Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	292,968	T→C	intergenic (‑20/+252)	yagK ← / ← yagL	CP4‑6 prophage; uncharacterized protein YagK/CP4‑6 prophage; resolvase‑like catalytic domain‑containing protein YagL

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	292,968	0	T	C	100.0%	223.1 / NA	62	intergenic (‑20/+252)	yagK/yagL	CP4‑6 prophage; uncharacterized protein YagK/CP4‑6 prophage; resolvase‑like catalytic domain‑containing protein YagL
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (31/31);  total (31/31)

CACGTACAGCAATTAACCTAGGATACCGGTTAGTCAAATAACATAATAATTTATTAATCTTACTCTGATATTCGAGGATATGTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGTCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTCACTGTTGTCGGTATATACTGGTATCAGATTTTAGTACGGACATACTGATCTGATTACTACTCTTACTGGTGAATAC  >  NC_000913/292837‑293101                                                                                                                                    |                                                                                                                                      cacGTACAGCAATTAACCTAGGATACCGGTTAGTCAAATAACATAATAATTTATTAATCTTACTCTGATATTCGAGGATATGTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTa                                                                                                                                   >  2:184762/1‑136 (MQ=255) cacGTACAGCAATTAACCTAGGATACCGGTTAGTCAAATAACATAATAATTTATTAATCTTACTCTGATATTCGAGGATATGTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTa                                                                                                                                   <  1:184762/136‑1 (MQ=255) cacGTACAGCAATTAACCTAGGATACCGGTTAGTCAAATAACATAATAATTTATTAATCTTACTCTGATATTCGAGGATATGTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGt                                                                                                                               >  1:504150/1‑140 (MQ=255) cacGTACAGCAATTAACCTAGGATACCGGTTAGTCAAATAACATAATAATTTATTAATCTTACTCTGATATTCGAGGATATGTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGt                                                                                                                               >  2:711763/1‑140 (MQ=255) cacGTACAGCAATTAACCTAGGATACCGGTTAGTCAAATAACATAATAATTTATTAATCTTACTCTGATATTCGAGGATATGTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGt                                                                                                                               >  2:64449/1‑140 (MQ=255)           aaTTAACCTAGGATACCGGTTAGTCAAATAACATAATAATTTATTAATCTTACTCTGATATTCGAGGATATGTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGa                                                                                                                     <  2:612554/140‑1 (MQ=255)                  cTAGGATACCGGTTAGTCAAATAACATAATAATTTATTAATCTTACTCTGATATTCGAGGATATGTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACa                                                                                                              <  1:711763/140‑1 (MQ=255)                    aGGATACCGGTTAGTCAAATAACATAATAATTTATTAATCTTACTCTGATATTCGAGGATATGTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAgg                                                                                                            >  1:373593/1‑140 (MQ=255)                     ggATACCGGTTAGTCAAATAACATAATAATTTATTAATCTTACTCTGATATTCGAGGATATGTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAggg                                                                                                           <  1:593371/140‑1 (MQ=255)                       aTACCGGTTAGTCAAATAACATAATAATTTATTAATCTTACTCTGATATTCGAGGATATGTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGTAGACCGTACAGGGAt                                                                                                         >  2:857721/1‑140 (MQ=255)                       aTACCGGTTAGTCAAATAACATAATAATTTATTAATCTTACTCTGATATTCGAGGATATGTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGAt                                                                                                         <  2:881770/140‑1 (MQ=255)                           cGGTTAGTCAAATAACATAATAATTTATTAATCTTACTCTGATATTCGAGGATATGTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAggg                                                                                                           >  1:186819/1‑134 (MQ=255)                           cGGTTAGTCAAATAACATAATAATTTATTAATCTTACTCTGATATTCGAGGATATGTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAggg                                                                                                           <  2:186819/134‑1 (MQ=255)                                aGTCAAATAACATAATAATTTATTAATCTTACTCTGATATTCGAGGATATGTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATAcag                                                                                                >  2:778885/1‑140 (MQ=255)                                aGTCAAATAACATAATAATTTATTAATCTTACTCTGATATTCGAGGATATGTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATAcag                                                                                                >  2:751012/1‑140 (MQ=255)                                  tCAAATAACATAATAATTTATTAATCTTACTCTGATATTCGAGGATATGTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATAcaggc                                                                                              <  2:373593/140‑1 (MQ=255)                                  tCAAATAACATAATAATTTATTAATCTTACTCTGATATTCGAGGATATGTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATAcaggc                                                                                              <  1:64449/140‑1 (MQ=255)                                  tCAAATAACATAATAATTTATTAATCTTACTCTGATATTCGAGGATATGTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATAcaggc                                                                                              >  2:322184/1‑140 (MQ=255)                                                aatTTATTAATCTTACTCTGATATTCGAGGATATGTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTgg                                                                                >  1:504647/1‑140 (MQ=255)                                                   ttattaATCTTACTCTGATATTCGAGGATATGTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTCa                                                                             <  2:949865/140‑1 (MQ=255)                                                     attaATCTTACTCTGATATTCGAGGATATGTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTc                                                                                    <  1:48219/131‑1 (MQ=255)                                                     attaATCTTACTCTGATATTCGAGGATATGTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTc                                                                                    >  2:48219/1‑131 (MQ=255)                                                         aTCTTACTCTGATATTCGAGGATATGTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGc                                                                                         >  2:589390/1‑122 (MQ=255)                                                         aTCTTACTCTGATATTCGAGGATATGTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGc                                                                                         <  1:589390/122‑1 (MQ=255)                                                         aTCTTACTCTGATATTCGAGGATATGTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTCACtgttg                                                                       <  2:513590/140‑1 (MQ=255)                                                         aTCTTACTCTGATATTCGAGGATATCTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTCACtgttg                                                                       <  2:81440/140‑1 (MQ=255)                                                          tCTTACTCTGATATTCGAGGATATGTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTCACtgttgt                                                                      <  2:158712/140‑1 (MQ=255)                                                              aCTCTGATATTCGAGGATATGTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTCACtgttg                                                                       <  2:155860/135‑1 (MQ=255)                                                              aCTCTGATATTCGAGGATATGTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTCACtgttg                                                                       >  1:155860/1‑135 (MQ=255)                                                               ctctGATATTCGAGGATATGTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTCa                                                                             >  2:843045/1‑128 (MQ=255)                                                               ctctGATATTCGAGGATATGTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTCa                                                                             <  1:843045/128‑1 (MQ=255)                                                                tctGATATTCGAGGATATGTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTCACTGTTGTCGGtat                                                                <  2:651837/140‑1 (MQ=255)                                                                    atatTCGAGGATATGTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTc                                                                              <  1:778490/122‑1 (MQ=255)                                                                    atatTCGAGGATATGTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTc                                                                              >  2:778490/1‑122 (MQ=255)                                                                    atatTCGAGGATATGTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTCACTGTTGTCGGTATATAc                                                            >  1:165340/1‑140 (MQ=255)                                                                                atGTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTCACTGTTGTCGGTATATACTGGTATCAGAtt                                                <  2:165340/140‑1 (MQ=255)                                                                                 tGTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTCACTGTTGTCGGTATATACTGGTATCAGAttt                                               >  2:669720/1‑140 (MQ=255)                                                                                      tCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTCACTGTTGTCGGTATATACTGGTATCAGATTTTAGTa                                          <  1:669720/140‑1 (MQ=255)                                                                                       ccATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTCACTGTTGTCGGTATATACTGGTATCAGATTTTAGTAc                                         >  1:104143/1‑140 (MQ=255)                                                                                        cATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTCACTGTTGTCGGTATATACTGGTATCAGATTTTAGTACg                                        >  1:365985/1‑140 (MQ=255)                                                                                          tGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTCACTGTTGTCGGTATATACTGGTATCAGATTTTAGTa                                          <  1:126245/136‑1 (MQ=255)                                                                                          tGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTCACTGTTGTCGGTATATACTGGTATCAGATTTTAGTa                                          >  2:126245/1‑136 (MQ=255)                                                                                          tGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTCACTGTTGTCGGTATATACTGGTATCAGATTTTAGTACGGa                                      >  2:259161/1‑140 (MQ=255)                                                                                             gTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATCCCTGGTCACTGTTGTCGGTATATACTGGTATCAGATTTTAGt                                           <  1:150479/132‑1 (MQ=255)                                                                                             gTACCTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATCCCTGGTCACTGTTGTCGGTATATACTGGTATCAGATTTTAGt                                           >  2:150479/1‑132 (MQ=255)                                                                                                ccTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTCACTGTTGTCGGTATATACTGGTATCAGATTTTAGTACGGACATAct                                >  2:220485/1‑140 (MQ=255)                                                                                                ccTTGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTCACTGTTGTCGGTATATACTGGTATCAGATTTTAGTACGGACATAct                                >  1:474474/1‑140 (MQ=255)                                                                                                  ttGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTCACTGTTGTCGGTATATACTGGTATCAGATTTTAGTa                                          >  2:259931/1‑128 (MQ=255)                                                                                                  ttGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTCACTGTTGTCGGTATATACTGGTATCAGATTTTAGTa                                          <  1:259931/128‑1 (MQ=255)                                                                                                   tGATATGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTCACTGTTGTCGGTATATACTGGTATCAGATTTTAGTACGGACATActgat                             >  2:150362/1‑140 (MQ=255)                                                                                                        tGTTTTCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTCACTGTTGTCGGTATATACTGGTATCAGATTTTAGTACGGACATActgatctgat                        >  2:197363/1‑140 (MQ=255)                                                                                                          ttttCATAATATATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTCACTGTTGTCGGTATATACTGGTATCAGATTTTAGTACGGACATACTGATCTGATta                      <  2:104143/140‑1 (MQ=255)                                                                                                            ttCATAATATATACCTGTATTTGGCCCTACGGTCTATAGTAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTCACTGTTGTCGGTATATACTGGTATCAGATTTTAGTACGGACATACTGATCTGATtact                    <  1:857721/140‑1 (MQ=255)                                                                                                               ataataTATACCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTCACTGTTGTCGGTATATACTGGTATCAGATTTTAGTACGGACATACTGATCTGATTactact                 >  2:381196/1‑140 (MQ=255)                                                                                                                   tatataCCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTCACTGTTGTCGGTATATACTGGTATCAGATTTTAGTACGGACATACTGATCTGATTACTACTCTTa             <  2:474474/140‑1 (MQ=255)                                                                                                                   tatataCCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTCACTGTTGTCGGTATATACTGGTATCAGATTTTAGTACGGACATACTGATCTGATTACTACTCTTa             <  1:150362/140‑1 (MQ=255)                                                                                                                      ataCCTGTATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTCACTGTTGTCGGTATATACTGGTATCAGATTTTAGTACGGACATACTGATCTGATTACTACTCTTACTg          <  1:259161/140‑1 (MQ=255)                                                                                                                             tATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTCACTGTTGTCGGTATATACTGGTATCAGATTTTAGTACGGACATACTGATCTGATTACTACTCTTACTGGTGAATa   >  2:661145/1‑140 (MQ=255)                                                                                                                             tATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTCACTGTTGTCGGTATATACTGGTATCAGATTTTAGTACGGACATACTGATCTGATTACTACTCTTACTGGTGAATa   <  2:504150/140‑1 (MQ=255)                                                                                                                             tATTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTCACTGTTGTCGGTATATACTGGTATCAGATTTTAGTACGGACATACTGATCTGATTACTACTCTTACTGGTGAATa   <  1:197363/140‑1 (MQ=255)                                                                                                                              aTTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTCACTGTTGTCGGTATATACTGGTATCAGATTTTAGTACGGACATACTGATCTGATTACTACTCTTACTGGTGAATAc  <  2:595269/140‑1 (MQ=255)                                                                                                                              aTTTGGCCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTCACTGTTGTCGGTATATACTGGTATCAGATTTTAGTACGGACATACTGATCTGATTACTACTCTTACTGGTGAATAc  >  2:445244/1‑140 (MQ=255)                                                                                                                                    |                                                                                                                                      CACGTACAGCAATTAACCTAGGATACCGGTTAGTCAAATAACATAATAATTTATTAATCTTACTCTGATATTCGAGGATATGTACTCCATGAGTACCTTGATATGTTTTCATAATATATACCTGTATTTGGTCCTACGGTCTATAGCAGACCGTACAGGGATGCCATACAGGCAGGGCTATTCCTGGTCACTGTTGTCGGTATATACTGGTATCAGATTTTAGTACGGACATACTGATCTGATTACTACTCTTACTGGTGAATAC  >  NC_000913/292837‑293101

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑