:1025348/1‑99 (MQ=255)                         aaTACAATTATAGATTTTTGAAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGc                                                                     <  1:1366409/99‑1 (MQ=255)                          aTACAATTATAGATTTTTGGAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGcc                                                                    >  2:1258611/1‑99 (MQ=255)                           tACAATTATAGATTTTTGGAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCa                                                                   >  1:1421762/1‑99 (MQ=255)                            aCAATTATAGATTTTTGGAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCaa                                                                  <  2:159123/99‑1 (MQ=255)                             cAATTATAGATTTTTGGAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTCGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAAt                                                                 >  2:940689/1‑99 (MQ=255)                                 tataGATTTTTGGAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGc                                                             >  1:161161/1‑99 (MQ=255)                                   tataTTTTAGAAAAACCACCCCAAGAAACCCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTa                                                           <  1:1465854/96‑1 (MQ=255)                                   taGATTTTTGGAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTa                                                           <  2:640990/99‑1 (MQ=255)                                     gATTTTTGGAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATg                                                         >  1:260883/1‑99 (MQ=255)                                       tttttGGAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGaa                                                       >  1:543638/1‑99 (MQ=255)                                       tttttGGAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGCTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGaa                                                       >  2:1192133/1‑99 (MQ=255)                                         tttGGAAAATCAGCCCCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGa                                                     <  1:342398/99‑1 (MQ=255)                                         tttGGAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGa                                                     <  1:1589704/99‑1 (MQ=255)                                          ttGGAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGAc                                                    >  2:98310/1‑99 (MQ=255)                                           tGGAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACt                                                   <  1:1308716/99‑1 (MQ=255)                                            ggAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTg                                                  >  2:736897/1‑99 (MQ=255)                                             gAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTgc                                                 >  2:1362316/1‑99 (MQ=255)                                               aaaCCAGCCCCAAAAAACCCGAAAATGAACCTTTGGTTTTTGGAATCTTTTAAAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTgca                                                <  1:487810/99‑1 (MQ=255)                                                aaTCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTgcaag                                              <  2:1295383/99‑1 (MQ=255)                                                  tCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTgcaagca                                            >  1:1015103/1‑99 (MQ=255)                                                  tCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTgcaagca                                            >  1:1112184/1‑99 (MQ=255)                                                  tCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTgcaagca                                            >  1:813064/1‑99 (MQ=255)                                                  tCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTgcaagca                                            >  1:596002/1‑99 (MQ=255)                                                  tCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTgcaagca                                            >  1:736928/1‑99 (MQ=255)                                                  ccAGCCCAAGAAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTgcaagca                                            <  1:159968/98‑1 (MQ=255)                                                     gCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTGCaagcaagc                                         >  1:613935/1‑99 (MQ=255)                                                       aCCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTGCAAGCAagcag                                       >  2:1145774/1‑99 (MQ=255)                                                           gTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTGCAAGCAAGCAGCAAc                                   <  2:143718/99‑1 (MQ=255)                                                           gTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTGCAAGCAAGCAGCAAc                                   >  2:1184198/1‑99 (MQ=255)                                                           gTAAACCCGAAAATGAACCATGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTGCAAGCAAGCAGCAAc                                   <  1:915668/99‑1 (MQ=255)                                                            tAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTTGTCAGGCCAATTTGCTATGAAGACTGCAAGCAAGCAGCAACt                                  >  1:524436/1‑99 (MQ=255)                                                               aCCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTGCAAGCAAGCAGCAACTAAt                               >  2:553213/1‑99 (MQ=255)                                                               aCCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTGCAAGCAAGCAGCAACTAAt                               >  2:588537/1‑99 (MQ=255)                                                               aCCCGAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGACAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTGCAAGCAAGCAGCAACTAAt                               <  1:5539/99‑1 (MQ=255)                                                                   gAAAATGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTGCAAGCAAGCAGCAACTAATAGCt                           <  2:340214/99‑1 (MQ=255)                                                                     aaaTGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTGCAAGCAAGCAGCAACTAATAGCTAg                         <  2:1276730/99‑1 (MQ=255)                                                                     aaaTGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTGCAAGCAAGCAGCAACTAATAGCTAg                         >  2:1125289/1‑99 (MQ=255)                                                                      aaTGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTGCAAGCAAGCAGCAACTAATAGCTAGt                        <  2:1257927/99‑1 (MQ=255)                                                                       aTGAACCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTGCAAGCAAGCAGCAACTAATAGCTAGTg                       >  1:974559/1‑99 (MQ=255)                                                                          aaCCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCTTGGTCAGGCCAATTTGCTATGAAGACTGCAAGCAAGCAGCAACTAATAGCTAGTGGaa                    <  1:1523481/99‑1 (MQ=255)                                                                          aaCCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTGCAAGCAAGCAGCAACTAATAGCTAGTGGaa                    <  2:684576/99‑1 (MQ=255)                                                                          aaCCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTGCAAGCAAGCAGCAACTAATAGCTAGTGGaa                    >  1:804697/1‑99 (MQ=255)                                                                           aCCTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTGCAAGCAAGCAGCAACTAATAGCTAGTGGAAt                   <  1:1403070/99‑1 (MQ=255)                                                                             cTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTGCAAGCAAGCAGCAACTAATAGCTAGTGGAATGa                 <  2:224665/99‑1 (MQ=255)                                                                             cTTGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTGCAAGCAAGCAGCAACTAATAGCTAGTGGAATGa                 <  1:692617/99‑1 (MQ=255)                                                                              ttGGGTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTGCAAGCAAGCAGCAACTAATAGCTAGTGGAATGAc                <  2:868942/99‑1 (MQ=255)                                                                                 ggTTCTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTGCAAGCAAGCAGCAACTAATAGCTAGTGGAATGACCCa             >  2:351246/1‑99 (MQ=255)                                                                                     cTTGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTGCAAGCAAGCAGCAACTAATAGCTAGTGGAATGACCCaaaaa         <  1:1150906/99‑1 (MQ=255)                                                                                      ttGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTGCAAGCAAGCAGCAACTAATAGCTAGTGGAATGACCCAAAAat        <  2:1067334/99‑1 (MQ=255)                                                                                       tGAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTGCAAGCAAGCAGCAACTAATAGCTAGTGGAATGACCCAAAAata       <  2:1599050/99‑1 (MQ=255)                                                                                        gAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTGCAAGCAAGCAGCAACTAATAGCTAGTGGAATGACCCAAAAatat      <  1:1509358/99‑1 (MQ=255)                                                                                        gAATCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTGCAAGCAAGCAGCAACTAATAGCTAGTGGAATGACCCAAAAatat      <  1:1662482/99‑1 (MQ=255)                                                                                         aaTCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTGCAAGCAAGCAGCAACTAATAGCTAGTGGAATGACCCAAAAATAtt     >  1:1491632/1‑99 (MQ=255)                                                                                         aaTCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTGCAAGCAAGCAGCAACTAATAGCTAGTGGAATGACCCAAAAATAtt     >  1:541424/1‑99 (MQ=255)                                                                                         aaTCCTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTGCAAGCAAGCAGCAACTAATAGCTAGTGGAATGACCCAAAAATAtt     >  1:1077264/1‑99 (MQ=255)                                                                                            ccTTTG‑AAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTGCAAGCAAGCAGCAACTAATAGCTAGTGGAATGACCCAAAAATATTCAg  <  1:1439147/99‑1 (MQ=255)                                                                                                  |                                                                                              CAGGATATGAAAGCAAAATTAGGAAATACAATTATAGATTTTTGGAAAATCAGCACCAGTAAACCCGAAAATGAACCTTGGGTTCTTGAATCCTTTGAAAAAAAGGCAGATTTCCTGGTCAGGCCAATTTGCTATGAAGACTGCAAGCAAGCAGCAACTAATAGCTAGTGGAATGACCCAAAAATATTCAG  >  CP002094/1319279‑1319469

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑