Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913	401,670	Δ728 bp		[phoA]	[phoA]

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	401670	402397	728	37 [3]	[7] 41	[phoA]	[phoA]

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 401669	3 (0.070)	34 (0.810)	32/470	0.3	88.4%	intergenic (+23/‑78)	iraP/phoA	anti‑adaptor protein IraP/alkaline phosphatase
	?	NC_000913	402398 =	6 (0.140)					coding (652/1416 nt)	phoA	alkaline phosphatase

CAAAAAGAAGAAGAGTCGAAAGAACTGTGTGCGCAGGTAGAAGCTTTGGAGATTATCGTCACTGCAATGCTTCGCAATATGGCGCAAAATGACCAACAGCGGTTGATTGATCAGGTAGAGGGGGCGCTGTACGAGGTAAAGCCCGATGCCAGCATTCCTGACGACGATACGGAGCTGCTGCGCGATTACGTAAAGAAGTTATTGAAGCATCCTCGTCAGTAAAAAGTTAATCTTTTCAACAGCTGTCATAAAGTTGTCACGGCCGAGACTTATAGTCGCTTTGTTTTTATTTTTTAATGTATTTGTACATGGAGAAAATAAAGTGAAACAAAGCACTATTGCACTGGCACTCTTACCGTTACTGTTTACCCCTGTGACAAAAGCCCGGACACCAGAAATGCCTGTTCTGGAAAACCGGGCTGCTCAGGGCGATATTACTGCACCCGGCGGTGCTCGCCGTTTAACGGGTGATCAGACTGC  >  NC_000913/401425‑401904                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                            cAAAAAGAAGAAGAGTCGAAAGAACTGTGTGCGCAGGTAGAAGCTTTGGAGATTATCGTCACTGCAATGCTTCGCAATATGGCGCAAAATGACCAACAGCGGTTGATTGATCAGGTAGAGGGGGCGCTGTACGAGGTAAAGCCCGATGCCAGCATTCCTGACGACGATACGGAGCTGCTGCGCGATTACGTAAAGAAGTTATTGAAGCATCCTCGTCAGTAAAAAGTTAATCTTTTCAACAGCTGcttaac                                                                                                                                                                                                                                       >  1:437659‑M1/1‑245 (MQ=255)      agaagaagaGTCGAAAGAACTGTGTGCGCAGGTAGAAGCTTTGGAGATTATCGTCACTGCAATGCTTCGCAATATGGCGCAAAATGACCAACAGCGGTTGATTGATCAGGTAGAGGGGGCGCTGTACGAGGTAAAGCCCGATGCCAGCATTCCTGACGACGATACGGAGCTGCTGCGCGATTACGTAAAGAAGTTATTGAAGCATCCTCGTCAGTAAAAAGTTAATCTTTTCAACAGCTGcttaacgctcg                                                                                                                                                                                                                                  <  1:284‑M1/251‑12 (MQ=255)                           gtgtgCGCAGGTAGAAGCTTTGGAGATTATCGTCACTGCAATGCTTCGCAATATGGCGCAAAATGACCAACAGCGGTTGATTGATCAGGTAGAGGGGGCGCTGTACGAGGTAAAGCCCGATGCCAGCATTCCTGACGACGATACGGAGCTGCTGCGCGATTACGTAAAGAAGTTATTGAAGCATCATCGTCAGTAAAAAGTTAATCTTTTCAACAGCTGcttaacgctcgtgccgacgttacgcttggcgg                                                                                                                                                                                                             >  1:382280‑M1/1‑219 (MQ=255)                                  cAGGTAGAAGCTTTGGAGATTATCGTCACTGCAATGCTTCGCAATATGGCGCAAAATGACCAACAGCGGTTGATTGATCAGGTAGAGGGGGCGCTGTACGAGGTAAAGCCCGATGCCAGCATTCCTGACGACGATACGGAGCTGCTGCGCGATTACGTAAAGAAGTTATTGAAGCATCCTCGTCAGTAAAAAGTTAATCTTTTCAACAGCTGcttaacgctcgtgccgacgttacgcttggcggcggcgca                                                                                                                                                                                                      <  1:411156‑M1/251‑40 (MQ=255)                                       aGAAGCTTTGGAGATTATCGTCACTGCAATGCTTCGCAATATGGCGCAAAATGACCAACAGCGGTTGATTGATCAGGTAGAGGGGGCGCTGTACGAGGTAAAGCCCGATGCCAGCATTCCTGACGACGATACGGAGCTGCTGCGCGATTACGTAAAGAAGTTATTGAAGCATCCTCGTCAGTAAAAAGTTAATCTTTTCAACAGCTGcttaacgctcgtgccgacgttacgcttggcggcggcgcaaaaac                                                                                                                                                                                                 <  1:449356‑M1/251‑45 (MQ=255)                                              ttGGAGATTAGCGTCAATGCAATGCTACGCAATATGGCGCAAAATGACCAACAGCGGTTGATTGAACAGGTAGAGGGGGCGCTGTACGAGGTAAAGCCCGATGCCAGAATTCCTGACGACGATACGGAGCTGCTGCGCGATTACGTAAAGAAGTTATTGAAGCATCTTCGTCAGTAAAAAGTTAATCTTTTCAACAGCTGcttaacgctcgtgccgacgttacgcttggcggcggcgcaaaaaccgttgc                                                                                                                                                                                           <  2:10182‑M1/250‑51 (MQ=255)                                                          gTCACTGCAAAGCTTCGCAATATGGCGCAAAATGACCAACAGCGGTTGATTGATCAGGTAGAGGGGGCGCTGTACGAGGTAAAGCCCGATGCCAGCATTCCTGACGACGATACGGAGCTGCTGCGCGATTACGTAAAGAAGTTATTGAAGCATCCTCGTCAGTAAAAAGTTAATCTTTTCAACAGCTGcttaacgctcgtgccgacgttacgcttggcggcggcgcaaaaacctttgctgaaacggcaacc                                                                                                                                                                              <  2:335222‑M1/251‑64 (MQ=255)                                                           tCACTGCAATGCTTCGCAATATGGCGCAAAATGACCAACAGCGGTTGATTGATCAGGTAGAGGGGGCGCTGTACGAGGTAAAGCCCGATGCCAGCATTCCTGACGACGATACGGAGCTGCTGCGCGATTACGTAAAGAAGTTATTGAAGCATCCTCGTCAGTAAAAAGTTAATCTTTTCAACAGCTGTCATAAAGTTGTCACGGCCGAGACTTATAGTCGCTTTGTTTTTATTTTTTAATGTATTTGTat                                                                                                                                                                              >  1:204899/1‑249 (MQ=255)                                                                gCAATGCTTCGCAATATGGCGCAAAATGACCAACAGCGGTTGATTGATCAGGTAGAGGGGGCGCTGTACGAGGTAAAGCCCGATGCCAGCATTCCTGACGACGATACGGAGCTGCTGCGCGATTACGTAAAGAAGTTATTGAAGCATCCTCGTCAGTAAAAAGTTAATCTTTTCAACAGCTGcttaacgctcgtgccgacgttacgcttggcggcggcgcaaaaacctttgctgaaacggcaaccgctggt                                                                                                                                                                        <  1:265886‑M1/251‑70 (MQ=255)                                                                   aTGCTTCGCAATATGGAGCAAAATGACCAACAGCGGTTGATTGATCAGGTAGAGGGGGCGCTGTACGAGGTAAAGGCCGATGCCAGCATTCCTGAAGACGATACGGAGCTGCTGCGCGATTACGTAAAGAAGTTATTGAAGCATCCTCGTCAGTAAAGAGTTAATCTTTTCAACAGATGcttaacgctcgtaccgacgatacgcgtggctgaggagcaaacacctttgctgaaccggacaccgctcgggc                                                                                                                                                                      >  2:163650‑M1/1‑179 (MQ=255)                                                                             atatGGGGCAAAAGGTACAACAGCTGTTGATTGACTATGTAGAGGGGGAGCTGTAAGAGGTAAATACCGATGCCAGCATTCCTGACGACGATACGGATCTGCTGCGCTATTACGTAAAGAAGTTATTGAAGCATCCTCGTCAGTAAAAAGCTAATCTTTTCAACAGCTGcttaacgtgcgtgccgacgttacgcttggcggcggcgcaaaaaccttggctgaaacggcaaccgctggtgaatggcagggaa                                                                                                                                                           <  2:18656‑M1/251‑83 (MQ=255)                                                                                     cAAAATGACCAACAGCGGTTGATTGATCAGGTAGAGGGGGCGCTGTACGAGGTAAAGCCCGATGCCAGCATTCCTGACGACGATACGGAGCTGCTGCGCGATTACGTAAAGAAGTTATTGAAGCATCCTCGTCAGTAAAAAGTTAATCTTTTCAACAGCTGcttaacgctcgtgccgacgttacgcttggcggcggcgcaaaaacctttgctgaaacggcaaccgctggtgaatggcagggaaaaacgctg                                                                                                                                                   <  1:49540‑M1/251‑91 (MQ=255)                                                                                            aCCAACATCGGTTGATTGATCAGGTAGAGGGGGCGCTGTACGAGGGAGTCCCCGATGCCTTCATTCCTGACGACGTTACGGAGCTGCTGCGCGATTACGTAAAGAAGTTATTGAAGCATCCTCGTCAGTAAAAAGTTAATCTTTTCAACAGCTGtttaacgctcgtgccgacgttactcttggcggcggcgcaaaaacctttgctgaaacggcaaccgcgggtgaatggcagggaaatacgcggcgtgaac                                                                                                                                            <  2:278727‑M1/251‑98 (MQ=255)                                                                                                    cGGTTGATTGATCAGGTAGAGGGGGCGCTGTACGAGGTAAAGCCCGATGCCAGCATTCCTGACGACGATACGGAGCTGCTGCGCGATTACGTAAAGAAGTTATTGAAGCATCCTCGTCAGTAAAAAGTTAATCTTTTCAACAGCTGcttaacgctcgtgccgacgttacgcttggcggcggcgcaaaaacctttgctgaaacggcaaccgctggtgaatggccgggaaaaacgctgcgtgaacaggcaa                                                                                                                                      >  2:349368‑M1/1‑146 (MQ=255)                                                                                                                     agagGGGGCGCTGTACGAGGTAAAGCCCGATGCCAGCATTCCTGACGACGATACGGAGCTGCTGCGCGATTACGTAAAGAAGTTATTGAAGCATCCTCGTCAGTAAAAAGTTAATCTTTTCAACAGCTGcttaacgctcgtgccgacgttacgcttggcggcggcgcaaaaacctttgctgaaacggcaaccgctggtgaatggcagggaaaaacgctgcgtgaacaggcacaggcgcgtggttatcagtt                                                                                                                   <  2:437659‑M1/251‑123 (MQ=255)                                                                                                                     agagGGGGCGCTGTACGAGGTAAAGCCCGATGCCAGCATTCCTGACGACGATACGGAGCTGCTGCGCGATTACGTAAAGAAGTTATTGAAGCATCCTCGTCAGTAAAAAGTTAATCTTTTCAACAGCTGcttaacgctcgtgccgacgttacgcttggcggcggcgcaaaaacctttgctgaaacggcaaccgctggtgaatggcagggaaaaacgctgcgtgaacaggcacaggcgcgtggttatcagtt                                                                                                                   <  1:94584‑M1/251‑123 (MQ=255)                                                                                                                                      aGGTAAAGCCCGATGCCAGCATTCCTGACGACGATACGGAGCTGCTGCGCGATTACGTAAAGAAGTTATTGAAGCATCCTCGTCAGTAAAAAGTTAATCTTTTCAACAGCTGcttaacgctcgtgccgacgttacgcttggcggcggcgcaaaaacctttgctgaaacggcaaccgctggtgaatggcagggaaaaacgctgcgtgaacaggcacaggcgcgtggttatcagttggtgagcgatgctgcct                                                                                                  <  1:184609‑M1/251‑140 (MQ=255)                                                                                                                                        gTAAAGCCCGATGCCAGCATTCCTGACGACGATACGGAGCTGCTGCGCGATTACGTAAAGAAGTTATTGCAGCCTCCTCGTCAGTAAAAAGTTAATCTTTTCAACAGCTGcttaacgctcgggccgccgttacgcttggcggcggcgcaaaaacctttgcggaaacggcaaccgctggtgaatggcagggaaaaacgctgcgtgaacaggcacaggcgcgtggttatcagttggtgagcgatgctgcctca                                                                                                <  1:313884‑M1/251‑142 (MQ=255)                                                                                                                                        gTAAAGCCCGATGCCAGCATTCCTGACGACGATACGGAGCTGCTGCGCGATTACGTAAAGAAGTTATTGAAGCATCCTCGTCAGTAAAAAGTTAATCTTTTCAACAGCTGcttaacgctcgtgccgacgttacgcttggcggcggcgcaaaaacctttgctgaaacggcaaccgctggtgaatggcagggaaaaacgctgcgtgaacaggcacaggcgcgtggttatcagttggtgagcgatgctgcctca                                                                                                <  1:463076‑M1/251‑142 (MQ=255)                                                                                                                                                                   gacgaTACGGAGCTGCTGCGCGATTACGTAAAGAAGTTATTGAAGCATCCTCGTCAGTAAAAAGTTAATCTTTTCAACAGCTGcttaacgctcgtgccgacgttacgcttggcggcggcgcaaaaacctttgctgaaacggcaaccgctggtgaatggcagggaaaaacgctgcgtgaacaggcacaggcgcgtggttatcagttggtgagcgatgctgcctaactgaattcggtgacggaagcgaatc                                                                       >  1:298761‑M1/1‑83 (MQ=255)                                                                                                                                                                                 gctgcGCGATTACGTAAAGAAGTTATTGAAGCATCCTCGTCAGTAAAAAGTTAATCTTTTCAACAGCTGcttaacgctcgtgccgacgttacgcttggcggcggcgcaaaaacctttgctgaaacggcaaccgctggtgaatggcagggaaaaacgctgcgtgaacaggcacaggcgcgtggttatcagttggtgagcgatgctgcctcactgaattcggtgacggaagcgaatcagcaaaaacccctg                                                         <  1:418083‑M1/249‑181 (MQ=255)                                                                                                                                                                                    gcgcGATTACGTAAAGAAGTTATTGAAGCATCCTCGTCAGTAAAAAGTTAATCTTTTCAACAGCTGcttaacgctcgtgccgacgttacgcttggcggcggcgcaaaaacctttgctgaaacggcaaccgctggtgaatggcagggaaaaacgctgcgtgaacaggcacaggcgcgtggttatcagttggtgagcgatgctgcctcactgaattcggtgacggaagcgaatcagcaaaaacccctgcttg                                                     <  1:166798‑M1/250‑185 (MQ=255)                                                                                                                                                                                            aCGTAAAGAAGTTATTGAAGCATCCTCGTCAGTAAAAAGTTAATCTTTTCAACAGCTGcttaacgctcgtgccgacgttacgcttggcggcggcgcaaaaacctttgctgaaacggcaaccgctggtgaatggcagggaaaaacgctgcgtgaacaggcacaggcgcgtggttatcagttggtgagcgatgctgcctcactgaattcggtgacggaagcgaatcagcaaaaacccctgcttggcctgtttg                                            >  1:49413‑M1/1‑58 (MQ=255)                                                                                                                                                                                               tAAAGAAGTTATTGAAGCATCCTCGTCAGTAAAAAGTTAATCTTTTCAACAGCTGcttaacgctcgtgccgacgttacgcttggcggcggcgcaaaaacctttgctgaaacggcaaccgctggtgaatggcagggaaaaacgctgcgtgaacaggcacaggcgcgtggttatcagttggtgagcgatgctgcctcactgaattcggtgacggaagcgaatcagcaaaaacccctgcttggcctgtttgctg                                         >  1:185316‑M1/1‑55 (MQ=255)                                                                                                                                                                                                aaaGAAGTTATTGAAGCATCCTCGTCAGTAAAAAGTTAATCTTTTCAACAGCTGTCATAAAGTTGTCACGGCCGAGACTTATAGTCGCTTTGTTTTTATTTTTTAATGTATTTGTACATGGAGAAAATAAAGTGAAACAAAGCAc                                                                                                                                                  >  1:470585/1‑145 (MQ=255)                                                                                                                                                                                                aaaGAAGTTATTGAAGCATCCTCGTCAGTAAAAAGTTAATCTTTTCAACAGCTGTCATAAAGTTGTCACGGCCGAGACTTATAGTCGCTTTGTGTTTATTTTTTAATGTATTTGTACATGGAGAAAATAAAGTGAACCAAAGCAc                                                                                                                                                  <  2:470585/145‑1 (MQ=255)                                                                                                                                                                                                      gTTATTGAAGCATCCTCGTCAGTAAAAAGTTAATCTTTTCAACAGCTGcttaacgctcgtgccgacgttacgcttggcggcggcgcaaaaacctttgctgaaacggcaaccgctggtgaatggcagggaaaaacgcggcgtgaacaggcacaggcgcgtggttatcagttggtgagcgaggctgcctcaccgacgtcggggacggaagcgaatcagcaaaaacccctgcttggcctggtgtctgtaggca                                   >  2:357463‑M1/1‑48 (MQ=255)                                                                                                                                                                                                       ttATTGAAGCATACTCGTCAGTAAAAAGTTAATCTTTTCAACAGCTGcttaacgctcgtgccgacgttacgcttggcggcggcgcaaaaacctttgctgaaacggcaaccgctggtgaatggcagggaaaaacgctgcgtgaacaggcacaggcgcgtggttatcagttggtgagcgatgctgcctcactgaattcggtgacggaagcgaatcagcaaaaacccctgcttggcctgtttgctgacggcaat                                 >  1:95435‑M1/1‑47 (MQ=255)                                                                                                                                                                                                        aatTGAAGCATCCTCGACAGTAAAAAGTTAGTGTTTTCAACAGCTGcttaacgctcgtgccgacgttacggttggcggcggggaaaaaacctttgctgaaacggcaaccgctggtgaatggcagggaaaatcgctgcgttaacaggcacaggcgcgtggttatcaggtggtgagcgatgctgcctcactgaattcggtgatggaagcgaatcagcaaaaacccctgcttggcctgtttgctgacggcaata                                <  1:181700‑M1/250‑206 (MQ=255)                                                                                                                                                                                                         aTTGAAGCATCCTCGTCAGTACAAAGTTACTCTTTTCAACAGCTGcttaacgctcgtgccgacgttccgcttggcggcggcgcaaaaacctttgctgaacaggcaaccgctggtgactggcagggaaaaacgctccgtgaacaggaccagacgcgtggttatcagttggtgagcggtgctgcctcactgaattcggggacggaagcgcatccgcaaaaaccactgcttggcctggttgctgacggc                                    >  2:284872‑M1/1‑45 (MQ=255)                                                                                                                                                                                                         aTTGAAGCACCCTCGTAATTAAAAAGTTAATCTTTTCAACAGCTGcttaacgctcgtgccgccgttacgcttggcggcggcgcaaaaacctttgctgaaacggcaaccgctggtgaatggcagggaaaaacgctgcgtgaacaggcacaggcgcgtggttatcagttggtgagcgatgctgcctcactgaactcggtgacggaagcgaatcagcaaaaacccctgcttggcctgtttgctgacggc                                    <  1:284872‑M1/246‑202 (MQ=255)                                                                                                                                                                                                            gAAGCATCCTAGTCAGTAAAAAGTTAATCTTTTCAACAGCTGcttaacgcccgtgccgacgttacgcttggcggcggcgcaaaaacctttgctgaaacggcaaccgctggtgaatggcagggaaaaacgctgcgtgaacaggcacaggcgcgtggttatcagttggtgagcgatgctgcctcactgaattcggtgacggaagcgaatcagcaaaaacccctgcttggcctgtttgctgacggcaatatgc                             <  1:70923‑M1/250‑209 (MQ=255)                                                                                                                                                                                                                  tCCTCGTCAGTAAAAAGTTAATCTTTTCAACAGCTGcttaacgtccgggccgactttacgcttggcggcggcgcaaaaacctttgctgaaacggcaaccgctggtgaatggcagggaaaaacgctgcgtgaacaggcacaggcgcgtggttatcagttggtgagcgatgctgcctcactgaattcggtgacggaagcgaatcagcaaaaacccctgcttggcctgtttgctgacggcaatatgccagtgc                       <  1:184451‑M1/250‑215 (MQ=255)                                                                                                                                                                                                                    cTCGTGAGTAACAAGTTACTCTTTTCAACAGCTGcttaacgctcgtgccgacgttacgcttggcggcggcgcaaaaacctttgctgaaacggcaaccgctggagactggcagggaaaaacgctgcgtgaacaggcacaggcgcgtggctatcagttggtgagcgatgctgcctcactgaattcggtgacggaagcgaatcagcaaaaacccctgcttggcctgtttgctgacggcaatatgccagtgagcg                    >  2:194671‑M1/1‑34 (MQ=255)                                                                                                                                                                                                                          aGTAAAAAGTTAATCTTTTCAACAGCTGcttaacgctcgtgccgacgttacgcttggcggcggcgcaaaaacctttgctgaaacggcaaccgctggtgaatggcagggaaaaacgctgcgtgaacaggcacaggcgcgtggttatcagttggtgagcgatgctgcctcactgaattcggtgacggaagcgaatcagcaaaaacccctgcttggcctgtttgctgacggcaatatgccagtgcgctggctag              <  1:17927‑M1/251‑224 (MQ=255)                                                                                                                                                                                                                              aaaaGGTAATCTTTTCACCAGCTCcttaacgctcttgccgccgttacgcttcgcggcggcgcaaaatcctttgctttgaccgcacccgctggtgaatggcagggaaaaacgctgcgtgaacaggcacaggcgcgtttttatcagttggtgagcgatgctgcctcactgaattcgttgccggaagcgaatcagcaaaatcccctgcttggcctgtttgctgacggcaatatgccagtgcgctggctaggacc          <  1:188673‑M1/251‑228 (MQ=255)                                                                                                                                                                                                                                      atcatttcaacAGCTGcttaacgctcgtgccgacgttacgcttggcggcggcgcaaaaacctttgctgaaacggcaaccgctggtgaatggcagggaaaaacgctgcgggaacaggcacaggcgcgtggttagcagttggtgagcgatgctgcctcactgaattcggtgacggaagcgaatcagcaaaaccccctgcttggcctgtttgctgacggcaatatgtcagtgcgctggctaggaccgaaagcaa  <  2:61013‑M1/247‑236 (MQ=255)                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                            CAAAAAGAAGAAGAGTCGAAAGAACTGTGTGCGCAGGTAGAAGCTTTGGAGATTATCGTCACTGCAATGCTTCGCAATATGGCGCAAAATGACCAACAGCGGTTGATTGATCAGGTAGAGGGGGCGCTGTACGAGGTAAAGCCCGATGCCAGCATTCCTGACGACGATACGGAGCTGCTGCGCGATTACGTAAAGAAGTTATTGAAGCATCCTCGTCAGTAAAAAGTTAATCTTTTCAACAGCTGTCATAAAGTTGTCACGGCCGAGACTTATAGTCGCTTTGTTTTTATTTTTTAATGTATTTGTACATGGAGAAAATAAAGTGAAACAAAGCACTATTGCACTGGCACTCTTACCGTTACTGTTTACCCCTGTGACAAAAGCCCGGACACCAGAAATGCCTGTTCTGGAAAACCGGGCTGCTCAGGGCGATATTACTGCACCCGGCGGTGCTCGCCGTTTAACGGGTGATCAGACTGC  >  NC_000913/401425‑401904

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑