Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913	657,215	Δ25 bp	intergenic (+98/‑53)	pagP → / → cspE	phospholipid:lipid A palmitoyltransferase/constitutive cold shock family transcription antitermination protein; negative regulator of cspA transcription; RNA melting protein; ssDNA‑binding protein

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	657215	657239	25	55 [0]	[0] 56	pagP/cspE	phospholipid:lipid A palmitoyltransferase/constitutive cold shock family transcription antitermination protein; negative regulator of cspA transcription; RNA melting protein; ssDNA‑binding protein

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 657214	0 (0.000)	55 (0.910)	51/296	0.3	100%	intergenic (+97/‑78)	pagP/cspE	phospholipid:lipid A palmitoyltransferase/constitutive cold shock family transcription antitermination protein; negative regulator of cspA transcription; RNA melting protein; ssDNA‑binding protein
	?	NC_000913	657240 =	0 (0.000)					intergenic (+123/‑52)	pagP/cspE	phospholipid:lipid A palmitoyltransferase/constitutive cold shock family transcription antitermination protein; negative regulator of cspA transcription; RNA melting protein; ssDNA‑binding protein

ACAATGGCAATGTGTACTTTGCCTGGATGCGCTTTCAGTTTTGAGACAAATGAAGTTTTAGTAACTTCTTTAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTGGACAAAGCGTACCACAATTGGTGTACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTACTCCGGAAG  >  NC_000913/657074‑657361                                                                                                                                             |                                                                                                                                                    acaaTGGCAATGTGTACTTTGCCTGGATGCGCTTTCAGTTTTGAGACAAATGAAGTTTTAGTAACTTCTTTAAAATCAATAGCTAAAATAAGTAACATCAAAACTAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTactggtaacc                                                                                                                                           >  2:416420‑M1/1‑141 (MQ=255)  caaTGGCAATGTGTACTTTGCCTGGATGCGCTTTCAGTTTTGAGACAAATGAAGTTTTAGTAACTTCTTTAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTactggtaaccg                                                                                                                                          <  2:330105‑M1/151‑12 (MQ=255)         catGTGTACTTTGCCTGGATGCGCTTTCAGTTTTGAGACAAATGAAGTTTTAGTAACTTCTTTAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTactggtaaccgacacagc                                                                                                                                   >  2:777227‑M1/2‑133 (MQ=255)              gtACTTTGCCTGGATGCGCTTTCAGTTTTGAGACAAATGAAGTTTTAGTAACTTCTTTAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTactggtaaccgacacagcattt                                                                                                                               <  1:21928‑M1/150‑23 (MQ=255)                     gCCTGGATGCGCTTTCAGTTTTGAGACAAATGAAGTTTTAGTAACTTCTTTAAAAGCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTactggtaaccgacacagcatttgtgtcta                                                                                                                        <  2:242100‑M1/150‑30 (MQ=255)                            tGCGCTTTCAGTTTTGAGACAAATGAAGTTTTAGTAACTTCTTTAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcat                                                                                                                >  1:271194‑M1/1‑114 (MQ=255)                             gcgcTTTCAGTTTTGAGACAAATGAAGTTTTAGTAACTTCTTTAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatg                                                                                                               <  1:395111‑M1/151‑39 (MQ=255)                                 tttCAGTTTTGAGACAAATGAAGTTTTAGTAACTTCTTTAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaa                                                                                                            >  2:489200‑M1/1‑109 (MQ=255)                                  ttCAGTTTTGAGACAAATGAAGTTTTAGTAACTTCTTTAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaa                                                                                                            <  2:861527‑M1/149‑42 (MQ=255)                                   tCAGTTTTGAGACAAATGAAGTTTTAGTAACTTCTTTAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaagg                                                                                                         >  1:514611‑M1/1‑107 (MQ=255)                                   tCAGTTTTGAGACAAATGAAGTTTTAGTAACTTCTTTAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaag                                                                                                          <  1:411428‑M1/150‑44 (MQ=255)                                      gTTTTGAGACAAATGAAGTTTTAGTAACTTCTTTAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaa                                                                                                      <  1:427482‑M1/151‑48 (MQ=255)                                           gagaCAAATGAAGTTTTAGTAACTTCTTTAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaattttg                                                                                                 <  1:499913‑M1/151‑53 (MQ=255)                                                aaaTGAAGTTTTAGTAACTTCTTTAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACCTTTATCACTTTTTAGTAAAGTTACACTactggtaatcgacacagcatttgtgtctatttttcatgtaaaggtaattttgatgtc                                                                                            >  2:598665‑M1/1‑94 (MQ=255)                                                  aTGAAGTTTTAGTAACTTCTTTAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaattttgatgtcta                                                                                          <  2:540127‑M1/151‑60 (MQ=255)                                                    gAAGTTTTAGTAACTTCTTTAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaattttgatgtctaag                                                                                        <  2:105603‑M1/151‑62 (MQ=255)                                                      aGTTTTAGTAACTTCTTTAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaattttgatgtcta                                                                                          >  1:555956‑M1/1‑88 (MQ=255)                                                        ttttAGTAACTTCTTTAAAATCAAGAGCGAAAATAAGTAACATCAAAAATAACGCGGCTTTTATCACTTTTTAGTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaatggtaattttgatgcctaagatt                                                                                     >  2:956491‑M1/1‑86 (MQ=255)                                                         tttAGTAACTTCTTTAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaattttgatgtctaagatta                                                                                    <  1:728480‑M1/150‑66 (MQ=255)                                                            aGTAACTTCTTTAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaattttgatgtctaagattaaagg                                                                                >  1:68816‑M1/1‑82 (MQ=255)                                                             gTAACTTCTTTAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaattttgatgtctaagattaaaggt                                                                               <  1:620974‑M1/151‑71 (MQ=255)                                                                   tcttTAAAATCAATAGCTAAAATAATTAACATCAAAAATAACGCGACTTTTATCACTTTTTATTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaattttgatgtctaagattaaaggtaacg                                                                           <  2:476072‑M1/149‑75 (MQ=255)                                                                    cttTAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaattttgatgtctaagattaaaggtaacgtt                                                                         >  1:672992‑M1/1‑74 (MQ=255)                                                                      ttAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaattttgatgtctaagattaaaggtaacgtt                                                                         <  1:576291‑M1/148‑77 (MQ=255)                                                                         aaaTCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaattttgatgtctaagattaaaggtaacgttaagtgg                                                                   >  2:225216‑M1/1‑69 (MQ=255)                                                                             cAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaattttgatgtctaagattaaaggtaacgttaagtggttta                                                               <  2:911144‑M1/151‑87 (MQ=255)                                                                             cAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaattttgatgtctaagattaaaggtaacgttaagtggttt                                                                <  1:59783‑M1/150‑86 (MQ=255)                                                                              aaTAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaattttgatgtctaagattaaaggtaacgttaagtggttta                                                               >  2:558319‑M1/1‑64 (MQ=255)                                                                              aaTAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaattttgatgtctaagattaaaggtaacgttaagtggttt                                                                >  2:251287‑M1/1‑64 (MQ=255)                                                                                  gCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaattttgatgtctaagattaaaggtaacgttaagtggtttaatgag                                                          <  1:836406‑M1/151‑92 (MQ=255)                                                                                      aaaTAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaattttgatgtctaagattaaaggtaacgttaagtggtttaatgagtcc                                                       >  1:605383‑M1/1‑56 (MQ=255)                                                                                       aaTAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTATTAAAGTTTCACTactggtaaccgacacagcatttgtgtttatttttcatttaaaggtaattttgatgtctaagattaaaagtaacgttaggtggtttaatgagtcca                                                      <  2:963036‑M1/150‑96 (MQ=255)                                                                                         tAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaattttgatgtctaagattaaaggtaacgttaagtggtttaatgagtccaa                                                     >  1:432478‑M1/1‑53 (MQ=255)                                                                                              aaCATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaattttgatgtctaagattaaaggtaacgttaagtggtttaatgagtccaaaggattc                                              >  1:792936‑M1/1‑48 (MQ=255)                                                                                                     aaaaTAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaattttgatgtctaagattaaaggtaacgttaagtggtttaatgagtccaaaggattcggtttc                                        >  1:303000‑M1/1‑41 (MQ=255)                                                                                                     aaaaTAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggaaattttgatgtctaagattaaaggtaacgttaagtggtttaatgagtccaaaggattcggtttc                                        >  2:104218‑M1/1‑41 (MQ=255)                                                                                                        aTAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaattttgatgtctaagattaaaggtaacgttaagtggtttaatgagtccaaaggattcggtttcatt                                     >  2:474339‑M1/1‑38 (MQ=255)                                                                                                         tAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaattttgatgtctaagattaaaggtaacgttaagtggtttaatgagtccaaaggattcggtttcattac                                   >  1:558976‑M1/1‑37 (MQ=255)                                                                                                          aaCGCGACTTTTATCACTTTTTAGTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaattttgatgtctaagattaaaggtaacgttaagtggtttaatgagtccaaaggattcggtttcattact                                  >  2:198506‑M1/1‑36 (MQ=255)                                                                                                           aCGCGACTTTTATCACTTTTTAGTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaattttgatgtctaagattaaaggtaacgttaagtggtttaatgagtccaaaggattcggtttcattactc                                 >  1:13556‑M1/1‑35 (MQ=255)                                                                                                                      aTCACTTTTTAGTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaattttgatgtctaagattaaaggtaacgttaagtggtttaatgagtccaaaggattcggtttcattactccggaagacggc                      <  2:544704‑M1/151‑128 (MQ=255)                                                                                                                      aTCACTTTTTAGTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaattttgatgtctaagattaaaggtaacgttaagtggtttaatgagtccaaaggattcggtttcattactccggaagacgg                       <  1:563977‑M1/150‑127 (MQ=255)                                                                                                                       tCACTTTTTAGTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaattttgatgtctaagattaaaggtaacgttaagtggtttaatgagtccaaaggattcggtttcattactccggaagacggc                      <  1:233585‑M1/150‑128 (MQ=255)                                                                                                                            ttttAGTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaattttgatgtctaagattaaaggtaacgttaagtggtttaatgagtccaaaggattcggtttcattactccggaagacggcagcaa                 <  1:674050‑M1/150‑133 (MQ=255)                                                                                                                            ttttAGTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaattttgatgtctaagattaaaggtaacgttaagtggtttaatgagtccaaaggattcggtttcattactccggaagacggcagca                  <  2:108576‑M1/149‑132 (MQ=255)                                                                                                                             tttAGTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaattttgatgtctaagattaaaggtaacgttaagtggtttaatgagtccaaaggattcggtttcattactccggaagacggcagcaaa                <  1:142181‑M1/150‑134 (MQ=255)                                                                                                                                 gTAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaattttgatgtctaagattaaaggtaacgttaagtggtttaatgagtccaaaggattcggtttcattactccggaagacggcagcaaagacgt           <  1:57957‑M1/151‑139 (MQ=255)                                                                                                                                  tAAAGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaattttgatgtctaagattaaaggtaacgttaagtggtttaatgagtccaaaggattcggtttcattactccggaagacggcagcaaagacgt           >  1:822826‑M1/1‑12 (MQ=255)                                                                                                                                   aaaGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaattttgatgtctaagattaaaggtaacgttaagtggtttaatgagtccaaaggattcggtttcattactccggaagacggcagcaaagacgtgt         <  2:320404‑M1/151‑141 (MQ=255)                                                                                                                                    aaGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaattttgatgtctaagattaaaggtaacgttaagtggtttaatgagtccaaaggattcggtttcattactccggaagacggcagcaaagacgtgtt        >  2:126034‑M1/1‑10 (MQ=255)                                                                                                                                    aaGTTACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaattttgatgtctaagattaaaggtaacgttaagtggtttaatgagtccaaaggattcggtttcattactccggaagacggcagcaaagacgtgtt        <  1:561293‑M1/151‑142 (MQ=255)                                                                                                                                       ttACACTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaattttgatgtctaagattaaaggtaacgttaagtggtttaatgagtccaaaggattcggtttcattactccggaagacggcagcaaagacgtgttcgt     >  2:3377‑M1/1‑7 (MQ=255)                                                                                                                                        tACACTactggtaaccgactcagcatttgtgtctatttttcatgtaaaggtatttttgatgtctaagattaaaggtaacgttaagtggtttaatgagtccaaaggattcggtttcattactccggaagacggcagcaaagacgtgttcgt     >  2:664137‑M1/1‑6 (MQ=255)                                                                                                                                         acacTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaattttgatgtctaagattaaaggtaacgttaagtggtttaatgagtccaaaggattcggtttcattactccggaagacggcagcaaagacgtgttcgtac   <  2:432282‑M1/151‑147 (MQ=255)                                                                                                                                          cacTactggtaaccgacacagcatttgtgtctatttttcatgtaaaggtaattttgatgtctaagattaaaggtaacgttaagtggtttaatgagtccaaaggattcggtttcattactccggaagacggcagcaaagacgtgttcgtaca  <  1:672942‑M1/151‑148 (MQ=255)                                                                                                                                             |                                                                                                                                                    ACAATGGCAATGTGTACTTTGCCTGGATGCGCTTTCAGTTTTGAGACAAATGAAGTTTTAGTAACTTCTTTAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTGGACAAAGCGTACCACAATTGGTGTACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTACTCCGGAAG  >  NC_000913/657074‑657361

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑