Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913	257,908	Δ776 bp		insB9–[crl]	insB9, insA9, [crl]

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	257908–258675	258683	9–776	77 [0]	[0] 77	insB9–[crl]	insB9,insA9,[crl]

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 257907	0 (0.000)	70 (2.100)	27/112	0.0	100%	intergenic (+8/+16)	crl/insB9	RNA polymerase holoenzyme assembly factor Crl/IS1 transposase B
	?	NC_000913	258684 =	0 (0.000)					pseudogene (9/331 nt)	crl	RNA polymerase holoenzyme assembly factor Crl

CTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACC  >  NC_000913/258620‑258747                                                                 |                                                                ggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaa                                                                 >  1:2671508‑M2/65‑65 (MQ=255)  gacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggaaAg                                                                >  1:1729940‑M2/64‑65 (MQ=255)   acacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGt                                                               <  1:1137645‑M2/3‑1 (MQ=255)   acacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGt                                                               >  1:860275‑M2/63‑65 (MQ=255)   acacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGt                                                               <  1:1759959‑M2/3‑1 (MQ=255)   acacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGt                                                               <  1:1378912‑M2/3‑1 (MQ=255)   acacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGt                                                               <  1:603578‑M2/3‑1 (MQ=255)   acacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGt                                                               <  1:350180‑M2/3‑1 (MQ=255)    cacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTg                                                              >  1:2882730‑M2/62‑65 (MQ=255)      cccgaagagcagatcgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCa                                                            >  1:1643654‑M2/60‑65 (MQ=255)        cgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCaaa                                                          <  1:1945041‑M2/8‑1 (MQ=255)        cgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCaaa                                                          <  1:663985‑M2/8‑1 (MQ=255)          aagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGa                                                        <  1:2976166‑M2/10‑1 (MQ=255)          aagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGa                                                        <  1:2670166‑M2/10‑1 (MQ=255)          aagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGa                                                        <  1:2494832‑M2/10‑1 (MQ=255)          aagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGa                                                        <  1:1326664‑M2/10‑1 (MQ=255)           agagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGAt                                                       <  1:2650740‑M2/11‑1 (MQ=255)             agcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgacggtaAGTGCAAAGATaa                                                     >  1:2555511‑M2/53‑65 (MQ=255)             agcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATaa                                                     >  1:1017776‑M2/53‑65 (MQ=255)             agcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATaa                                                     >  1:2076308‑M2/53‑65 (MQ=255)             agcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATaa                                                     >  1:1100051‑M2/53‑65 (MQ=255)             agcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATaa                                                     >  1:2604488‑M2/53‑65 (MQ=255)             agcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATaa                                                     >  1:2471401‑M2/53‑65 (MQ=255)             agcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATaa                                                     >  1:1758229‑M2/53‑65 (MQ=255)             agcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATaa                                                     >  1:1164463‑M2/53‑65 (MQ=255)              gcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAAt                                                    <  1:537011‑M2/14‑1 (MQ=255)                  attgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGAt                                                <  1:566063‑M2/18‑1 (MQ=255)                   ttgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGAtt                                               >  1:1229260‑M2/47‑65 (MQ=255)                     gatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCt                                             <  1:2783847‑M2/21‑1 (MQ=255)                      atcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCtt                                            <  1:2454620‑M2/22‑1 (MQ=255)                              atttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGAtt                                    <  1:1594919‑M2/30‑1 (MQ=255)                              atttaccgcaccaggcccgcatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGAtt                                    <  1:778887‑M2/30‑1 (MQ=255)                                ttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGt                                  <  1:848806‑M2/32‑1 (MQ=255)                                ttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGt                                  <  1:1635217‑M2/32‑1 (MQ=255)                                gtaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGt                                  <  1:2954945‑M2/32‑1 (MQ=255)                                    cgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTgg                              <  1:1764423‑M2/36‑1 (MQ=255)                                    cgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTgg                              <  1:25671‑M2/36‑1 (MQ=255)                                    cgcactaggcacgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTgg                              <  1:2143000‑M2/36‑1 (MQ=255)                                      cgctaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCt                            <  1:2576488‑M2/38‑1 (MQ=255)                                      cactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCt                            <  1:1993823‑M2/38‑1 (MQ=255)                                      cactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCt                            <  1:280918‑M2/38‑1 (MQ=255)                                      cactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCt                            <  1:2959168‑M2/38‑1 (MQ=255)                                      cactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCt                            <  1:929896‑M2/38‑1 (MQ=255)                                        ctaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGt                          <  1:1072336‑M2/40‑1 (MQ=255)                                        ctaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGt                          <  1:2278855‑M2/40‑1 (MQ=255)                                        ctaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGt                          <  1:2013318‑M2/40‑1 (MQ=255)                                        ctaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGt                          <  1:1640473‑M2/40‑1 (MQ=255)                                        ctaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGt                          <  1:1152437‑M2/40‑1 (MQ=255)                                        ctaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGt                          <  1:191663‑M2/40‑1 (MQ=255)                                        ctaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGt                          <  1:1252259‑M2/40‑1 (MQ=255)                                          aggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTAt                        <  1:1561494‑M2/42‑1 (MQ=255)                                            gcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGc                      <  1:949911‑M2/44‑1 (MQ=255)                                            gcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGc                      <  1:564608‑M2/44‑1 (MQ=255)                                            gcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGc                      <  1:1566863‑M2/44‑1 (MQ=255)                                             cccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCg                     <  1:2917470‑M2/45‑1 (MQ=255)                                             cccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCg                     >  1:1650361‑M2/21‑65 (MQ=255)                                             cccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCg                     >  1:1969047‑M2/21‑65 (MQ=255)                                             cccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCg                     >  1:2682683‑M2/21‑65 (MQ=255)                                             cccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCg                     >  1:689335‑M2/21‑65 (MQ=255)                                             cccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCg                     >  1:520415‑M2/21‑65 (MQ=255)                                             cccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCg                     >  1:1322179‑M2/21‑65 (MQ=255)                                             cccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCg                     <  1:1496282‑M2/45‑1 (MQ=255)                                             cccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCg                     >  1:583182‑M2/21‑65 (MQ=255)                                             cccgcatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGGatggg                     >  1:2033135‑M2/21‑63 (MQ=255)                                                  atattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAAc                >  1:50992‑M2/16‑65 (MQ=255)                                                    attcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGt              >  1:158169‑M2/14‑65 (MQ=255)                                                    attcgtgaaggtaAGTGCAAAGAGAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTGTACGt              >  1:331985‑M2/14‑65 (MQ=255)                                                      tcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGa            >  1:2496967‑M2/12‑65 (MQ=255)                                                       cgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGaa           >  1:2891885‑M2/11‑65 (MQ=255)                                                       cgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGaa           >  1:250284‑M2/11‑65 (MQ=255)                                                         tgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAAc         >  1:116324‑M2/9‑65 (MQ=255)                                                            aggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCgg      <  1:1401656‑M2/60‑1 (MQ=255)                                                             ggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGc     >  1:2831585‑M2/5‑65 (MQ=255)                                                              gtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCa    <  1:492689‑M2/62‑1 (MQ=255)                                                                aAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCAcc  <  1:6331‑M2/64‑1 (MQ=255)                                                                aAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCAcc  <  1:541449‑M2/64‑1 (MQ=255)                                                                aAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCAcc  <  1:1294511‑M2/64‑1 (MQ=255)                                                                 |                                                                CTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACC  >  NC_000913/258620‑258747

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑