Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913	402,391	Δ723 bp	coding (645‑1367/1416 nt)	phoA →	alkaline phosphatase

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	402391	403113	723	34 [0]	[0] 34	phoA	alkaline phosphatase

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 402390	0 (0.000)	34 (0.620)	31/482	0.7	100%	coding (644/1416 nt)	phoA	alkaline phosphatase
	?	NC_000913	403114 =	0 (0.000)					coding (1368/1416 nt)	phoA	alkaline phosphatase

GTGTCAAAACCTATAACGGCGCGCTGGGCGTCGATATTCACGAAAAAGATCACCCAACGATTCTGGAAATGGCAAAAGCCGCAGGTCTGGCGACCGGTAACGTTTCTACCGCAGAGTTGCAGGATGCCACGCCCGCTGCGCTGGTGGCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAACAGCTGCTTAACGCTCGTGCCGACGTTACGCTTGGCGGCGGCGCAAAAACCTTTGCTGAAACGGCAACCGCTGGTGAATGGCAGGGAAAAACGCTGCGTGAACAGGCACAGGCGCGTGGTTATCAGTTGGTGAGCGATGCTGCCTCACTGAATTCGGTGACGGAAGCGAATCAGCAAAAACCCCTGCTTGGCCTGTTTGCTGACGGCAATATGCCAGTGCGCTGGCTAGGACCGAAAGCA  >  NC_000913/402147‑402631                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                                  gtgtCAAAACCTATAACGGCGCGCTGGGCGTCGATATTCACGAAAAAGATCACCCAACGATTCTGGAAATGGCAAAAGCCGCAGGTCTGGCGACCGGTAACGTTTCTACCGCAGAGTTGCAGGATGCCACGCCCGCTGCGCTGGTGGCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagacc                                                                                                                                                                                                                                            <  2:152121‑M1/251‑8 (MQ=255)     cAAATCCTATAACGGCGCGCTGGTCGTCGATATTCACGAAAAAGATCTCCCAACGATTCTGGAAATGGCAAAAGCCGCAGGTCTGGCGACCGGTAACGTTTCTTCCGCAGAGTTGCAGGATGCCACGCCCGCTGCGCTGGTGGCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGTCCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatc                                                                                                                                                                                                                                        <  1:82920‑M1/251‑12 (MQ=255)             ataACGGCGCGCTGGGCGTCGATATTCACGAAAAAGATCACCCAACGATTCTGGAAATGGCAAAAGCCGCAGGTCTGGCGACCGGTAACGTTTCTACCGCAGAGTTGCAGGATGCCACGCCCGCTGCGCTGGTGGCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctac                                                                                                                                                                                                                                >  1:191841‑M1/1‑232 (MQ=255)                          gggCGTCGATATTCACGAAAAAGATCACCCAACGATTCTGGAAATGGCAAAAGCCGCAGGTCTGGCGACCGGTAACGTTTCTACCGCAGAGTTGCAGGATGCCACGCCCGCTGCGCTGGTGGCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaaagc                                                                                                                                                                                                                     <  1:375258‑M1/249‑31 (MQ=255)                              gTCGATATTCACGAAAAAGATCACCCAACGATTCTGGAAATGGCAAAAGCCGCAGGTCTGGCGACCGGTAACGTTTCTACCGCAGAGTTGCAGGATGCCACGCCCGCTGCGCTGGTGGCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaaagccgctct                                                                                                                                                                                                               >  1:179416‑M1/1‑215 (MQ=255)                                  atatTCACGAAAAAGATCACCCAACGATTCTGGAAATGGCAAAAGCCGCAGGTCTGGCGACCGGTAACGTTTCTACCGCAGAGTTGCAGGATGCCACGCCCGCTGCGCTGGTGGCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaaagccgctctgggg                                                                                                                                                                                                           >  1:12940‑M1/1‑211 (MQ=255)                                  atatTCACGAAAAAGATCACCCAACGATTCTGGAAATGGCAAAAGCCGCAGGTCTGGCGACCGGTAACGTTTCTACCGCAGAGTTGCAGGATGCCACGCCCGCTGCGCTGGTGGCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaaagccgctctgggg                                                                                                                                                                                                           >  1:519468‑M1/1‑211 (MQ=255)                                       cACGAAAAAGATCCCCCAACGATTCTGGAAATGGCAAAAGCCGCAGGTCTGGCGACCGGTAACGTTTCTACCGCAGAGTTGCAGGATGCCACGCCCGCTGCGCTGGTGGCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaaagccgctctggggctga                                                                                                                                                                                                       <  2:376745‑M1/250‑45 (MQ=255)                                            aaaaGATCACCCAACGATTCTGGAAATGGCACAAGCCGCAGGTCTGGCGACCGGTAACGTTTCTACCGCAGAGTTGCAGGATGCCACGCCCGCTGCGCTGGTGGCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagcccgatctcttctacaccatgaaagccgctctggggctgaaataa                                                                                                                                                                                                  >  2:338477‑M1/1‑201 (MQ=255)                                                          cGATTCTGGAAATGGCAAAAGCCGCAGGTCTGGCGACCGGTAACGTTTCTACCGCAGAGTTGCAGGATGCCACGCCCGCTGCGCTGGTGGCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaaagccgctctggggctgaaataaaaccgcgcccggcag                                                                                                                                                                                   <  2:314315‑M1/251‑65 (MQ=255)                                                                          aaaaGCCGCAGGTCTGGCGACCGGTAACGTTTCTACCGCAGAGTTGCAGGATGCCACGCCCGCTGCGCTGGTGGCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaaagccgctctggggctgaaataaaaccgcgcccggcagtgaattttcgctgccg                                                                                                                                                                   >  1:486081‑M1/1‑171 (MQ=255)                                                                                         ggCGACCGGTAACGTTTCTACCGCAGAGTTGCAGGATGCCACGCCCGCTGCGCTGGTGGCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatcgcgtctacaccatgaaagccgctctggggctgaaataaaaccgcgcccggcagtgaattttcgcggccggggggtttttttg                                                                                                                                                      <  2:83442‑M1/249‑94 (MQ=255)                                                                                                                       gCAGGATGCCACGCCCGCTGCGCTGGTGGCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaaagccgctctggggctgaaataaaaccgcgcccggcagtgaattttcgctgccgggtggtttttttgctgttagcaaccagacttaatggcagatcacg                                                                                                                      <  1:555918‑M1/251‑126 (MQ=255)                                                                                                                        cAGGATGCCACGCCCGCTGCGCTGGTGGCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaaagccgctctggggctgaaataaaaccgcgcccggcagtgaattttcgctgccgggtggtttttttgctgttagcaaccagacttaatggcagatcacgg                                                                                                                     >  1:191576‑M1/1‑125 (MQ=255)                                                                                                                                  cGCCCGCTGCGCTGGTGGCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaaagccgctctggggctgaaataaaaccgcgcccggcagtgaattttcgctgccgggtggtttttttgctgttagcaaccagacttaatggcagatcacgggcgcatacgc                                                                                                           <  1:181545‑M1/251‑137 (MQ=255)                                                                                                                                           cgctgGTGGCACATGTGACCGCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaaagccgctctggggctgaaataaaaccgcgcccggcagtgaattttcgctgccgggtggtttttttgctgttagcaaccagacttaatggcagatcacgggcgcatacgctcatggtta                                                                                                  <  2:114681‑M1/251‑146 (MQ=255)                                                                                                                                                gtggCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaaagccgctctggggctgaaataaaaccgcgcccggcagtgaattttcgctgccgggtggtttttttgctgttagcaaccagacttaatggcagatcacgggcgcatacgctcatggttaaaac                                                                                              >  1:106872‑M1/1‑101 (MQ=255)                                                                                                                                                            aCCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaaagccgctctggggctgaaataaaaccgcgccaggcagtgaattttcgctgccgggtggtttttttgctgttagcaaccagacttaatggcagatcacgggcgcatacgctcatggttaaaacttgaagagggatg                                                                                 >  2:491037‑M1/1‑89 (MQ=255)                                                                                                                                                                cgcgCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaaagccgctctggggctgaaataaaaccgcgcccggcagtgaattttcgctgccgggtggtttttttgctgttagcaaccagacttaatggcagatcacgggcgcatacgctcatggttaaaacatgaagagggatggtg                                                                              <  2:15388‑M1/250‑166 (MQ=255)                                                                                                                                                                           tACGGTCCGAGCGCGACCAGTGAAAAATGGCCGGGTAACGCTCTGGAAAAAGGCAGAAAAGGATCGATTACCGAccagaccgatctcttctacaccaggaaagccgctctggggctgaaataaaaccgcgcccggcagtgaattttcgctgccgggtggtttttttgctgttagcaaccagacttaatggcagatcacgggcgcatacgctcatggttaaaacatgaagagggatggttctatgaaaata                                                                   <  2:59316‑M1/250‑177 (MQ=255)                                                                                                                                                                                           ccAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaaagccgctctggggctgaaataaaaccgcgcccggcagtgaattttcgctgccgggtggtttttttgctgttagcaaccagacttaatggcagatcacgggcgcatacgctcatggttaaaacatgaagagggatggtgctatgaaaataacattactggttacctt                                                  >  1:73417‑M1/1‑58 (MQ=255)                                                                                                                                                                                              gggaaAAATGGCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaaagccgctctggggctgaaataaaaccgcgcccggcagtgaattttcgctgccgggtggtttttttgctgttagcaaccagacttaatggcagatcacgggcgcatacgctcatggttaaaacaggaagagggatggtgctatgaaaataacattactggttaccttgct                                               <  1:335791‑M1/249‑197 (MQ=255)                                                                                                                                                                                                gAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaaagccgctctggggctgaaataaaaccgcgcccggcagtgaattttcgctgccgggtggtttttttgctgttagcaaccagacttaatggcagatcacgggcgcatacgctcatggttaaaacatgaagagggatggtgctatgaaaataacattactggttaccttgctt                                              <  2:558091‑M1/250‑198 (MQ=255)                                                                                                                                                                                                  aaaaTGTCCGGGTCACGATCTGGACAAAGGCGGCAAAGGATAGATTACAGAccagaccgatctcttctacaccatgaaagccgctctggggctgaaataaaaccgcgcccggcagtgaattttcgctgccgggtggtttttttgctgttagcaaccagacttaatggcagataacgggcgcataagctcatggttaaaacatgacgagggatggtgctaagaaaataacattactggttaccttgcttttt                                           >  2:389642‑M1/1‑51 (MQ=255)                                                                                                                                                                                                   aaaTGTCCGTGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaaagccgcgctggggctgaaataaaaccgcgcccggcagtgaatgttcgctgccgggtggttttttggctgttagcaaccagacttaatggcagatcacgggcgcagacgctcatggttaaagcattaagagggatggtgctatgaaaataacattactggttaccttgcttttcg                                          <  1:82704‑M1/251‑202 (MQ=255)                                                                                                                                                                                                         ccGGGTAACGCTCTTGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaaagccgctctggggctgaaataaaaccgcgcccggcagtgaattttcgctgccgggtggtttttttgctgttagcaaccagacttaatggcagatcacgggcgcatacgctcatggttaaaacatgaagagggatggtgctatgaaaataacattactggttaccttgcttttcggtctgg                                    <  1:461624‑M1/251‑208 (MQ=255)                                                                                                                                                                                                          cGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaaagccgctctggggctgaaataaaaccgcgcccggcagtgaattttcgctgccgggtggtttttttgctgttagcaaccagacttaatggcagatcacgggcgcatacgctcatggttaaaacatgaagagggatggtgctatgaaaataacattactggttaccttgcttttcggtctggt                                   >  1:307919‑M1/1‑43 (MQ=255)                                                                                                                                                                                                          cGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaaagccgctctggggctgaaataaaaccgcgcccggcagtgaattttcgctgccgggtggtttttttgctgttagcaaccagacttaatggcagatcacgggc                                                                                                                   <  1:498341‑M1/171‑129 (MQ=255)                                                                                                                                                                                                          cGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaaagccgctctggggctgaaataaaaccgcgcccggcagtgaattttcgctgccgggtggtttttttgctgttagcaaccagacttaatggcagatcacgggc                                                                                                                   >  2:498341‑M1/1‑43 (MQ=255)                                                                                                                                                                                                              tAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaaagccgctctggggctgaaataaaaccgcgcccggcagtgaattttcgctgccgggtggtttttttgctgttagcaaccagacttaatggcagatcacgggcgcatacgctcatggttaaaacatgaagagggatggtgctatgaaaataacattactggttaccttgcttttcggtctggttttt                               >  1:37565‑M1/1‑39 (MQ=255)                                                                                                                                                                                                              tAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaaagccgctctggggctgaaataaaaccgcgcccggcagtgaattttcgctgccgggtggtttttttgctgttagcaaccagacttaatggcagatcacgggcgcatacgctcatggttaaaacatgaagagggatggtgctatgaaaataacattactggttaccttgcttttcggtctggttttt                               >  2:19152‑M1/1‑39 (MQ=255)                                                                                                                                                                                                                                        gATCGATTACCGGccagaccgatctcgtctacgccatgaaagccgctctggggctgaaataaacccgcgcccggcagtgaattttcgctgccgggtggtttttttgatgttagcaaccagacttaatggcagatcacgggcgcatacgctcatggttaaaacatgaagagggatggtgctatgaaaataacattactggttaccttgcttttcggtctggtttttttaaccaccgtcggcgctgccgagag     <  1:96685‑M1/251‑239 (MQ=255)                                                                                                                                                                                                                                         aTCGATTACCGAccagaccgatctcttctacaccatgaaagccgctctggggctgaaataaaaccgcgcccggcagtgaattttcgctgccgggtggtttttttgctgttagcaaccagccttaatggcagatcacgggcgcatacactcatggttaaaacatgaagagggatggtgctatgaaaataacattactggttaccttgcttttcggtctggtatttttaaccaccgtcggcgctgccgag       >  1:490881‑M1/1‑12 (MQ=255)                                                                                                                                                                                                                                           cGATTACCGAccagaccgatctcttctacaccatgaaagccgctctggggctgaaataaaaccgcgcccggcagtgaattttcgctgccgggtggtttttttgctgttagcaaccagacttaatggcagatcacgggcgcatacgctcatggttaaaacatgaagagggatggtgctatgaaaataacattactggttaccttgcttttcggtctggtttttttaaccaccgtcggcgctgccgagagaac  <  1:428995‑M1/251‑242 (MQ=255)                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                                  GTGTCAAAACCTATAACGGCGCGCTGGGCGTCGATATTCACGAAAAAGATCACCCAACGATTCTGGAAATGGCAAAAGCCGCAGGTCTGGCGACCGGTAACGTTTCTACCGCAGAGTTGCAGGATGCCACGCCCGCTGCGCTGGTGGCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAACAGCTGCTTAACGCTCGTGCCGACGTTACGCTTGGCGGCGGCGCAAAAACCTTTGCTGAAACGGCAACCGCTGGTGAATGGCAGGGAAAAACGCTGCGTGAACAGGCACAGGCGCGTGGTTATCAGTTGGTGAGCGATGCTGCCTCACTGAATTCGGTGACGGAAGCGAATCAGCAAAAACCCCTGCTTGGCCTGTTTGCTGACGGCAATATGCCAGTGCGCTGGCTAGGACCGAAAGCA  >  NC_000913/402147‑402631

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑