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

GATGCGCTTTCAGTTTTGAGACAAATGAAGTTTTAGTAACTTCTTTAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTGGACAAAGCGTACCACAATTGGTGTACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTACTCCGGAAGACGGCAGCAAAGACGTGTTCGTACACTTC  >  NC_000913/657099‑657390                                                                                                                                              |                                                                                                                                                       acaatggcaatgtgtactttgcctggatgcgctttcagttttgagacaaatgaagttttagtaacttctttaaaatcaatagctaaaataagtaacatcaaaactaacgcgacttttatcactttttagtaaagttacactACTGGTAAcc                                                                                                                                               >  2:416420‑M2/142‑151 (MQ=255)  caatggcaatgtgtactttgcctggatgcgctttcagttttgagacaaatgaagttttagtaacttctttaaaatcaatagctaaaataagtaacatcaaaaataacgcgacttttatcactttttagtaaagttacactACTGGTAACCg                                                                                                                                              <  2:330105‑M2/11‑1 (MQ=255)         catgtgtactttgcctggatgcgctttcagttttgagacaaatgaagttttagtaacttctttaaaatcaatagctaaaataagtaacatcaaaaataacgcgacttttatcactttttagtaaagttacactACTGGTAACCGACACAGc                                                                                                                                       >  2:777227‑M2/134‑151 (MQ=255)              gtactttgcctggatgcgctttcagttttgagacaaatgaagttttagtaacttctttaaaatcaatagctaaaataagtaacatcaaaaataacgcgacttttatcactttttagtaaagttacactACTGGTAACCGACACAGCAttt                                                                                                                                   <  1:21928‑M2/22‑1 (MQ=255)                     gcctggatgcgctttcagttttgagacaaatgaagttttagtaacttctttaaaagcaatagctaaaataagtaacatcaaaaataacgcgacttttatcactttttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTa                                                                                                                            <  2:242100‑M2/29‑1 (MQ=255)                            tgcgctttcagttttgagacaaatgaagttttagtaacttctttaaaatcaatagctaaaataagtaacatcaaaaataacgcgacttttatcactttttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCAt                                                                                                                    >  1:271194‑M2/115‑151 (MQ=255)                             gcgctttcagttttgagacaaatgaagttttagtaacttctttaaaatcaatagctaaaataagtaacatcaaaaataacgcgacttttatcactttttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATg                                                                                                                   <  1:395111‑M2/38‑1 (MQ=255)                                 tttcagttttgagacaaatgaagttttagtaacttctttaaaatcaatagctaaaataagtaacatcaaaaataacgcgacttttatcactttttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTaa                                                                                                                >  2:489200‑M2/110‑150 (MQ=255)                                  ttcagttttgagacaaatgaagttttagtaacttctttaaaatcaatagctaaaataagtaacatcaaaaataacgcgacttttatcactttttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTaa                                                                                                                <  2:861527‑M2/41‑1 (MQ=255)                                   tcagttttgagacaaatgaagttttagtaacttctttaaaatcaatagctaaaataagtaacatcaaaaataacgcgacttttatcactttttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAgg                                                                                                             >  1:514611‑M2/108‑151 (MQ=255)                                   tcagttttgagacaaatgaagttttagtaacttctttaaaatcaatagctaaaataagtaacatcaaaaataacgcgacttttatcactttttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAg                                                                                                              <  1:411428‑M2/43‑1 (MQ=255)                                      gttttgagacaaatgaagttttagtaacttctttaaaatcaatagctaaaataagtaacatcaaaaataacgcgacttttatcactttttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTaa                                                                                                          <  1:427482‑M2/47‑1 (MQ=255)                                           gagacaaatgaagttttagtaacttctttaaaatcaatagctaaaataagtaacatcaaaaataacgcgacttttatcactttttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTg                                                                                                     <  1:499913‑M2/52‑1 (MQ=255)                                                aaatgaagttttagtaacttctttaaaatcaatagctaaaataagtaacatcaaaaataacgcgacctttatcactttttagtaaagttacactACTGGTAATCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTc                                                                                                >  2:598665‑M2/95‑151 (MQ=255)                                                  atgaagttttagtaacttctttaaaatcaatagctaaaataagtaacatcaaaaataacgcgacttttatcactttttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTa                                                                                              <  2:540127‑M2/59‑1 (MQ=255)                                                    gaagttttagtaacttctttaaaatcaatagctaaaataagtaacatcaaaaataacgcgacttttatcactttttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAg                                                                                            <  2:105603‑M2/61‑1 (MQ=255)                                                      agttttagtaacttctttaaaatcaatagctaaaataagtaacatcaaaaataacgcgacttttatcactttttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTa                                                                                              >  1:555956‑M2/89‑147 (MQ=255)                                                        ttttagtaacttctttaaaatcaagagcgaaaataagtaacatcaaaaataacgcggcttttatcactttttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAATGGTAATTTTGATGCCTAAGAtt                                                                                         >  2:956491‑M2/87‑150 (MQ=255)                                                         tttagtaacttctttaaaatcaatagctaaaataagtaacatcaaaaataacgcgacttttatcactttttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTa                                                                                        <  1:728480‑M2/65‑1 (MQ=255)                                                            agtaacttctttaaaatcaatagctaaaataagtaacatcaaaaataacgcgacttttatcactttttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAgg                                                                                    >  1:68816‑M2/83‑151 (MQ=255)                                                             gtaacttctttaaaatcaatagctaaaataagtaacatcaaaaataacgcgacttttatcactttttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGt                                                                                   <  1:620974‑M2/70‑1 (MQ=255)                                                                   tctttaaaatcaatagctaaaataattaacatcaaaaataacgcgacttttatcactttttattaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACg                                                                               <  2:476072‑M2/74‑1 (MQ=255)                                                                    ctttaaaatcaatagctaaaataagtaacatcaaaaataacgcgacttttatcactttttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACGtt                                                                             >  1:672992‑M2/75‑150 (MQ=255)                                                                      ttaaaatcaatagctaaaataagtaacatcaaaaataacgcgacttttatcactttttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACGtt                                                                             <  1:576291‑M2/76‑1 (MQ=255)                                                                         aaatcaatagctaaaataagtaacatcaaaaataacgcgacttttatcactttttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTgg                                                                       >  2:225216‑M2/70‑151 (MQ=255)                                                                             caatagctaaaataagtaacatcaaaaataacgcgacttttatcactttttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGttt                                                                    <  1:59783‑M2/85‑1 (MQ=255)                                                                             caatagctaaaataagtaacatcaaaaataacgcgacttttatcactttttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTa                                                                   <  2:911144‑M2/86‑1 (MQ=255)                                                                              aatagctaaaataagtaacatcaaaaataacgcgacttttatcactttttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGttt                                                                    >  2:251287‑M2/65‑149 (MQ=255)                                                                              aatagctaaaataagtaacatcaaaaataacgcgacttttatcactttttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTa                                                                   >  2:558319‑M2/65‑150 (MQ=255)                                                                                  gctaaaataagtaacatcaaaaataacgcgacttttatcactttttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAg                                                              <  1:836406‑M2/91‑1 (MQ=255)                                                                                      aaataagtaacatcaaaaataacgcgacttttatcactttttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTcc                                                           >  1:605383‑M2/57‑150 (MQ=255)                                                                                       aataagtaacatcaaaaataacgcgacttttatcactttttattaaagtttcactACTGGTAACCGACACAGCATTTGTGTTTATTTTTCATTTAAAGGTAATTTTGATGTCTAAGATTAAAAGTAACGTTAGGTGGTTTAATGAGTCCa                                                          <  2:963036‑M2/95‑1 (MQ=255)                                                                                         taagtaacatcaaaaataacgcgacttttatcactttttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCaa                                                         >  1:432478‑M2/54‑149 (MQ=255)                                                                                              aacatcaaaaataacgcgacttttatcactttttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTc                                                  >  1:792936‑M2/49‑151 (MQ=255)                                                                                                     aaaataacgcgacttttatcactttttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTc                                            >  1:303000‑M2/42‑150 (MQ=255)                                                                                                     aaaataacgcgacttttatcactttttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGAAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTc                                            >  2:104218‑M2/42‑150 (MQ=255)                                                                                                        ataacgcgacttttatcactttttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCAtt                                         >  2:474339‑M2/39‑150 (MQ=255)                                                                                                         taacgcgacttttatcactttttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTAc                                       >  1:558976‑M2/38‑151 (MQ=255)                                                                                                          aacgcgacttttatcactttttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTACt                                      >  2:198506‑M2/37‑151 (MQ=255)                                                                                                           acgcgacttttatcactttttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTACTc                                     >  1:13556‑M2/36‑151 (MQ=255)                                                                                                                      atcactttttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTACTCCGGAAGACgg                           <  1:563977‑M2/126‑1 (MQ=255)                                                                                                                      atcactttttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTACTCCGGAAGACGgc                          <  2:544704‑M2/127‑1 (MQ=255)                                                                                                                       tcactttttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTACTCCGGAAGACGgc                          <  1:233585‑M2/127‑1 (MQ=255)                                                                                                                            ttttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTACTCCGGAAGACGgcagca                      <  2:108576‑M2/131‑1 (MQ=255)                                                                                                                            ttttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTACTCCGGAAGACGGCAGCaa                     <  1:674050‑M2/132‑1 (MQ=255)                                                                                                                             tttagtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTACTCCGGAAGACGGCAGCaaa                    <  1:142181‑M2/133‑1 (MQ=255)                                                                                                                                 gtaaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTACTCCGGAAGACGGCAGCAAAGACgt               <  1:57957‑M2/138‑1 (MQ=255)                                                                                                                                  taaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTACTCCGGAAGACGGCAGCAAAGACgt               >  1:822826‑M2/13‑150 (MQ=255)                                                                                                                                   aaagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTACTCCGGAAGACGGCAGCAAAGACgtgt             <  2:320404‑M2/140‑1 (MQ=255)                                                                                                                                    aagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTACTCCGGAAGACGGCAGCAAAGACGTGtt            <  1:561293‑M2/141‑1 (MQ=255)                                                                                                                                    aagttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTACTCCGGAAGACGGCAGCAAAGACGTGtt            >  2:126034‑M2/11‑151 (MQ=255)                                                                                                                                       ttacactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTACTCCGGAAGACGGCAGCAAAGACGTGTTCGt         >  2:3377‑M2/8‑151 (MQ=255)                                                                                                                                        tacactACTGGTAACCGACTCAGCATTTGTGTCTATTTTTCATGTAAAGGTATTTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTACTCCGGAAGACGGCAGCAAAGACGTGTTCGt         >  2:664137‑M2/7‑150 (MQ=255)                                                                                                                                         acactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTACTCCGGAAGACGGCAGCAAAGACGTGTTCGTac       <  2:432282‑M2/146‑1 (MQ=255)                                                                                                                                          cactACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTACTCCGGAAGACGGCAGCAAAGACGTGTTCGTaca      <  1:672942‑M2/147‑1 (MQ=255)                                                                                                                                              aCTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTACTCCGGAAGACGGCAGCAAAGACGTGTTCGTACACTtc  <  2:400122/151‑1 (MQ=255)                                                                                                                                              |                                                                                                                                                       GATGCGCTTTCAGTTTTGAGACAAATGAAGTTTTAGTAACTTCTTTAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTGGACAAAGCGTACCACAATTGGTGTACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTACTCCGGAAGACGGCAGCAAAGACGTGTTCGTACACTTC  >  NC_000913/657099‑657390

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: ‑