Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	1,207,981	G→A	100%	A161T (GCC→ACC)	stfP →	e14 prophage; uncharacterized protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,207,981	0	G	A	98.7%	225.4 / ‑5.0	72	A161T (GCC→ACC)	stfP	e14 prophage; uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base G (0/1);  new base A (32/39);  total (32/40)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.62e-01

GCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACTTCGTTTTTATTACG  >  NC_000913/1207884‑1208075                                                                                                  |                                                                                               gCAATCAGTACTCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAACACTGTTGTATTCCCGGTTGCGTTTAATAATAcc                                                                                              <  2:1680023/100‑1 (MQ=255) gCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATAcc                                                                                              <  1:2153416/100‑1 (MQ=255)     tCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCtgtg                                                                                          >  1:569513/1‑100 (MQ=255)      cAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTgtgt                                                                                         >  1:218645/1‑100 (MQ=255)      cAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTgtgt                                                                                         <  1:1817476/100‑1 (MQ=255)       aGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTgtgt                                                                                         <  2:1528554/99‑1 (MQ=255)         tAATCATTCAGTGGGGGTGGCATGCCGCAAAAGCATCTGCCTCTGGGGGGGGTGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGc                                                                                      >  2:526547/1‑100 (MQ=255)          naTCATTCAGTGGGGGTGGAGTGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGcc                                                                                     >  2:1253103/2‑100 (MQ=255)           aTCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCg                                                                                    <  2:2496301/100‑1 (MQ=255)             cATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCgtt                                                                                  <  2:1219414/100‑1 (MQ=255)              aTTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCgttg                                                                                 <  1:779881/100‑1 (MQ=255)               ttCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCgttgt                                                                                <  1:752590/100‑1 (MQ=255)                 cAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGttgttg                                                                              <  1:766914/100‑1 (MQ=255)                 cAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGttgttg                                                                              <  1:598214/100‑1 (MQ=255)                 cAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGttgttg                                                                              <  1:1844726/100‑1 (MQ=255)                 cAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCAGTGTTGCCGttgttg                                                                              >  1:2520190/1‑100 (MQ=255)                 cAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACACTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGttgttg                                                                              <  1:1478288/100‑1 (MQ=255)                  aGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGc                                                                             <  2:1964070/100‑1 (MQ=255)                     gggggTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCaaa                                                                          >  2:172557/1‑100 (MQ=255)                     gggggTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCaaa                                                                          <  1:1697008/100‑1 (MQ=255)                      ggggTGGAATACCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACATGTGTTGCCGTTGTTGCAAAt                                                                         >  2:790902/1‑100 (MQ=255)                       gggTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAAtt                                                                        >  2:809120/1‑100 (MQ=255)                        ggTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTa                                                                       <  1:1048011/100‑1 (MQ=255)                        ggTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTa                                                                       <  1:827075/100‑1 (MQ=255)                        ggTGGAATGCCGCAAAAGCATCTGCCGCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTa                                                                       <  1:2268031/100‑1 (MQ=255)                          tGGAATGCCGCAAAAGGATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATg                                                                     <  2:2228771/100‑1 (MQ=255)                           ggAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGa                                                                    >  2:360446/1‑100 (MQ=255)                             aaTGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGAc                                                                   >  1:1124183/1‑99 (MQ=255)                                gCCTCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATg                                                               <  2:1311910/100‑1 (MQ=255)                                 ccGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGt                                                              <  2:387947/100‑1 (MQ=255)                                 ccGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGt                                                              >  1:342040/1‑100 (MQ=255)                                  cGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTc                                                             <  1:580275/100‑1 (MQ=255)                                  cGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTc                                                             >  2:1414376/1‑100 (MQ=255)                                  cGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTc                                                             <  2:1311649/100‑1 (MQ=255)                                  cGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTc                                                             >  2:2188284/1‑100 (MQ=255)                                  cGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCGGTGTTGCCGTTGTTGCAAATTATGACAATGt                                                              >  1:816634/1‑99 (MQ=255)                                         gaaTCTGCCGCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCa                                                       <  1:2287380/97‑1 (MQ=255)                                          cATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCAcc                                                     <  1:981871/100‑1 (MQ=255)                                            tCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTa                                                   <  2:2520175/100‑1 (MQ=255)                                              tGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATc                                                 <  2:2260854/100‑1 (MQ=255)                                                 ctctGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAAt                                              >  2:1088029/1‑100 (MQ=255)                                                   ctGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGc                                            <  2:988752/100‑1 (MQ=255)                                                    tGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCa                                           >  2:1128031/1‑100 (MQ=255)                                                       gggggATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTg                                        >  1:1719775/1‑100 (MQ=255)                                                        ggggATGGAAATACAGTTGTATTCCTGGTTGCGTTTAATAATGCCTCTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTgg                                       <  1:1476163/100‑1 (MQ=255)                                                        ggggATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTgg                                       <  1:2468499/100‑1 (MQ=255)                                                                   tACAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGa                            <  1:2169839/100‑1 (MQ=255)                                                                     cAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGTGGGat                           >  1:1394746/1‑99 (MQ=255)                                                                     cAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGata                          >  1:1094380/1‑100 (MQ=255)                                                                     cAGTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGata                          >  1:1102294/1‑100 (MQ=255)                                                                       gTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGAtata                        >  2:2188971/1‑100 (MQ=255)                                                                       gTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGAtata                        >  2:628035/1‑100 (MQ=255)                                                                       gTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGAtata                        >  1:518354/1‑100 (MQ=255)                                                                       gTTGTATTCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGAtata                        <  1:801423/100‑1 (MQ=255)                                                                             ttCCCGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCa                  <  2:1760323/100‑1 (MQ=255)                                                                             ttCCCGGTTGCGTTTAATAATACCTGTGTTGCCGATGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAAcc                   <  2:353037/99‑1 (MQ=255)                                                                               cccGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACt                >  2:716730/1‑100 (MQ=255)                                                                               cccGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACt                >  2:1106474/1‑100 (MQ=255)                                                                                 cGGTTGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACTTc              >  2:2156618/1‑100 (MQ=255)                                                                                     tGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACTTCGttt          >  1:2361005/1‑100 (MQ=255)                                                                                     tGCGTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACTTCGttt          <  2:299491/100‑1 (MQ=255)                                                                                       ngTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACTTCGttttt        >  2:1160423/2‑100 (MQ=255)                                                                                       cGTTTAATAATACCTGGGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACTACTTCGttttt        <  2:1966009/100‑1 (MQ=255)                                                                                        gTTTAATCATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACTTCGTTTtta       >  1:1342983/1‑100 (MQ=255)                                                                                        gTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACTTCGTTTtta       >  2:283171/1‑100 (MQ=255)                                                                                        gTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACTTCGTTTtta       >  1:130752/1‑100 (MQ=255)                                                                                        gTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACTTCGTTTtta       <  1:231021/100‑1 (MQ=255)                                                                                        gTTTAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGAGGGATATACAACCACTTCGTTTtta       >  2:2551326/1‑100 (MQ=255)                                                                                         tttAATAATACCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACTTCGTTTttat      <  1:1401912/100‑1 (MQ=255)                                                                                          ttAGTAATACCTGTGTTGCCGTTAATGCAAATTATGACAATGTTAGCGCAACTATCTATACAGTAGTAACGGGGGCATATACGATCACCTCGTTTttat      <  2:288901/99‑1 (MQ=255)                                                                                           taatagTACCGGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGAACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACTTGGTTTttat      <  2:605386/98‑1 (MQ=255)                                                                                           taataaTACCTGTGTGGCCGTGGTTTCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACTTCGTTTttat      <  1:472820/98‑1 (MQ=255)                                                                                             ataataCCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAGCGGGGGGATATACAACCACTTCGTTTTTATTACg  >  2:1352732/1‑100 (MQ=255)                                                                                                  |                                                                                               GCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATGGAAATACAGTTGTATTCCCGGTTGCGTTTAATAATGCCTGTGTTGCCGTTGTTGCAAATTATGACAATGTCAGCGCACCTATCAATGCAGTGGCAACGGGGGGATATACAACCACTTCGTTTTTATTACG  >  NC_000913/1207884‑1208075

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: ‑