Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	CP009273	354,080	Δ9 bp	coding (314‑322/900 nt)	cynR ←	transcriptional activator of cyn operon; autorepressor

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	CP009273	354080	354088	9	38 [0]	[0] 40	cynR	transcriptional activator of cyn operon; autorepressor

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	= 354079	0 (0.000)	37 (0.670)	22/134	0.7	100%	coding (323/900 nt)	cynR	transcriptional activator of cyn operon; autorepressor
	?	CP009273	354089 =	0 (0.000)					coding (313/900 nt)	cynR	transcriptional activator of cyn operon; autorepressor

CTCCTGCGACATTTCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTAAAGGTGGGGGTGACGGCGATACGCAGCGATCCTCGCGTCAGATCGG  >  CP009273/354012‑354145                                                                    |                                                                   ctcCTGCGACATTTCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAgg                                                                    <  1:4001249/68‑1 (MQ=255)   ccTGCGTGATTTCCTGTAGCTGGAGGGTGATGCTGGGATAGCGCGCATAGAACTCCGCCATTAAGGag                                                                  >  1:1764107‑M1/1‑66 (MQ=255)   ccTGCGACATTTCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGag                                                                  >  1:438070‑M1/1‑66 (MQ=255)   ccTGCGACATTTCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCAGCCATTAAGGag                                                                  >  1:4096864‑M1/1‑66 (MQ=255)      gCGACATTTCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGagtag                                                               <  1:2934847‑M1/68‑6 (MQ=255)      gCGACATTTCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGagtag                                                               <  1:2201544‑M1/68‑6 (MQ=255)         aCATTTCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGagtagctc                                                            <  1:1757383‑M1/68‑9 (MQ=255)           aTTTCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGagtagctcgt                                                          <  1:3778441‑M1/68‑11 (MQ=255)             ttCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGagtagctcgtaa                                                        >  1:1690439‑M1/1‑56 (MQ=255)                cTGTAGCTGGAGCGTGATGCTGGGTTAGCGCGCATAGAAATCCGCCATTAAGGagtagctcgtaaagg                                                     <  1:4686891‑M1/68‑16 (MQ=255)                    aGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGagtagctcgtaaaggtggg                                                 >  1:1644240‑M1/1‑49 (MQ=255)                     gCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGagtagctcgtaaaggtgggg                                                >  1:26014‑M1/1‑48 (MQ=255)                     gCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGagtagctcgtaaaggtgggg                                                >  1:4085115‑M1/1‑48 (MQ=255)                     gCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGagtagctcgtaaaggtgggg                                                >  1:2088408‑M1/1‑48 (MQ=255)                         gAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGagaagctcgtaaaggtgggggtga                                            >  1:1093409‑M1/1‑44 (MQ=255)                             gTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGagtagctcgtaaaggtgggggtgacggc                                        <  1:3293276‑M1/68‑29 (MQ=255)                                 tGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGagtagctcgtaaaggtgggggtgacggcgata                                    >  1:2257786‑M1/1‑36 (MQ=255)                                       gATAGCGCGCATAGAAATCCGCCATTAAGGagtagctcgtaaaggtgggggtgacggtgatacgcagc                              >  1:2465347‑M1/1‑30 (MQ=255)                                        aTAGCGCGCATAGAAATCCGCCATTAAGGagtagctcgtaaaggtgggggtgacggcgatacgcagcg                             >  1:328638‑M1/1‑29 (MQ=255)                                        aTAGCGCGCATAGAAATCCGCCATTAAGGagtagctcgtaaaggtgggggtgacggcgatacgcagcg                             >  1:1154678‑M1/1‑29 (MQ=255)                                         tAGCGCGCATAGAAATCCGCCATTAAGGagtagctcgtaaaggtgggggtgacggcgatccgcagcga                            >  1:450531‑M1/1‑28 (MQ=255)                                         tAGCGCGCATAGAAATCCGCCATTAAGGagtagctcgtaaaggtgggggtgacggcgatacgcagcga                            >  1:3720763‑M1/1‑28 (MQ=255)                                            cgcgcATAGAAATCCGCCATTAAGGagtagctcgtaaaggtgggggtgacggcgatacgcagcgatcc                         >  1:3843870‑M1/1‑25 (MQ=255)                                                   aGAAATCCGCCATTAAGGagtagctcgtaaaggtgggggtgacggcgatacgcagcgatcctcgcgtc                  >  1:1738893‑M1/1‑18 (MQ=255)                                                         ccGCCATTAAGGagtagctcgtaaaggtgggggtgacggcgatacgcagcgatcctcgcgtcagatcg            >  1:31262‑M1/1‑12 (MQ=255)                                                         ccGCCATTAAGGagtagctcgtaaaggtgggggtgacggcgatacgcagcgatcctcgcgtcagatcg            <  1:320516‑M1/68‑57 (MQ=255)                                                         ccGCCATTAAGGagtagcgcgtaaaggtgggggtgacggcgatacgcagcgatcctcgcgtcagatcg            <  1:314249‑M1/68‑57 (MQ=255)                                                           gCCATTAAGGagtagctcgtaaaggtgggggtgacggcgatacgcagcgatcctcgcgtcagatcggc          >  1:1119943‑M1/1‑10 (MQ=255)                                                            agattAAGGagtagctcgtaaaggtgggggtgacggcgatacgcagcgatcctcgcgtcagatcggca         <  1:2817488‑M1/66‑60 (MQ=255)                                                               ttAAGGagtagctcgtaaaggtgggggtgacggcgatacgcagcgatcctcgcgtcagatcggcaaca      <  1:3898301‑M1/68‑63 (MQ=255)                                                               ttAAGGagtagctcgtaaaggtgggggtgacggcgatacgcagcgatcctcgcgtcagatcggcaaca      <  1:2551434‑M1/68‑63 (MQ=255)                                                                tAAGGagttgctcgtaaaggtgggggtgacggcgatacgcagcgatcctcgcgtcagatcggcaacat     <  1:1184669‑M1/68‑64 (MQ=255)                                                                tAAGGagtagctcgtaaaggtgggggtgacggcgatacgcagcgatcctcgcgtcagatcggcaacat     <  1:27279‑M1/68‑64 (MQ=255)                                                                tAAGGagtagctcgtaaaggtgggggtgacggcgatacgcagcgatcctcgcgtcagatcggcaacat     <  1:4351097‑M1/68‑64 (MQ=255)                                                                tAAGGagtagctcgtaaaggtgggggtgacggcgatacgcagcgatcctcgcgtcagatccgcaacat     <  1:2022799‑M1/68‑64 (MQ=255)                                                                   ggagtagctcgtaaaggtgtgggtgacggcgatacgcagcgatcctcgcgtcagttcggcaacatcat  >  1:2008217‑M1/1‑2 (MQ=255)                                                                   ggagtagctcgtaaaggtgggggtgacggcgatacgcagcgatcctcgcgtcagatcggcaacatcat  >  1:2929631‑M1/1‑2 (MQ=255)                                                                   ggagtagctcgtaaaggtgggggtgacggcgatacgcagcgatcctcgcgtcagatcggcaacatcat  >  1:253511‑M1/1‑2 (MQ=255)                                                                    |                                                                   CTCCTGCGACATTTCCTGTAGCTGGAGCGTGATGCTGGGATAGCGCGCATAGAAATCCGCCATTAAGGGGCCGATAAAGTAGCTCGTAAAGGTGGGGGTGACGGCGATACGCAGCGATCCTCGCGTCAGATCGG  >  CP009273/354012‑354145

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑