Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	4,142,509	T→G	5.9%	intergenic (‑288/‑21)	frwA ← / → frwC	putative PTS enzyme: Hpr, enzyme I and II components/putative enzyme IIC component of PTS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,142,509	0	T	G	5.9%	247.3 / 5.8	68	intergenic (‑288/‑21)	frwA/frwC	putative PTS enzyme: Hpr, enzyme I and II components/putative enzyme IIC component of PTS
Reads supporting (aligned to +/- strand):  ref base T (32/32);  new base G (2/2);  total (34/34)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.84e-01

TCCGGTTTATCGCAAGTTATGAGGCGGATCGCATTTTTGTACTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTCCCTTCG  >  NC_000913/4142369‑4142605                                                                                                                                             |                                                                                                 tCCGGTTTATCGCAAGTTATGAGGCGGATCGCATTTTTGTACTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAg                                                                                            >  3:163173/1‑147 (MQ=255) tCCGGTTTATCGCAAGTTATGAGGCGGATCGCATTTTTGTACTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAg                                                                                            <  4:163173/147‑1 (MQ=255)                    tGAGGCGGATCGCATTTTTGTACTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTGCGAAAGcccat                                                                                       <  2:859518/133‑3 (MQ=255)                    tGAGGCGGATCGCATTTTTGTACTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTGCGAAAGcccat                                                                                       >  1:859518/1‑131 (MQ=255)                              cGCATTTTTGTACTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGc                                                              >  3:857627/1‑148 (MQ=255)                                cATTTTTGTACTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAg                                                                     >  2:267969/1‑139 (MQ=255)                                cATTTTTGTACTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAg                                                                     <  1:267969/139‑1 (MQ=255)                                         aCTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTatgaa                                                                         <  3:360268/126‑1 (MQ=255)                                         aCTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTatgaa                                                                         >  4:360268/1‑126 (MQ=255)                                              tatTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTgg                                                                 <  1:5266/129‑1 (MQ=255)                                              tatTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTgg                                                                 >  2:5266/1‑129 (MQ=255)                                              tatTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATAc                                              <  4:857627/148‑1 (MQ=255)                                                  aCAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGt                                          >  3:628810/1‑148 (MQ=255)                                                              tAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCttt                                                                                                  <  3:327493/80‑1 (MQ=255)                                                              tAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCttt                                                                                                  >  4:327493/1‑80 (MQ=255)                                                              tAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATc                                                         >  3:28369/1‑121 (MQ=255)                                                              tAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATc                                                         <  4:28369/121‑1 (MQ=255)                                                                     ccTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCtt                                                                              >  1:540043/1‑93 (MQ=255)                                                                     ccTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCtt                                                                              <  2:540043/93‑1 (MQ=255)                                                                       tttttATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATa                                               <  4:1111567/122‑1 (MQ=255)                                                                       tttttATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATa                                               >  3:1111567/1‑122 (MQ=255)                                                                        ttttATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGagcagc                                                                                <  1:875512/88‑1 (MQ=255)                                                                        ttttATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGagcagc                                                                                >  2:875512/1‑88 (MQ=255)                                                                              ccACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATg                              <  1:157330/132‑1 (MQ=255)                                                                              ccACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATg                              >  2:157330/1‑132 (MQ=255)                                                                              ccACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTGCGAAAGccc                                                                                         >  2:970403/1‑73 (MQ=255)                                                                              ccACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTGGCGAAAGccc                                                                                         <  1:970403/73‑1 (MQ=255)                                                                                aCTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGAt                                                          <  4:197449/102‑1 (MQ=255)                                                                                aCTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGAt                                                          >  3:197449/1‑102 (MQ=255)                                                                                 cTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTatga                                                                          <  3:691857/85‑1 (MQ=255)                                                                                 cTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTatga                                                                          >  4:691857/1‑85 (MQ=255)                                                                                  tGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCGGCATTTAATGACGGGCGTTTCACACATGAt          <  4:628810/148‑1 (MQ=255)                                                                                   gTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGtt                     <  1:245192/136‑1 (MQ=255)                                                                                   gTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGtt                     >  2:245192/1‑136 (MQ=255)                                                                                     ctGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCg                                                                                        <  3:878705/66‑1 (MQ=255)                                                                                     ctGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCg                                                                                        >  4:878705/2‑67 (MQ=255)                                                                                          ccGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGt                                                                >  4:553878/1‑86 (MQ=255)                                                                                          ccGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGt                                                                <  3:553878/86‑1 (MQ=255)                                                                                            gCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGt                                          <  4:614320/106‑1 (MQ=255)                                                                                            gCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGt                                          >  3:614320/1‑106 (MQ=255)                                                                                                    ttGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTatgaatg                                                                       >  4:942387/1‑69 (MQ=255)                                                                                                    ttGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTatgaatg                                                                       <  3:942387/69‑1 (MQ=255)                                                                                                          aTTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGt                                                                >  1:795416/1‑70 (MQ=255)                                                                                                          aTTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGt                                                                <  2:795416/70‑1 (MQ=255)                                                                                                          aTTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTa                                 >  1:753820/1‑101 (MQ=255)                                                                                                          aTTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTa                                 <  2:753820/101‑1 (MQ=255)                                                                                                          aTTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGAc                            >  2:543815/1‑106 (MQ=255)                                                                                                          aTTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGAc                            <  1:543815/106‑1 (MQ=255)                                                                                                          aTTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCg                       <  2:368801/111‑1 (MQ=255)                                                                                                          aTTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCg                       >  1:368801/1‑111 (MQ=255)                                                                                                            tGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGt                      >  1:1084351/1‑110 (MQ=255)                                                                                                            tGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGt                      <  2:1084351/110‑1 (MQ=255)                                                                                                               ttCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACg                           >  2:484365/1‑102 (MQ=255)                                                                                                               ttCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACg                           <  1:484365/102‑1 (MQ=255)                                                                                                                tcctccATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTCCCTTCg  <  3:1045035/126‑1 (MQ=255)                                                                                                                tcctccATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTCCCTTCg  >  4:1045035/1‑126 (MQ=255)                                                                                                                        cAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTcacac               >  1:9489/1‑105 (MQ=255)                                                                                                                        cAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTcacac               <  2:9489/105‑1 (MQ=255)                                                                                                                               atGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATa                                               >  1:960040/1‑66 (MQ=255)                                                                                                                               atGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATa                                               <  2:960040/66‑1 (MQ=255)                                                                                                                                   aCATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACg                           >  2:61496/1‑82 (MQ=255)                                                                                                                                   aCATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACg                           <  1:61496/82‑1 (MQ=255)                                                                                                                                        ggCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTCGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACg                           <  1:383687/77‑1 (MQ=255)                                                                                                                                        ggCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTCGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACg                           >  2:383687/1‑77 (MQ=255)                                                                                                                                         tcTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTCCCTTCg  <  4:763345/100‑1 (MQ=255)                                                                                                                                         gCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTCCCTTCg  >  3:763345/1‑101 (MQ=255)                                                                                                                                          cTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTc                                         <  2:242891/61‑1 (MQ=255)                                                                                                                                          cTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTc                                         >  1:242891/1‑61 (MQ=255)                                                                                                                                          cTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTCCCt     >  2:827560/1‑97 (MQ=255)                                                                                                                                          cTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTCCCt     <  1:827560/97‑1 (MQ=255)                                                                                                                                            ttCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGt                                          >  1:187246/1‑58 (MQ=255)                                                                                                                                            ttCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGt                                          <  2:187246/58‑1 (MQ=255)                                                                                                                                            ttCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTccc      >  3:32465/1‑94 (MQ=255)                                                                                                                                            ttCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTccc      <  4:32465/94‑1 (MQ=255)                                                                                                                                             |                                                                                                 TCCGGTTTATCGCAAGTTATGAGGCGGATCGCATTTTTGTACTGATATTACAAAAGTCCAGTAAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGCCTATTGTTTCCTCCATCAAAAATATGGACATGGGCTTTCGCAAGCCCGGGAGCAGCTTATGAATGAGTTGGTGCAGATCCTGAAAAATACCCGTCAGCATTTAATGACGGGCGTTTCACACATGATTCCCTTCG  >  NC_000913/4142369‑4142605

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑