Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913	4,124,266	Δ103 bp	coding (89‑191/1026 nt)	cytR ←	DNA‑binding transcriptional repressor CytR

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	4124266	4124368	103	28 [0]	[1] 29	cytR	DNA‑binding transcriptional repressor CytR

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 4124265	0 (0.000)	28 (1.030)	27/460	0.2	100%	coding (192/1026 nt)	cytR	DNA‑binding transcriptional repressor CytR
	?	NC_000913	4124369 =	0 (0.000)					coding (88/1026 nt)	cytR	DNA‑binding transcriptional repressor CytR

TACGCTGTTCCTCAATGCTGGCATCAAACGGCAGCCTTGAACCCAGCAACAACATGCCATCAATTTGCTTGGTGATGATCAAATCGATAAAGGTTTTTTCCTGCTG‑ATTTTGATGCGCACAGTCGCCAATCAGCACCAGATATCCGTGATTTGCCGCCGTAACTTCGATACCGCGAATAATTTCGCTAAAGAAGGGATCGCAGATATCCGGGACAATCACCAGAATGGTGCGGGATTCATTACGCTTGACGTTGCGCCCCATAGGCTGCGGTAAATAACCCACTTCCCGGGCCGCTTTTTCAACCCGATTACGGGTGGCCTGGGAGACTTTATCGGGATTCATTAATGCTCGGGAGACGGTCGCTGTAGAGACTTTTGCCTTGAGGGCAACGTCTTTCATGGTCGCGGCAGTTTCCTGCTTCTTCGCTTTCACACTCACTCCTCGCCTGGCACGTCAGGC  >  NC_000913/4124024‑4124483                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                           tACGCTTTTCCTCAATGCTGGCATCAAACGGCAGCCTTGAACCCAGCAACAACAGGCCATCAATTTGCTTGGTGATGATCAAATCGATAAAGGTTTTTTCCTGCTG‑ATTTTGATGCTCAAAGTCGCCAATCAGCACCAGATATCCGTGATTTGCCGCCGTAACTTCGATACCGCGAATAATTTCGCTAAAGAAGGGATCGCAGATATCCGGGACAATCACCAGAATGGTGCGGGATTCATTAatgctcgg                                                                                                                                                                                                                    <  2:187711‑M1/250‑9 (MQ=255)   cGCTGTTCCTCAATGCTGGCATCAAACGGCAGCCTTGAACCCAGCAACAACATGCCATCAATTTGCTTGGTGATGTTCAAATCGATAAAGGTTTTTTCCTGCTG‑ATTTTGATGCGCACAGTCGCCAATCAGCACCAGATATCCGTGATTTGCCGCCGTAACTTCGATACCGCGAATAATTTCGCTAAAGAAGGGATCGCAGATATCCGGGACAATCACCAGAATGGTGCGGGATTCATTAatgctcgggag                                                                                                                                                                                                                 <  1:80967‑M1/251‑12 (MQ=255)       gTTCCTCAATGCTGGCATCAAACGGCAGCCTTGAACCCAGCAACAACATGCCATCAATTTGCTTGGTGATGATCAAATCGATAAAGGTTTTTTCCTGCTG‑ATTTTGATGCGCACAGTCGCCAATCAGCACCAGATATCCGTGATTTGCCGCCGTAACTTCGATACCGCGAATAATTTCGCTAAAGAAGGGATCGCAGATATCCGGGACAATCACCAGAATGGTGCGGGATTCATTAatgctcgggagacgg                                                                                                                                                                                                             <  2:9837‑M1/251‑16 (MQ=255)       gTTCCTCAATGCTGGCATCAAACGGCAGCCTTGAACCCAGCAACAACATGCCATCAATTTGCTTGGTGATGATCAAATCGATAAAGGTTTTTTCCTGCTG‑ATTTTGATGCGCACAGTCGCCAATCAGCACCAGATATCCGTGATTTGCCGCCGTAACTTCGATACCGCGAATAATTTCGCTAAAGAAGGGATCGCAGATATCCGGGACAAGCTCCAGAATGGTGCGGGATTCATTAatgctcgggagacg                                                                                                                                                                                                              <  1:13434‑M1/250‑15 (MQ=255)       gTTCCTCAATGCTGGCATCAAACGGCAGCCTTGAACCCAGCAACAACATGCCATCAATTTGCTTGGTGATGATCAAATCGATAAAGGTTTTTTCCTGCTG‑ATTTTGATGCGCACAGTCGCCAATCAGCACCAGATATCCGTGAGTTGCCGCCGTAACTTCGATACCGCGAATAATTTCGCTAAAGAAGGGATCGCAGATATCCGGGACAATCACCAGAATGGTGCGGGATTCATTAatgctcgggagac                                                                                                                                                                                                               <  1:207838‑M1/249‑14 (MQ=255)                           accggCATCCTTGAACCCAGCCACAACATGTCATCAATGTGCTGGGTGATGTTCAAATCGATAAAGGTTTTTTCCTG‑TGTATTTTTATGCGCACAGTCGCCAATCAGCACCAGATATCCGGGATTTGCCGCCGTAACTTCGATACCGCGAATAATTTCGCTAAAGAAGTGATCGCAGATATCCGGGACAATCACCAGAATGGCGCGGGATTCATTAattctcgggagacggtcgctgcagcgacttttgcc                                                                                                                                                                                         <  2:181246‑M1/249‑36 (MQ=255)                                      tGAACCCAGCAACAACATGCCATCAATTTGCTTGGTGATGATCAAATCGATAAAGGTTTTTTCCTGCTG‑ATTTTGATGCGCACAGTCGCCAATCAGCACCAGATATCCGTGATTTGCCGCCGTAACTTCGATACCGCGAATAATTTCGCTAAAGAAGGGATCGCAGATATCCGGGACAATCACCAGAATGGTGCGGGATTCATTAatgctcgggagacggtcgctgtagagacttttgccttgagggcaa                                                                                                                                                                               <  1:57394‑M1/250‑46 (MQ=255)                                                              aaTTTGCTTGGTGATGATCAAATCGATAAAGGTTTTTTCCTCATG‑ATTTTGATGCGCACCGTCGCCAATCAGCACCAGATATCCGTGATTTGCCGCCGTAACTTCGATACCGCGAATAATTTCGCTAAAGAAGGGATCGCAGATATCCGGGACAATCACCAGAATGGTGCGGGATTCATTAatgctcgggagacggtcgctgtagagacttttgccttgagggcaacgtctttcatggtcgcggcagtttc                                                                                                                                                      >  1:43378‑M1/1‑181 (MQ=255)                                                                 ttGCTTGGTGATGATCAAATCGATAAAGGTTTTTTCCTGCTG‑ATTTTGATGCGCACAGTCGCCAATCAGCACCAGATATCCGTGATTTGCCGCCGTAACTTCGATACCGCGAATAATTTCGCTAAAGAAGGGATCGCAGATATCCGGGACAATCACCAGAATGGTGCGGGATTCATTAatgctcgggagacggtcgctgtagagacttttgccttgagggcaacgtctttcatggtc                                                                                                                                                                 <  2:63092‑M1/237‑60 (MQ=255)                                                                 ttGCTTGGTGATGATCAAATCGATAAAGGTTTTTTCCTGCTG‑ATTTTGATGCGCACAGTCGCCAATCAGCACCAGATATCCGTGATTTGCCGCCGTAACTTCGATACCGCGAATAATTTCGCTAAAGAAGGGATCGCAGATATCCGGGACAATCACCAGAATGGTGCGGGATTCATTAatgctcgggagacggtcgctgtagagacttttgccttgagggcaacgtctttcatggtc                                                                                                                                                                 >  1:63092‑M1/1‑178 (MQ=255)                                                                                     cGATAAAGGTTTTTTCCGGCTG‑ATTTTGATGCGCACAGTCGCCAATCAGCCCCAGATATCTGTGATTTGCCGCCGTAACTTCGATACCGCGAATAATTTCGCTAAAGAAGGGATCGCAGATATCCGGGACAATCACCAGAATGGTGCGGGATTCATTAatgctcgggagacggtcgctgtagagacttttgccttgagggcaacgtctttcatggtcgcggcagtttcctgcttcttcgctttcacactca                                                                                                                               <  2:201389‑M1/251‑94 (MQ=255)                                                                                                      tgctg‑cTTTTGATGCGCACAGTCGCCAATCAGCACCAGATATCCGTGATTTGCCGCCGTAACTTCGATACCGCGAATAATTTCGCTAAAGAAGGGATCGCAGATATCCGGGACAATCACCAGAATGGTGCGGGATTCATTAatgctcgggagacggtcgctgtagagacttttgccttgagggcaacgtctttcatggtcgcggcagtttcctgcttcttcgctttcacactcactcctcgcctggcacgg                                                                                                              >  2:48812‑M1/1‑141 (MQ=255)                                                                                                                             cGCCAATCAGCACCAGATATCCGTGATTTGCCGCCGTAACGTCGATACCGCGAATAATTTCGCTAAAGAAGGGATCGCAGATATCCGGGACAATCACCAGAATGGTGCGGGATTCATTAatgctcgggagacggtcgctgtagagacttttgccttgagggcaacgtctttcatggtcgcggcagtttcctgcttcttcgctttcacactcactcctcgcctggcacgtcaggcgtactacatccatgttt                                                                                        <  1:104095‑M1/251‑133 (MQ=255)                                                                                                                                                 ccGTGATTTGCCGCCGTAACTTCGATACCGCGAATAATTTCGCTAAAGAAGGGATCGCAGATATCCGGGACAATCACCAGAATGGTGCGGGATTCATTAatgctcgggagacggtcgctgtagagacttttgccttgagggcaacgtctttcatggtcgcggcagtttcctgcttcttcgctttcacactctctcctcgcctggcacgtcaggcgtactacatccatgtttacttcacatcggcaacatt                                                                     <  1:96072‑M1/250‑152 (MQ=255)                                                                                                                                                 ccGTGATTTGCCGCCGTAACTTCGATACCGCGAATAATTTCGCTAAAGAAGGGATCGCAGATATCCGGGACAATCACCAGAATGGTGCGGGATTCATTAatgctcgggagacggtcgctgtagagacttttgccttgagggcaacgtctttcatggtcgcggcagtttcctgcttcttcgctttcacactcactcctcgcctggcacgtcaggcgtactacatccatgtttacttcacatcggcaacatt                                                                     <  1:97926‑M1/250‑152 (MQ=255)                                                                                                                                                         tGCCGCCGTAACTTCGATACCGCGAATAATTTAGCTAAAGAAGGGATCGCAGATGTCCGGGACAATCACCAGAATGGTGCGGGATTCATTActgctcgggagacggtcgctgtagagacttttgccttgagggcaacgtctttcatggtcgcggcagtttcctgcttcttcgctttcacactcactcctcgcctggcacgtcaggagtactacatccatgtttacttcacatcggcaacatttttagc                                                               >  1:184828‑M1/1‑91 (MQ=255)                                                                                                                                                                  aaCTTCGATACCGCGAATAATTTCGCTAAAGAAGGGATCGCAGATATCCGGGACAATCACCAGAATGGTGCGGGATTCATTAatgctcgggagacggtcgctgtagagacttttgccttgagggcaacgtctttcatggtcgcggcagtttcctgcttcttcgctttcacactcactcctcgcctggcacgtcaggcgtactacatccatgtttacttcacatcggcaacatttttagcagatagcgcgtg                                                   <  1:287730‑M1/251‑170 (MQ=255)                                                                                                                                                                                   taatTTCGCTAAAGAAGGGATCGCAGATATCCGGGACAATCACCAGAATGGTGCGGGATTCATTAatgctcgggagacggtcgctgtagagacttttgccttgagggcaacgtctttcatggtcgcggcagtttcctgcttcttcgctttcacactcactcctcgcctggcacgtcaggcgtactacatccatgtttacttcacatcggcaacatttttagcagatagcgcgtgaaaacggttacagaatt                                  >  1:55356‑M1/1‑65 (MQ=255)                                                                                                                                                                                     atTTCGTTAAAGAAGGGATCGCAGATATCCGGGACAATCACCAGAATGGTGCGGGATTCATTAatgctcgggagacggtcgctgtagagacttttgccttgagggcaacgtctttcatggtcgcggcagtttcctgcttcttcgctttcacactcactcctcgcctggcacgtcaggcgtactacatccatgtttacttcacatcggcaacatttttagcagatagcgcgtgaaaacggttacagaatttt                                >  1:92585‑M1/1‑63 (MQ=255)                                                                                                                                                                                           cTAAAGAAGGGATCGCAGATATCCGGGACAATCACCAGAATGGTGCGGGATTCATTAatgctcgggagacggtcgctgtagagacttttgccttgagggcaacgtctttcatggtcgcggcagtttcctgcttcttcgctttcacactcactcctcgcctggcacgtcaggcgtactacatccatgtttacttcacatcggcaacatttttagcagatagcgcgtgaaaacggttacagaattttcatga                           >  2:250340‑M1/1‑57 (MQ=255)                                                                                                                                                                                             aaaGAAGGGATCGCAGATATCCGGGACAATCACCAGAATGGTGCGGGATTCATTAatgctcgggagacggtcgctgtagagacttttgccttgagggcaacgtctttcatggtcgcggcagtttcctgcttcttcgctttcacacgcactcctcgcctggcacgtcaggcgtactacatccatgtttacttcacatcggcaacatttttagcagatagcgcgtgaaaacggttacagaattttcatgaaa                         <  1:51270‑M1/250‑196 (MQ=255)                                                                                                                                                                                               agaagGGATCGCAGATATCCGGGACAATCACCAGAATGGTGCGGGATTCATTAatgctcgggagacggtcgctgtagagacttttgccttgagggcaacgtctttcatggtcgcggcagtttcctgcttcttcgctttcacactcactcctcgcctggcacgtcaggcgtactacatccatgtttacttcacatcggcaacatttttagcagatagcgcgtgaaaacggttacagaattttcatgaaaagt                      <  1:250340‑M1/251‑199 (MQ=255)                                                                                                                                                                                                gaagGGATCGCAGATATCCGGGACAATCACCAGAATGGTGCGGGATTCATTAatgctcgggagacggtcgctgtagagacttttgccttgagggcaacgtctttcatggtcgcggcagtttcctgcttcttcgctttcacactcactcctcgcctggcacgtcaggcgtactacatccatgtttacttcacatcggcaacatttttagcagatagcgcgtgaaaacggttacagaattttcatgaaaagtg                     >  2:214730‑M1/1‑52 (MQ=255)                                                                                                                                                                                                 aagGGATCGCAGATATCCGGGACAATCACCAGAATGGTGCGGGATTAATTAatgctcgggagacggtcgctgtagagacttttgccttgagggcaacgtctttcatggtcgcggcagtttcctgcttcttcgctttcacactcactcctcgcctggcacgtcaggcgtactacatccatgtttacttcacatcggcaacatttttagcagatagcgcgtgaaaacggttacagacttttcatgaaaagtgt                    >  2:35871‑M1/1‑51 (MQ=255)                                                                                                                                                                                                      aTCGCAGATATCCGGGACAATCACCAGACTGGTGCGGGATTCATTAatgctcgggagacggtcgctgtagagacttttgccttgagggcaacgtctttcatggtcgcggcagtttcctgcttcttcgctttcacactcactcctcgcctggcacgtcaggcgtactacatccatgtttacttcacatcggcaccatttttagcagatagcgcgtgaaaacggttacagaattttcatgaaaagtgtgatg                >  2:305075‑M1/1‑46 (MQ=255)                                                                                                                                                                                                                  cGGGACAATCACCAGAATGGTGCGGGATTCCTTAatgctcgggagacggtcgctgtagagacttttgccttgagggcaacgtctttcatggtcgcggcagtttcctgcttcttcgctttcacactcactcctcgcctggcacgtcaggcgtactacatccatgtttacttcacatcggcaacatttttagcagatagcgcgtgaaaacggttccagaattttcatgaatagtgtgatgaatattgaatttt   >  1:293588‑M1/1‑34 (MQ=255)                                                                                                                                                                                                                   gggACAATCACCAGAATGGTGCGGGATTCATTAatgctcgggagacggtcgctgtagagacttttgccttgagggcaacgtctttcatggtcgcggcagtttcctgcttcttcgctttcacactcactcctcgcctggcacgtcaggcgtactacatccatgtttacttcacatcggcaacatttttagcagatagcgagttaaaacgtttacagaattttcatgaaaagtgtgatgaatattgaattttt  <  2:313105‑M1/251‑219 (MQ=255)                                                                                                                                                                                                                                    ggTGCGGGATTCATTAatgctcgggagacggtcgctgtagagacttttgccttgagggcaacgtctttcatggtcgcggcagtttcctgcttcttcgctttcacactcactcctcgcctggcacgtcaggcgtactacatccatgtttacttcacatcggca                                                                          <  1:208575‑M1/162‑147 (MQ=255)                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                           TACGCTGTTCCTCAATGCTGGCATCAAACGGCAGCCTTGAACCCAGCAACAACATGCCATCAATTTGCTTGGTGATGATCAAATCGATAAAGGTTTTTTCCTGCTG‑ATTTTGATGCGCACAGTCGCCAATCAGCACCAGATATCCGTGATTTGCCGCCGTAACTTCGATACCGCGAATAATTTCGCTAAAGAAGGGATCGCAGATATCCGGGACAATCACCAGAATGGTGCGGGATTCATTACGCTTGACGTTGCGCCCCATAGGCTGCGGTAAATAACCCACTTCCCGGGCCGCTTTTTCAACCCGATTACGGGTGGCCTGGGAGACTTTATCGGGATTCATTAATGCTCGGGAGACGGTCGCTGTAGAGACTTTTGCCTTGAGGGCAACGTCTTTCATGGTCGCGGCAGTTTCCTGCTTCTTCGCTTTCACACTCACTCCTCGCCTGGCACGTCAGGC  >  NC_000913/4124024‑4124483

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑