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

GTTGCTGATGCAGGATCATCCCGGCTTCAATGGTTTTCCCTAAACCCACTTCGTCAGCCAGCAGGACGCGCGGCGCGTGGCGGCGACCAACATCATGAGCGATGTTGAGCTGATGCGGGATCAGGCTGGTACGCTGACCGCGCAGGCCGCTGTACGGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGATAACGCAGCGCAAAGCGGTCCATACGGTCAATCTGCCCGGCAAACAGACGGTCCTGCGGTTTGCTGAACACCAGTTTGCTATCAAGG  >  NC_000913/62682‑62962                                                                                                                                            |                                                                                                                                              gTTGCTGATGCAGGATCATCCCGGCTTCAATGGTTTTCCCTAAACCCACTTCGTCAGCCAGCAGGACGCGCGGCGCGTGGCGGCGACCAACATCATGAGCGCTGTTGAGCTGATGCGGGATCAGGCTGGTACGCTGACCGggc                                                                                                                                            >  2:277529‑M1/1‑140 (MQ=255)        aTGCAGGATCACCCGGGCTTCCATGGTTTTCCCTAAACCCACTTCGTCAGCCAGCAGGACGCGCGGCGCGTGGCGGCGACCAACATCATGAGCGATGTTGAGCTGATGCGGGATCAGGCTGGTACGCTGACCGgcatacggaa                                                                                                                                     <  1:199480‑M1/143‑11 (MQ=255)                 cagcccggcTTCGATGGTTTTCCCTAAACCCACGTCGTCAGCCAGCAGGACGCGCGGCGCGTGGCGGCGACCAACATCGTGAGCGATGTTGAGCTGATGCGGGATCAGGCTGGTACGCTGACCGgcatacggaactgttcgct                                                                                                                            <  1:79866‑M1/140‑20 (MQ=255)                            cAATGGTGGTCCCGAAGCCGCCTGCGTCCGCCAGCAGGACGCGCGGCGCGTGGCGGCGACCAACATCATGAGCGATGTTGAGCTGATGCGGGATCAGGCTGGTACGCTGACCGgcatacggaactgttcgctggaatattgac                                                                                                                 <  2:412550‑M1/143‑31 (MQ=255)                              aTGGTTTTCCCTAAACCCACTTCGTCAGCCAGCAGGACCCGCGGCGCGTGGCGGCGACCAACATCATGAGCGATGTTGAGCTGATGCAGGATCAGGCTGGTACGCTGACCGgcatacggaactgttcgctggaatatttacgc                                                                                                               >  1:398072‑M1/1‑111 (MQ=255)                                ggTTTTCCCTAAACCCACTTCGTCAGCCAGCAGGACGCGCGGCGCGTGGCGGCGACCAACATCATGAGCGATGTTGAGCTGATGCGGGATCAGGCTGGTACGCTGAACGgaccacggaactgttagacgctatatttacgcgc                                                                                                             >  2:873818‑M1/1‑109 (MQ=255)                                      cccTAAACCCACTTCGTCAGCCAGCAGGACGCGCGGCGCGTGGCGGCGACCAACATCATGAGCGATGTTGAGCTGATGCGGGATCAGGCTGGTACGCTGACCGgcatacggaactgttcgctggaatatttacgcgcgcgata                                                                                                       <  1:947928‑M1/143‑41 (MQ=255)                                        cTAAACCCACTTCGTCAGCCAGCAGGACGCGCGGCGCGTGGCGGCGACCAACATCATGAGCGATGTTGAGCTGATGCGGGATCAGGCTGGTACGCTGACCGgcatacggaactgttcgctggaatatttacgcgcgcgatgac                                                                                                     >  2:931091‑M1/1‑101 (MQ=255)                                         tAAACCCACTTCGTCAGCCAGCAGGACGCGCGGCGCGTGGCGGCGACCAACATCATGAGCGATGTTGAGCTGATGCGGGATCAGGCTGGTACGCTGACCGgcatacggaactgttcgctggaatatttacgcgcccgataacg                                                                                                    >  1:767299‑M1/1‑100 (MQ=255)                                           aaCCCACTTCGTCAGCCAGCAGGACGCGCGGCGCGTGGCGGCGACCAACATCATGAGCGATGTTGAGCTGATGCGGGATCAGGCTGGTACGCTGACCGgcatacggaactgttcgctggaatatttacgcgcgcgataacgca                                                                                                  <  1:544547‑M1/143‑46 (MQ=255)                                             cccACTTCGTCAGCCAGCAGGACGCGCGGCGCGTGGCGGCGACCAACATCATGAGCGATGTTGAGCTGATGTGGGGGCAGGCTGGTACGCTGACCGgcatacggaactgttcgctggaatatttccgagcgcgataacgcagc                                                                                                >  1:609450‑M1/1‑96 (MQ=255)                                             cccACTTCGTCAGCCAGCAGGACGCGCGGCGCGTGGCGGCGACCAACATCATGAGCGATGTTGAGCTGATGCGGGATCAGGCTGGTACGCTGACCGgcatacggaactgttcgctggaatatttacgcgcgcgataacgcagc                                                                                                <  1:919984‑M1/143‑48 (MQ=255)                                                aCTTCGTCAGCCAGCAGGACGCGCGGCGCGTGGCGGCGACCAACATCATGAGCGATGTTGAGCTGATGCGGGATCAGGCTGGTACGCTGACCGgcatacggaactgttcgctggaatatttacgcgcgcgataacgcagcgca                                                                                             <  2:398303‑M1/143‑51 (MQ=255)                                                  ttCGTCAGCCAGCAGGACGCGCGGCGCGTGGCGGCGACCAACATCATGAGCGATGTTGAGCTGATGCGGGATCAGGCTGGTACGCTGACCGgcatacggaactgttcgctggaatatttacgcgcgcgataacgcagcgcaaa                                                                                           <  1:445751‑M1/143‑53 (MQ=255)                                                   tCGTCAGCCAGCAGGACGCGCGGCGCGTGGCGGCGACCAACATCATGAGCGATGTTGAGCTGATGCGGGATCAGGCTGGTACGCTGACCGgcatacggaactgttcgctggaatatttacgcgcgcgataacgcagcgcaaag                                                                                          <  2:262891‑M1/143‑54 (MQ=255)                                                     gTCGGCCGGCAGGACGCGCGGCGCGTGGCGGCGACCAACATCATGAGCGATGTTGAGCTGATGCGGGATCAGGCTGGTACGCTGACCGgcatacggaactgttcgctggaatatttacgcgcgcgataacgcagcgcaaagcg                                                                                        <  2:484157‑M1/143‑56 (MQ=255)                                                      tCAGCCAGCAGGACGCGCGGCGCGTGGCGGCGACCAACATCATGAGCGATGTTGAGCTGATGCGGGATCAGGCTGGTACGCTGACCGgcatacggagctgttcgcgggaatatttacgcgcgcgatagcgcagcgcaaagcgg                                                                                       >  1:222484‑M1/1‑87 (MQ=255)                                                        agccagcAGGACGCGCGGCGCGTGGCGGCGACCAACATCATGAGCGATGTTGAGCTGATGCGGGATCAGGCTGGTACGCTGACCGgcatacggaactgttcgctggaatatttacgcgcgcgataacgcagcgcaaagcggtc                                                                                     <  1:254564‑M1/143‑59 (MQ=255)                                                          ccagcAGGACGCGCGGCGCGTGGCGGCGACCAACATCATGGGCGATGTTGAGCTGAGGCGGGATCAGGCTGGTACGCTGACCGgcatgcggaagtgttcgctgaaataataacgcgcgcgcgaacacagagcaaaacggtaca                                                                                   >  2:541009‑M1/1‑83 (MQ=255)                                                          ccagcAGGACGCGCGGCGCGTGGCGGCGACCAACATCATGAGCGATGTTGAGCTGATGCGGGATCAGGCTGGTACGCTGACCGgcatacggaactgttcgctggaatatttacgcgcgcgatcacgcagcgcaaagcggtcca                                                                                   >  1:745839‑M1/1‑83 (MQ=255)                                                              cagcgcgcgcggcgcgTGGCGGCGACCAACATGATGAGCGATGTTGAGCTGATGCGGGATCAGGCTGGTACGCTGATCGgcatacgtaactgttcgctggaatatttacgcgcgcatgaacgtggctcaaagcggtccatacg                                                                               <  2:618684‑M1/138‑65 (MQ=255)                                                              cagGACGCGCGGCGCGTGGCGGCGACCAACATCATGAGCGATGTTGAGCTGATGCGGGATCAGGCTGGTACGCTGACCGgcatacggaactgttcgctggaatatttacgcgcgcgataacgcagcgcaaagcggtccatacg                                                                               <  2:489515‑M1/143‑65 (MQ=255)                                                                gggtgcggggcgctgggcGGCGGCCAACATCATGAGCGATGTTGAGGTGATGCGGGATCAGGCTGGTACGCTGACCGgcatacggaactgttcgctggaatatttacgcgcgcgataacgcagcgcaaagcggtccatacggt                                                                             <  2:384725‑M1/139‑67 (MQ=255)                                                                ggACGCGCGGCGCGTGGCGGCGACCAACATCATGAGCGATGTTGAGCTGATGCGGGATCAGGCTGGTACGCTGACCGgcatacggaactgttcgctggaatatttacgcgcgcgataacgcagcgcaaagcggtccatacggt                                                                             <  1:567479‑M1/143‑67 (MQ=255)                                                                       cggcgcgGGGCGGCGACCAACATCATGAGCGATGTTGAGCTGATGCGGGAGCAGGCTGGTACGCTGACCGgcatacggaactgttcgctggaatatttacgcgcgcgataacgcagcgcaaagcggtccatacggtcaatctg                                                                      <  2:281763‑M1/143‑74 (MQ=255)                                                                         gcgcgTGGCGGCGACCAACATCATGAGCGATGTTGAGCTGATGCGGGATCAGGCTGGTACGCTGACCGgcatacggaactgttcgctggaatatttacgcgcgcgataacgcagcgcaaagcggtccatacggtccatctgcc                                                                    >  1:270582‑M1/1‑68 (MQ=255)                                                                            cgTGGCGGCGACCAACATCATGAGCGATGTTGAGCTGATGCGGGATCAGGCTGGTACGCTGACCGgcatacggaactgttcgctggaatatttacgcgcgcgataacgcagcgcaaagcggtccatacggtcaatctgcccgg                                                                 <  1:503015‑M1/143‑79 (MQ=255)                                                                              gggcggcgACCAGCATCATGAGCGATGTTGGGCTGAGGCGGGATCAGGCGGGTGCGCGGACCGgcatacggaactgttcgctgggatatttacgcgcgcgataacgcagcgcaaagcggtccatacggtcaatctgcccggca                                                               <  2:489104‑M1/142‑81 (MQ=255)                                                                                gcggcgACCAACATCATGAGCGATGTTGAGCTGATGCGGGATCAGGCTGGTACGCTGACCGgcatacgggacggttcgctggaatatttacgcgcgcgataacgcagcgcaaagcggtccatacggccaagctgcccggcaaa                                                             >  2:561167‑M1/1‑61 (MQ=255)                                                                                 cggcgACCAACATCATGAGCGATGTTGAGCTGATGCGGGATCAGGCTGGTACGCTGACCGgcatacggaactgttcgctggaatatttacgcgcgcgagaacgcagcgcaaagcgggccatacgggcaatctgcccggcaacc                                                            >  2:416309‑M1/1‑60 (MQ=255)                                                                                      aCCAACATCATGAGCGATGTTGAGCTGATGCGGGATCAGGCTGGTACGCTGACCGgcatacggaactgttcgctggaatatttacgcgcgcgataacgcagcgcaaagcggtccatacggtcaatctgcccggcaaacagacg                                                       <  1:892336‑M1/143‑89 (MQ=255)                                                                                                  aGCGATGTGGAGCTGATGCGTGATCAGGCTGGTACGCTGACCGgcatacggaactgttcgctggaatatttacgcgcgaaataactcagcgcaaagcggtccatacggtcaatctgcccggcaaacagacggtcctgcggttt                                           <  1:277300‑M1/143‑101 (MQ=255)                                                                                                   gCGATGGTGAGCGGAAGCGGGAGCAGGCGGGTACGCGGACCGgcatacggaactgttcgctggaatatttacgcgcgcgataacgcagcgcaaagcggtccatacggtcaatctgcccggcaaacagacggtcctgcggtttg                                          <  1:263007‑M1/143‑102 (MQ=255)                                                                                                    cGATGTTGAGCTGATGCGGGATCAGGCTGGTACGCTGACCGgcatacggaactgttcgctggaatatttacgcgcgcgataacgcagcgcaaagcggtccatacggtcgatctgcccggcaaacagacggtccggcggtttgc                                         >  1:661152‑M1/1‑41 (MQ=255)                                                                                                       tgtgGAGCTGATGCGGGATCAGGCTGGTACGCTGACCGgcatccggagctgtgcgctggaatatttccgcgcgcgataacgcagcgcaaagcggtccatacggtcaatctgcccggcaaacagacggtcctgcggtttgctga                                      <  1:463304‑M1/143‑106 (MQ=255)                                                                                                        gTTGAGCTGAGGCGGGATCAGGCTGGTACGCTGACCGgcatacggaactgttcgctggaatatttacgcgcgcgataacgcagcgcaaagcggtccatacggtcaatctgcccggcaaacagacggtcctgcggtttgctgaa                                     <  2:271533‑M1/143‑107 (MQ=255)                                                                                                          ggaGCTGATGCGGGAGCAGGCTGGTACGCTGACCGgcatacggaactgttcgctggaatattgacgcgcgcgataacgcagcgcaaagcggtccatacggtcaatctgcccggcaaacagacggtcctgcggtttgctgaaca                                   <  2:97338‑M1/142‑109 (MQ=255)                                                                                                              cTGATGCGGGATCAGGCTGGTACGCTGACCGgcatacggaactgttcgctggaatatttacgcgcgcgataacgcagcgcaaagcggtccatacggtcgatctgcccggcaaacagacggtccttcggtttgctgaacaccag                               >  1:84838‑M1/1‑31 (MQ=255)                                                                                                                gATGCGGGATCAGGCTGGTACGCTGACCGgcatacggaactgttcgctggaatatttacgcgcgcgataacgcagcgcaaagcggtccatacggtcaatctgcccggcaaacagacggtcctgcggtttgctgaacaccagtt                             >  1:432291‑M1/1‑29 (MQ=255)                                                                                                                   gCGGGATCAGGCTGGTACGCTGACCGgcatacggaactgttcgctggaatatttacgcgcgcgataacgcagcgcaaagcggtccatacggtcaatctgcccggcaaacagacggtcctgcggtttgctgaacaccagtttgc                          >  2:994718‑M1/1‑26 (MQ=255)                                                                                                                       gATCAGGCTGGTACGCTGACCGgcatacggaactgttcgctggaatatttacgcgcgcgataacgcagcgcaaagcggtccatacggtcaatctgcccggcaaacagacggtcctgcggtttgctgaacaccagtttgctatc                      >  2:149782‑M1/1‑22 (MQ=255)                                                                                                                       gATCAGGCTGGTACGCTGACCGgcatacggaactgttcgctggaatatttacgcgcgcgataacgcagcacaaagcggtccatacggtcaatctgcccggcaaacagacggtcctgcggtttgctgaacaccagtttgcgatc                      >  1:731226‑M1/1‑22 (MQ=255)                                                                                                                         tCAGGCTGGTACGCTGACCGgcatacggaactgttcgctggaatatttacgcgcgcgataacgcagcgcaaagcggtccatacggtcaatctgcccggcaaacagacggtcctgcggtttgctgaacaccagtttgctatcaa                    <  1:588650‑M1/143‑124 (MQ=255)                                                                                                                          cAGGCGGGTACGCTGACCGgcatacggaactgttcgctggaatatttacgcgcgcgataacgcagcgcaaagcggtccatacggtcaatctgcccggcaaacagacggtcctgcggtttgctgaacaccagtttgctatcaag                   <  2:7912‑M1/143‑125 (MQ=255)                                                                                                                           aGGCTGGTACGCTGACCGgcatacggaactgttcgctggaatatttacgcgcgcgataacgcagcgcaaagcggtccatacggtcaatctgcccggcaaacagacggtcctgccatttgctgcacaccagctcgctatcaagg                  >  2:347575‑M1/1‑18 (MQ=255)                                                                                                                            ggCTGGTACGCTGACCGgcatacggaactgttcgctggaatatttacgcgcgcgataacgcagcgcaaagcggtcgatacggtccatctgcccggcaaacagacggtactgcggtttgctggacacaaggttgcttacaagga                 >  2:279869‑M1/1‑17 (MQ=255)                                                                                                                            ggCTGGCACGCTGAGCGgcagacggcactgttcgctggaatatttacgcgcgcgataacgcagcgcaaagcggtccatacggtcaatctgccgggcaaacagacggtcctgcggtttgctgaataccagtttgctatcaagga                 <  2:831763‑M1/143‑127 (MQ=255)                                                                                                                             gCTGGTACGCTGACCGgcatacggaactgttcgctggaatatttacgcgcgcgataacgcagcgcaaagcggtccatacggtcaatctgcccggcaaacagacggtcctgcggtttgctgaacaccagttccgtatcaaggaa                >  2:543467‑M1/1‑16 (MQ=255)                                                                                                                                 gTACGCTGACCGgcatacgtaactgttcgctgaaatatttacgcgcgcgataacgcagcgcaaagcggtccatacggtcaatctgcccggcaaacagacggtcctgcggtttgctgaacaccagtttgctatcaaggaaaact            <  1:277529‑M1/143‑132 (MQ=255)                                                                                                                                   aCGCTGACCGgcctacggaactgttcgttggaatatttacgcgcgcgataacgcagcgcaaagcggtccatacggtcaatctgcccggcaaacagacggtcctgcggtttgctgaacaccagtttgctatcaaggaaaacttc          <  2:728559‑M1/143‑134 (MQ=255)                                                                                                                                       tGACCGgcatacggaactgttcgctggaatatttacgcgcgcgataacgcagcgcaaagcggtccatacggtcaatctgcccggcaaacagacggtcctgcggtttgctgaacaccagtttgctatcaaggaaaacttcacgc      >  1:806935‑M1/1‑6 (MQ=255)                                                                                                                                          ccGgcatacggaactgttcgctggaatatttacgcgcgcgataacgcagcgcaaagcggtccatacggtcaatctgcccggcaaacagacggtcctgcggtttgctgaacaccagtttgctatcaaggaaaacttcacgcagg   <  2:665621‑M1/143‑141 (MQ=255)                                                                                                                                           cGgcatacggaactgttcgctggaatatttacgcgcgcgataacgccgcgcacagcggtccatacggtcaatctgcccggcaaacagacggtccagcggtttgctgcacacccgtttggtatcaaggcaacgttcacgcaggg  >  2:663229‑M1/1‑2 (MQ=255)                                                                                                                                            |                                                                                                                                              GTTGCTGATGCAGGATCATCCCGGCTTCAATGGTTTTCCCTAAACCCACTTCGTCAGCCAGCAGGACGCGCGGCGCGTGGCGGCGACCAACATCATGAGCGATGTTGAGCTGATGCGGGATCAGGCTGGTACGCTGACCGCGCAGGCCGCTGTACGGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGATAACGCAGCGCAAAGCGGTCCATACGGTCAATCTGCCCGGCAAACAGACGGTCCTGCGGTTTGCTGAACACCAGTTTGCTATCAAGG  >  NC_000913/62682‑62962

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: ‑