Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913	62,822	Δ16 bp	coding (428‑443/2907 nt)	rapA ←	RNA polymerase remodeling/recycling factor ATPase; RNA polymerase‑associated, ATP‑dependent RNA translocase

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	62822	62837	16	53 [0]	[0] 54	rapA	RNA polymerase remodeling/recycling factor ATPase; RNA polymerase‑associated, ATP‑dependent RNA translocase

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 62821	0 (0.000)	52 (0.930)	48/280	0.1	100%	coding (444/2907 nt)	rapA	RNA polymerase remodeling/recycling factor ATPase; RNA polymerase‑associated, ATP‑dependent RNA translocase
	?	NC_000913	62838 =	0 (0.000)					coding (427/2907 nt)	rapA	RNA polymerase remodeling/recycling factor ATPase; RNA polymerase‑associated, ATP‑dependent RNA translocase

CATCCCGGCTTCAATGGTTTTCCCTAAACCCACTTCGTCAGCCAGCAGGACGCGCGGCGCGTGGCGGCGACCAACATCATGAGCGATGTTGAGCTGATGCGGGATCAGGCTGGTACGCTGACCGCGCAGGCCGCTGTACGGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGATAACGCAGCGCAAAGCGGTCCATACGGTCAATCTGCCCGGCAAACAGACGGTCCTGCGGTTTGCTGAACACCAGTTTGCTATCAAGGAAAACTTCACGCAGGG  >  NC_000913/62698‑62978                                                                                                                                             |                                                                                                                                             gttgctgatgcaggatcatcccggcttcaatggttttccctaaacccacttcgtcagccagcaggacgcgcggcgcgtggcggcgaccaacatcatgagcgctgttgagctgatgcgggatcaggctggtacgctgaccgggc                                                                                                                                            >  2:277529‑M2/141‑141 (MQ=255)        atgcaggatcacccgggcttccatggttttccctaaacccacttcgtcagccagcaggacgcgcggcgcgtggcggcgaccaacatcatgagcgatgttgagctgatgcgggatcaggctggtacgctgaccgGCATACGGaa                                                                                                                                     <  1:199480‑M2/10‑1 (MQ=255)                 cagcccggcttcgatggttttccctaaacccacgtcgtcagccagcaggacgcgcggcgcgtggcggcgaccaacatcgtgagcgatgttgagctgatgcgggatcaggctggtacgctgaccgGCATACGGAACTGTTCGCt                                                                                                                            <  1:79866‑M2/19‑1 (MQ=255)                            caatggtggtcccgaagccgcctgcgtccgccagcaggacgcgcggcgcgtggcggcgaccaacatcatgagcgatgttgagctgatgcgggatcaggctggtacgctgaccgGCATACGGAACTGTTCGCTGGAATATTGAc                                                                                                                 <  2:412550‑M2/30‑1 (MQ=255)                              atggttttccctaaacccacttcgtcagccagcaggacccgcggcgcgtggcggcgaccaacatcatgagcgatgttgagctgatgcaggatcaggctggtacgctgaccgGCATACGGAACTGTTCGCTGGAATATTTAcgc                                                                                                               >  1:398072‑M2/112‑143 (MQ=255)                                ggttttccctaaacccacttcgtcagccagcaggacgcgcggcgcgtggcggcgaccaacatcatgagcgatgttgagctgatgcgggatcaggctggtacgctgaacgGACCACGGAACTGTTAGACGCTATATTTAcgcgc                                                                                                             >  2:873818‑M2/110‑143 (MQ=255)                                      ccctaaacccacttcgtcagccagcaggacgcgcggcgcgtggcggcgaccaacatcatgagcgatgttgagctgatgcgggatcaggctggtacgctgaccgGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGATa                                                                                                       <  1:947928‑M2/40‑1 (MQ=255)                                        ctaaacccacttcgtcagccagcaggacgcgcggcgcgtggcggcgaccaacatcatgagcgatgttgagctgatgcgggatcaggctggtacgctgaccgGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGATGAc                                                                                                     >  2:931091‑M2/102‑143 (MQ=255)                                         taaacccacttcgtcagccagcaggacgcgcggcgcgtggcggcgaccaacatcatgagcgatgttgagctgatgcgggatcaggctggtacgctgaccgGCATACGGAACTGTTCGCTGGAATATTTACGCGCCCGATAACg                                                                                                    >  1:767299‑M2/101‑143 (MQ=255)                                           aacccacttcgtcagccagcaggacgcgcggcgcgtggcggcgaccaacatcatgagcgatgttgagctgatgcgggatcaggctggtacgctgaccgGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGATAACGCa                                                                                                  <  1:544547‑M2/45‑1 (MQ=255)                                             cccacttcgtcagccagcaggacgcgcggcgcgtggcggcgaccaacatcatgagcgatgttgagctgatgtgggggcaggctggtacgctgaccgGCATACGGAACTGTTCGCTGGAATATTTCCGAGCGCGATAACGCAgc                                                                                                >  1:609450‑M2/97‑143 (MQ=255)                                             cccacttcgtcagccagcaggacgcgcggcgcgtggcggcgaccaacatcatgagcgatgttgagctgatgcgggatcaggctggtacgctgaccgGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGATAACGCAgc                                                                                                <  1:919984‑M2/47‑1 (MQ=255)                                                acttcgtcagccagcaggacgcgcggcgcgtggcggcgaccaacatcatgagcgatgttgagctgatgcgggatcaggctggtacgctgaccgGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGATAACGCAGCGCa                                                                                             <  2:398303‑M2/50‑1 (MQ=255)                                                  ttcgtcagccagcaggacgcgcggcgcgtggcggcgaccaacatcatgagcgatgttgagctgatgcgggatcaggctggtacgctgaccgGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGATAACGCAGCGCaaa                                                                                           <  1:445751‑M2/52‑1 (MQ=255)                                                   tcgtcagccagcaggacgcgcggcgcgtggcggcgaccaacatcatgagcgatgttgagctgatgcgggatcaggctggtacgctgaccgGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGATAACGCAGCGCAAAg                                                                                          <  2:262891‑M2/53‑1 (MQ=255)                                                     gtcggccggcaggacgcgcggcgcgtggcggcgaccaacatcatgagcgatgttgagctgatgcgggatcaggctggtacgctgaccgGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGATAACGCAGCGCAAAGCg                                                                                        <  2:484157‑M2/55‑1 (MQ=255)                                                      tcagccagcaggacgcgcggcgcgtggcggcgaccaacatcatgagcgatgttgagctgatgcgggatcaggctggtacgctgaccgGCATACGGAGCTGTTCGCGGGAATATTTACGCGCGCGATAGCGCAGCGCAAAGCgg                                                                                       >  1:222484‑M2/88‑143 (MQ=255)                                                        agccagcaggacgcgcggcgcgtggcggcgaccaacatcatgagcgatgttgagctgatgcgggatcaggctggtacgctgaccgGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGATAACGCAGCGCAAAGCGGTc                                                                                     <  1:254564‑M2/58‑1 (MQ=255)                                                          ccagcaggacgcgcggcgcgtggcggcgaccaacatcatgggcgatgttgagctgaggcgggatcaggctggtacgctgaccgGCATGCGGAAGTGTTCGCTGAAATAATAACGCGCGCGCGAACACAGAGCAAAACGGTACa                                                                                   >  2:541009‑M2/84‑143 (MQ=255)                                                          ccagcaggacgcgcggcgcgtggcggcgaccaacatcatgagcgatgttgagctgatgcgggatcaggctggtacgctgaccgGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGATCACGCAGCGCAAAGCGGTCCa                                                                                   >  1:745839‑M2/84‑143 (MQ=255)                                                              caggacgcgcggcgcgtggcggcgaccaacatcatgagcgatgttgagctgatgcgggatcaggctggtacgctgaccgGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGATAACGCAGCGCAAAGCGGTCCATACg                                                                               <  2:489515‑M2/64‑1 (MQ=255)                                                              cagcgcgcgcggcgcgtggcggcgaccaacatgatgagcgatgttgagctgatgcgggatcaggctggtacgctgatcgGCATACGTAACTGTTCGCTGGAATATTTACGCGCGCATGAACGTGGCTCAAAGCGGTCCATACg                                                                               <  2:618684‑M2/64‑1 (MQ=255)                                                                gggtgcggggcgctgggcggcggccaacatcatgagcgatgttgaggtgatgcgggatcaggctggtacgctgaccgGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGATAACGCAGCGCAAAGCGGTCCATACGGt                                                                             <  2:384725‑M2/66‑1 (MQ=255)                                                                ggacgcgcggcgcgtggcggcgaccaacatcatgagcgatgttgagctgatgcgggatcaggctggtacgctgaccgGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGATAACGCAGCGCAAAGCGGTCCATACGGt                                                                             <  1:567479‑M2/66‑1 (MQ=255)                                                                       cggcgcggggcggcgaccaacatcatgagcgatgttgagctgatgcgggagcaggctggtacgctgaccgGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGATAACGCAGCGCAAAGCGGTCCATACGGTCAATCTg                                                                      <  2:281763‑M2/73‑1 (MQ=255)                                                                         gcgcgtggcggcgaccaacatcatgagcgatgttgagctgatgcgggatcaggctggtacgctgaccgGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGATAACGCAGCGCAAAGCGGTCCATACGGTCCATCTGcc                                                                    >  1:270582‑M2/69‑143 (MQ=255)                                                                            cgtggcggcgaccaacatcatgagcgatgttgagctgatgcgggatcaggctggtacgctgaccgGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGATAACGCAGCGCAAAGCGGTCCATACGGTCAATCTGCCCgg                                                                 <  1:503015‑M2/78‑1 (MQ=255)                                                                              gggcggcgaccagcatcatgagcgatgttgggctgaggcgggatcaggcgggtgcgcggaccgGCATACGGAACTGTTCGCTGGGATATTTACGCGCGCGATAACGCAGCGCAAAGCGGTCCATACGGTCAATCTGCCCGGCa                                                               <  2:489104‑M2/80‑1 (MQ=255)                                                                                gcggcgaccaacatcatgagcgatgttgagctgatgcgggatcaggctggtacgctgaccgGCATACGGGACGGTTCGCTGGAATATTTACGCGCGCGATAACGCAGCGCAAAGCGGTCCATACGGCCAAGCTGCCCGGCaaa                                                             >  2:561167‑M2/62‑143 (MQ=255)                                                                                 cggcgaccaacatcatgagcgatgttgagctgatgcgggatcaggctggtacgctgaccgGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGAGAACGCAGCGCAAAGCGGGCCATACGGGCAATCTGCCCGgcaacc                                                            >  2:416309‑M2/61‑141 (MQ=255)                                                                                      accaacatcatgagcgatgttgagctgatgcgggatcaggctggtacgctgaccgGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGATAACGCAGCGCAAAGCGGTCCATACGGTCAATCTGCCCGGCAAACAGACg                                                       <  1:892336‑M2/88‑1 (MQ=255)                                                                                                  agcgatgtggagctgatgcgtgatcaggctggtacgctgaccgGCATACGGAACTGTTCGCTGGAATATTTACGCGCGAAATAACTCAGCGCAAAGCGGTCCATACGGTCAATCTGCCCGGCAAACAGACGGTCCTGCGGttt                                           <  1:277300‑M2/100‑1 (MQ=255)                                                                                                   gcgatggtgagcggaagcgggagcaggcgggtacgcggaccgGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGATAACGCAGCGCAAAGCGGTCCATACGGTCAATCTGCCCGGCAAACAGACGGTCCTGCGGTTTg                                          <  1:263007‑M2/101‑1 (MQ=255)                                                                                                    cgatgttgagctgatgcgggatcaggctggtacgctgaccgGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGATAACGCAGCGCAAAGCGGTCCATACGGTCGATCTGCCCGGCAAACAGACGGTCCGGCGGTTTGc                                         >  1:661152‑M2/42‑143 (MQ=255)                                                                                                       tgtggagctgatgcgggatcaggctggtacgctgaccgGCATCCGGAGCTGTGCGCTGGAATATTTCCGCGCGCGATAACGCAGCGCAAAGCGGTCCATACGGTCAATCTGCCCGGCAAACAGACGGTCCTGCGGTTTGCTGa                                      <  1:463304‑M2/105‑1 (MQ=255)                                                                                                        gttgagctgaggcgggatcaggctggtacgctgaccgGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGATAACGCAGCGCAAAGCGGTCCATACGGTCAATCTGCCCGGCAAACAGACGGTCCTGCGGTTTGCTGaa                                     <  2:271533‑M2/106‑1 (MQ=255)                                                                                                          ggagctgatgcgggagcaggctggtacgctgaccgGCATACGGAACTGTTCGCTGGAATATTGACGCGCGCGATAACGCAGCGCAAAGCGGTCCATACGGTCAATCTGCCCGGCAAACAGACGGTCCTGCGGTTTGCTGAaca                                   <  2:97338‑M2/108‑1 (MQ=255)                                                                                                              ctgatgcgggatcaggctggtacgctgaccgGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGATAACGCAGCGCAAAGCGGTCCATACGGTCGATCTGCCCGGCAAACAGACGGTCCTTCGGTTTGCTGAACACCAg                               >  1:84838‑M2/32‑143 (MQ=255)                                                                                                                gatgcgggatcaggctggtacgctgaccgGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGATAACGCAGCGCAAAGCGGTCCATACGGTCAATCTGCCCGGCAAACAGACGGTCCTGCGGTTTGCTGAACACCAGtt                             >  1:432291‑M2/30‑143 (MQ=255)                                                                                                                   gcgggatcaggctggtacgctgaccgGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGATAACGCAGCGCAAAGCGGTCCATACGGTCAATCTGCCCGGCAAACAGACGGTCCTGCGGTTTGCTGAACACCAGTTTGc                          >  2:994718‑M2/27‑143 (MQ=255)                                                                                                                       gatcaggctggtacgctgaccgGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGATAACGCAGCGCAAAGCGGTCCATACGGTCAATCTGCCCGGCAAACAGACGGTCCTGCGGTTTGCTGAACACCAGTTTGCTATc                      >  2:149782‑M2/23‑143 (MQ=255)                                                                                                                       gatcaggctggtacgctgaccgGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGATAACGCAGCACAAAGCGGTCCATACGGTCAATCTGCCCGGCAAACAGACGGTCCTGCGGTTTGCTGAACACCAGTTTGCGATc                      >  1:731226‑M2/23‑143 (MQ=255)                                                                                                                         tcaggctggtacgctgaccgGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGATAACGCAGCGCAAAGCGGTCCATACGGTCAATCTGCCCGGCAAACAGACGGTCCTGCGGTTTGCTGAACACCAGTTTGCTATCaa                    <  1:588650‑M2/123‑1 (MQ=255)                                                                                                                          caggcgggtacgctgaccgGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGATAACGCAGCGCAAAGCGGTCCATACGGTCAATCTGCCCGGCAAACAGACGGTCCTGCGGTTTGCTGAACACCAGTTTGCTATCAAg                   <  2:7912‑M2/124‑1 (MQ=255)                                                                                                                           aggctggtacgctgaccgGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGATAACGCAGCGCAAAGCGGTCCATACGGTCAATCTGCCCGGCAAACAGACGGTCCTGCCATTTGCTGCACACCAGCTCGCTATCAAgg                  >  2:347575‑M2/19‑143 (MQ=255)                                                                                                                            ggctggtacgctgaccgGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGATAACGCAGCGCAAAGCGGTCGATACGGTCCATCTGCCCGGCAAACAGACGGTACTGCGGTTTGCTGGACACAAGGTTGCTTACAAGGa                 >  2:279869‑M2/18‑143 (MQ=255)                                                                                                                            ggctggcacgctgagcgGCAGACGGCACTGTTCGCTGGAATATTTACGCGCGCGATAACGCAGCGCAAAGCGGTCCATACGGTCAATCTGCCGGGCAAACAGACGGTCCTGCGGTTTGCTGAATACCAGTTTGCTATCAAGGa                 <  2:831763‑M2/126‑1 (MQ=255)                                                                                                                             gctggtacgctgaccgGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGATAACGCAGCGCAAAGCGGTCCATACGGTCAATCTGCCCGGCAAACAGACGGTCCTGCGGTTTGCTGAACACCAGTTCCGTATCAAGGaa                >  2:543467‑M2/17‑143 (MQ=255)                                                                                                                                 gtacgctgaccgGCATACGTAACTGTTCGCTGAAATATTTACGCGCGCGATAACGCAGCGCAAAGCGGTCCATACGGTCAATCTGCCCGGCAAACAGACGGTCCTGCGGTTTGCTGAACACCAGTTTGCTATCAAGGAAAACt            <  1:277529‑M2/131‑1 (MQ=255)                                                                                                                                   acgctgaccgGCCTACGGAACTGTTCGTTGGAATATTTACGCGCGCGATAACGCAGCGCAAAGCGGTCCATACGGTCAATCTGCCCGGCAAACAGACGGTCCTGCGGTTTGCTGAACACCAGTTTGCTATCAAGGAAAACTTc          <  2:728559‑M2/133‑1 (MQ=255)                                                                                                                                       tgaccgGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGATAACGCAGCGCAAAGCGGTCCATACGGTCAATCTGCCCGGCAAACAGACGGTCCTGCGGTTTGCTGAACACCAGTTTGCTATCAAGGAAAACTTCACGc      >  1:806935‑M2/7‑143 (MQ=255)                                                                                                                                          ccgGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGATAACGCAGCGCAAAGCGGTCCATACGGTCAATCTGCCCGGCAAACAGACGGTCCTGCGGTTTGCTGAACACCAGTTTGCTATCAAGGAAAACTTCACGCAgg   <  2:665621‑M2/140‑1 (MQ=255)                                                                                                                                          cccgCACACGTAACTGTTCGCTGGCCCATCTCCGCGCGCGATCAAGCACCACAAAGCGGACCATAAGGACAATCCGACCGGCAAACAGACCGTCCCGAGATTAACCGAAGAACAGCCTGCTATCAAGGAAAACTTCACGCAgg   <  2:942099/140‑1 (MQ=255)                                                                                                                                           cgGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGATAACGCCGCGCACAGCGGTCCATACGGTCAATCTGCCCGGCAAACAGACGGTCCAGCGGTTTGCTGCACACCCGTTTGGTATCAAGGCAACGTTCACGCAggg  >  2:663229‑M2/3‑143 (MQ=255)                                                                                                                                             |                                                                                                                                             CATCCCGGCTTCAATGGTTTTCCCTAAACCCACTTCGTCAGCCAGCAGGACGCGCGGCGCGTGGCGGCGACCAACATCATGAGCGATGTTGAGCTGATGCGGGATCAGGCTGGTACGCTGACCGCGCAGGCCGCTGTACGGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGATAACGCAGCGCAAAGCGGTCCATACGGTCAATCTGCCCGGCAAACAGACGGTCCTGCGGTTTGCTGAACACCAGTTTGCTATCAAGGAAAACTTCACGCAGGG  >  NC_000913/62698‑62978

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑