Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
MC JC	NC_000913	3,582,206	Δ1,222 bp	100%	IS1‑mediated	[yhhZ]–yrhA	[yhhZ], yrhA

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	3582206	3584130–3583427	1222–1925	108 [0]	[33] 36	[yhhZ]–[insB1]	[yhhZ], yrhA, insA, [insB1]

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 3582205	0 (0.000)	96 (1.020)	64/178	NT	100%	coding (343/1179 nt)	yhhZ	putative Hcp1 family polymorphic toxin protein; putative colicin‑like DNase/tRNase activity
	?	NC_000913	3583428 =	NA (NA)					noncoding (1/768 nt)	IS1	repeat region

GTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAA  >  NC_000913/3584102‑3584230                              |                                                                                                    gTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAtt                               <  1:1459251/100‑1 (MQ=31)     cTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTaata                           <  1:1766836/100‑3 (MQ=18)     cTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTaaaa                           >  2:878198/1‑100 (MQ=35)     cTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTaaaa                           <  2:1310946/100‑1 (MQ=35)     cTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTaaaa                           <  1:549528/100‑1 (MQ=35)      tGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAg                          <  1:1458381/100‑1 (MQ=38)      tGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAg                          <  1:300546/100‑1 (MQ=38)      ngTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAg                          >  2:1178417/2‑100 (MQ=38)       gTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCAGTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGt                         <  2:874213/100‑1 (MQ=255)        tCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTa                        <  1:1156041/100‑1 (MQ=40)          gTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAAc                      <  2:99580/100‑1 (MQ=255)           ttCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACt                     <  1:457550/100‑1 (MQ=255)            tctcAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTGAAAGTAACtt                    >  2:1703630/1‑100 (MQ=255)            tctcAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACtt                    >  2:2583934/1‑100 (MQ=255)             ctcAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACttt                   >  2:386551/1‑100 (MQ=255)               cAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACttttt                 >  1:850211/1‑100 (MQ=255)               cAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACttttt                 >  2:1403844/1‑100 (MQ=255)                aaaaTCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACtttttt                <  1:818601/100‑1 (MQ=255)                 aaaTCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTg               <  2:1342307/100‑1 (MQ=255)                  aagcGGTGGAGCTGCATGACAAAGTCATTGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCTACATTAAAAGTAACTTTTTTg               <  2:27849/96‑1 (MQ=255)                  aaTCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGa              >  1:1534379/1‑100 (MQ=255)                    tCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGaaa            <  2:920919/100‑1 (MQ=255)                      gggtgAGCTGCATGACAAAGTCATCGTGGAGTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACttttt                 <  2:1780816/89‑1 (MQ=17)                      ggTGGAGGTGCATGACAAAGTCATCGGGCAGTATCTGAACATAATACACTATCCGTAAGTTGCAGTCATTACCTACATTAAAAGTAACtttttt                <  2:2013693/94‑1 (MQ=17)                      ggTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAAtt          <  2:1008023/100‑1 (MQ=255)                      ggTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAAtt          >  2:676254/1‑100 (MQ=255)                        tGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTag        <  2:1809561/100‑1 (MQ=255)                        tGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTag        <  2:723463/100‑1 (MQ=255)                         ggAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTATCGACATTAAAAGTAACTCTTTTGAAATTaga       <  1:1750340/100‑1 (MQ=255)                         ggAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTaga       <  2:1161270/100‑1 (MQ=255)                          gAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTagag      <  1:802313/100‑1 (MQ=255)                          gAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTagag      <  2:512287/100‑1 (MQ=255)                            gCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGat    >  1:1133795/1‑100 (MQ=255)                              tGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGataa  >  1:2010975/1‑100 (MQ=255)                              tGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGataa  >  2:1234873/1‑100 (MQ=255)                              tGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGataa  >  1:639408/1‑100 (MQ=255)                              |                                                                                                    GTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAA  >  NC_000913/3584102‑3584230

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑