Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
MC JC	CP009273	1,613,357	Δ20 bp	100%	intergenic (‑192/‑1)	marC ← / → marR	UPF0056 family inner membrane protein/transcriptional repressor of multiple antibiotic resistance

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	CP009273	1613357	1613376	20	15 [0]	[0] 15	marC/marR	UPF0056 family inner membrane protein/transcriptional repressor of multiple antibiotic resistance

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	= 1613356	0 (0.000)	13 (0.740)	11/242	NT	100%	intergenic (‑191/‑21)	marC/marR	UPF0056 family inner membrane protein/transcriptional repressor of multiple antibiotic resistance
	?	CP009273	1613377 =	0 (0.000)					coding (1/435 nt)	marR	transcriptional repressor of multiple antibiotic resistance

AAAGTATAAGGGGTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGCATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAATTCATTCATTTGACTTATACTTGCCTGGGCAATATTATCCCCTGCAACTAATTACTTGCCAGGGCAACTAATGTGAAAAGTACCAGCGATCTGTTCAATGAAATTATTCCATTGGGTCGCTTAATCCATATGGTTAATCAGAAGAAAGATCGCCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGCGGCACAGTTTAAGGTGCTCTGCTCTATCCGCTGCG  >  CP009273/1613203‑1613530                                                                                                                                                                               |                                                                                                                                                          tgtatctgggttatcagcgaaaagtataaggggtaaacaaggataaagtgtcactctttagctagccttgcatcgcattgaacaaaacttgaaccgatttagcaaaacgtggcatcggtcaattcattcatttgacttatacttgcctgggcaatattatcccttgcaactaatGTGAAAAGTNCCAGCGATCTGTTCAATGAAATTATTCCATTGGGTCGCTTAATCCATATGGTTAATCAGAAGAAAGATCGCCTGCTTAACGAGTATCTGt                                                        >  1:317793‑M2/175‑274 (MQ=255)   tatctgggttatcagcgaaaagtataaggggtaaacaaggataaagtgtcactctttagctagccttgcatcgcattgaacaaaacttgaaccgatttagcaaaacgtggcatcggtcaattcattcatttgacttatacttgcctgggcaatattatcccctgcaactaatGTGAAAAGTACCAGCGATCTGTTCAATGaa                                                                                                                              >  1:153605‑M2/173‑202 (MQ=255)       tgggttatcagcgaaaagtataaggggtaaacaaggataaagtgtcactctttagctagccttgcatcgcattgaacaaaacttgaaccgatttagcaaaacgtggcatcggtcaattcattcatttgacttatacttgcctgggcaatattatcccctgcaactaatGTGAAAAGTACCAGCGATCTGTTCAATGAAatta                                                                                                                          <  2:153600‑M2/34‑1 (MQ=255)                                            aaaagtgtaaaattttagatagacttgcatcgcattgaccaaaactttaaccgatttagcaaaacgtggcatcggtcaattcattcatttgacttatacttgcctgggcaatattatcccctgcaactaatGTGAAAAGTACCAGCGATCTGTTCAATGAAATTATTCCATTGGGTCGCTTAATCCATATGGTTAATCAGAAGAAAGATCGCCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGCGGCACAGTTTAAGGTgctctgctct            <  2:317787‑M2/144‑1 (MQ=255)                                                   tcactctttagctagccttgcatcgcattgaacataacttgaaccgatttagcaaaacgtggcatcggtcaattcattcatttgacttatacttgcctgggcaatattatcccctgcaactaatGTGAAAAGTACCAGCGATCTGTTCAATGAAATTATTCCATTGGGTCGCTTAATCCATATGGTTAATCAGaagaaaga                                                                               >  1:276150‑M2/125‑201 (MQ=255)                                                      ctctttatctagccttgcattgcattgattaaaacttgaaccgagttagcaaagcgttgcatcggtcaattcattcatttgacttatacttgcctgggcaatattatcccctgcaactaatGTGAAAAGTACCAGCGATCTGTTCAATGAAATTATTCCATTGGGTCGCTTAATCCATATGGTTAATCAGAAGAAAGATCGCCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGCGGCACAGTTTAAGGTGCTCTGCTCTATCCGCTgcg  <  1:83464‑M2/154‑1 (MQ=255)                                                       tctttagctagccttgcatcgcattgaacaaaacttgaaccgatttagcaaaacgtggcatcggtcaattcattcatttgacttatacttgcctgggcaatattatcccctgcaactaatGTGAAAAGTACCAGCGATCTGTTCAATGAAATTATTCCATTGGGTCGCTTAATCCATATGGTTAATCAGAAGAAAGATCGc                                                                           <  2:276145‑M2/81‑1 (MQ=255)                                                              ctagccttgcatcgcattgaacaaaacttgaaccgatttagcaaaacgtggcatcggtcaattcattcatttgacttatacttgcctgggcaatattatcccctgcaactaatGTGAAAAGTACCAGCGATCTGTTCAATGAAATTATTCCATTGGGTCGCTTAATCCATATGGTTAATCAGAAGAAAGATCGCCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGCGGCACAGTTTAAGGTGCTCTGCTCTATCCGc      >  2:390168‑M2/114‑263 (MQ=255)                                                                 gccttgcatcgcattgaacaaaacttgaaccgatttagcaaaacgtggcatcggtcaattcattcatttgacttatacttgcctgggcaatattatcccctgcaactaatGTGAAAAGTACCAGCGATCTGTTCAATGaa                                                                                                                              >  2:359887‑M2/111‑140 (MQ=255)                                                                  ccttgcatcgcattgaacaaaacttgaaccgatttagcaaaacgtggcatcggtcaattcattcatttgacttatccttgcctgggcaatattatcccctgcaactaatGTGAAAAGTACCAGCGATCTGTTCAATGAAATTATTCCATTGGGTCGCTTAATCCATATGGTTAATCAGAAGAAAGATCGCCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGCGGCACAGTTTAAGGTGCTCTGCTCGATCCGCTgcg  <  1:390174‑M2/154‑1 (MQ=255)                                                                     tgcatcgcattgaacaaaacttgaaccgatttagcaaaacgtggcatcggtcaattcattcatttgacttatacttgcctgggcaatattatcccctgcaactaatGTGAAAAGTACCAGCGATCTGTTCAATGAAatta                                                                                                                          <  1:359893‑M2/34‑1 (MQ=255)                                                                                      aacttgaaccgatttagcaaaacgtggcatcggtcaattcattcatttgacttatacttgcctgggcaatattatcccctgcaactaatGTGAAAAGTACCAg                                                                                                                                              >  1:373412‑M2/90‑103 (MQ=255)                                                                                          tgaaccgatttagcaaaacgtggcatcggtcaattcattcatttgacttatacttgcctgggcaatattatcccctgcaactaatGTGAAAAGTACCAGCGAt                                                                                                                                          <  2:373406‑M2/18‑1 (MQ=255)                                                                                                                                                                          ctaatGTGAAAAGTACCAGCGATCTGTTCAATGAAATTATTCCATTGGGTCGCTTAATCCATATGGTTAATCAGAAGAAAGATCGCCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACcgc                                     >  2:293612‑M2/6‑124 (MQ=255)                                                                                                                                                                              tGTGAAAAGTACCAGCGATCTGTTCAATGAAATTATTCCATTGGGTCGCTTAATCCATATGGTTAATCAGAAGAAAGATCGCCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACTGCGGca                                 <  1:293618‑M2/123‑1 (MQ=255)                                                                                                                                                                               |                                                                                                                                                          AAAGTATAAGGGGTAAACAAGGATAAAGTGTCACTCTTTAGCTAGCCTTGCATCGCATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAATTCATTCATTTGACTTATACTTGCCTGGGCAATATTATCCCCTGCAACTAATTACTTGCCAGGGCAACTAATGTGAAAAGTACCAGCGATCTGTTCAATGAAATTATTCCATTGGGTCGCTTAATCCATATGGTTAATCAGAAGAAAGATCGCCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGCGGCACAGTTTAAGGTGCTCTGCTCTATCCGCTGCG  >  CP009273/1613203‑1613530

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑