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]	[1] 35	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 (0.690)	31/474	0.5	100%	coding (644/1416 nt)	phoA	alkaline phosphatase
	?	NC_000913	403114 =	0 (0.000)					coding (1368/1416 nt)	phoA	alkaline phosphatase

AACCGGTGTCAAAACCTATAACGGCGCGCTGGGCGTCGATATTCACGAAAAAGATCACCCAACGATTCTGGAAATGGCAAAAGCCGCAGGTCTGGCGACCGGTAACGTTTCTACCGCAGAGTTGCAGGATGCCACGCCCGCTGCGCTGGTG‑GCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAACAGCTGCTTAACGCTCGTGCCGACGTTACGCTTGGCGGCGGCGCAAAAACCTTTGCTGAAACGGCAACCGCTGGTGAATGGCAGGGAAAAACGCTGCGTGAACAGGCACAGGCGCGTGGTTATCAGTTGGTGAGCGATGCTGCCTCACTGAATTCGGTGACGGAAGCGAATCAGCAAAAACCCCTGCTTGGCCTGTTTGCTGACGGCAATATGCCAGTGCGCTGGCTAGGAC  >  NC_000913/402142‑402623                                                                                                                                                                                                                                                          |                                                                                                                                                                                                                                          aaCCGGTGTCAAAACCTATAACGGCGCGCTGGGCGTCGATATTCACGAAAAAGATCACCCAACGATTCTGGAAATGGCAAAAGCCGCAGGTCTGGCGACCGGTAACGTTTCTACCGCAGAGTTGCAGGATGCCACGCCCGCTGCGCTGGTG‑GCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAcc                                                                                                                                                                                                                                         <  1:307945‑M1/251‑3 (MQ=255)             aaCCTATAACGGCGCGGTGGGCGTCGATAGTCAAGAAAAAGATCCCCCCACGATTCTGGAAATTGCAAAAGCCGCAGGTCTGGCGACCGGTAACGTTTCTACCGCAGAGGTGCAGGATGCCACGCCCGCTGCGCTGGTG‑GCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGGCCGGTTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTTCCGAccagaccgatctct                                                                                                                                                                                                                             <  2:439922‑M1/251‑15 (MQ=255)                cTATAACGGCGCGCTGGGCGTCGATATTCACGAAAAAGATCACCCAACGATTCTGGAAATGGCAAAAGCCGCAGGTCTGGCGACCGGTAACGTTTCTACCGCAGAGTTGCAGGATGCCACGCCCGCTGCGCTGGTG‑GCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttct                                                                                                                                                                                                                          >  2:227155‑M1/1‑234 (MQ=255)                             cTGGGCGTCGATATTCACGAAAAAGATCACCCAACGATTCTGGAAATGGCAAAAGCCGCAGGTCTGGCGACCGGTAACGTTTCTACCGCAGAGTTGCAGGATGCCACGCCCGCTGCGCTGGTG‑GCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaaagc                                                                                                                                                                                                             >  1:48269‑M1/1‑221 (MQ=255)                                  cGTCTATATGCACGAAAAAGATCACCCAACGATTCTGGAAATGGCAAAAGCCGCAGGTCTGGCGACCGGTAACGTTTCTACCGCAGAGGTGCAGGATGCCACGCCCGCTGCGCTGGTG‑GCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagtccgatctcttctacaccacgaaagccgctc                                                                                                                                                                                                        <  2:360862‑M1/251‑36 (MQ=255)                                     cGATATTCACGAAAAAGATCACCCAACGATTCTGGAAATGGCAAAAGCCGCAGGTCTGGCGACCGGTAACGTTTCTACCGCAGAGTTGCAGGATGCCACGCCCGCTGCGCTGGTG‑GCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaaagccgctctg                                                                                                                                                                                                      <  1:35061‑M1/250‑38 (MQ=255)                                                 aaaaGATCACCCAACGATTCTGGAAATGGCAAAAGCCGCAGGTCTGGCGACCGGTAACGTTTCTACCGCAGAGTTGCAGGATGCCACGCCCGCTGCGCTGGTG‑GCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaaagccgctctggggctgaaataaa                                                                                                                                                                                         <  1:227155‑M1/251‑51 (MQ=255)                                                  aaaGATCACCCAACGATTCTGGAAATGGCAAAAGCCGCAGGTCTGGCGACCGGTAACGTTTCTACCGCAGAGTTGCAGGATGCCACGCCCGCTGCGCTGGTG‑GCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaaagccgctctggggctgaaataaaa                                                                                                                                                                                        <  1:270292‑M1/251‑52 (MQ=255)                                                    aGATCACCCAACGATTCTGGAAATGGCAAAAGCCGCAGGTCTGGCGACCGGTAACGTTTCTACCGCAGAGTTGCAGGATGCCACGCCCGCTGCGCTGGTG‑GCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaaagccgctctggggctgaaataaaacc                                                                                                                                                                                      <  1:40332‑M1/251‑54 (MQ=255)                                                                    cTGGAAATGGCAAAAGCCGCAGGTCTGGCGACCGGTAACGTTTCTACCGCAGAGTTGCAGGATGCCACGCCCGCTGCGCTGGTG‑GCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaaaaccgctctggggctgaaataacacagagcccagacgtgaat                                                                                                                                                                      >  2:167729‑M1/1‑182 (MQ=255)                                                                    cTGGAAATGGCAAAAGCCGCAGGTCTGGCGACCGGTAACGTTTCTACCGCAGAGTTGCAGGATGCCACGCCCGCTGCGCTGGTG‑GCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaa                                                                                                                                                                                                                >  2:73145‑M1/1‑182 (MQ=255)                                                                    cTGGAAATGGCAAAAGCCGCAGGTCTGGCGACCGGTAACGTTTCTACCGCAGAGTTGCAGGATGCCACGCCCGCTGCGCTGGTG‑GCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaa                                                                                                                                                                                                                <  1:73145‑M1/209‑28 (MQ=255)                                                                               aaaaGCCGCAGGTCTGGCGACCGGTAACGTTTCTACCGCAGAGTTGCAGGATGCCACGCCCGCTGCGCTGGTG‑GCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCTAccagaccgatctcttctacaccatgaaagccgctctggggctgaaataaaaccg                                                                                                                                                                                     <  1:254712‑M1/225‑55 (MQ=255)                                                                               aaaaGCCGCAGGACTGGCGACCGGAAACGTTTCTACCGCAGCGTTGCAGGATGCCACCCCCGATGCGCTGGGG‑GCACATGCGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATTTCCGGGTAACGCTCTGGAAAAAGGCGGCAAAGGATCGATTACCGAccaggccggtctcttctacaccatgaaagccgctctggggctgaaataaaaccgagatcggacgaccctcgtgtcgggt                                                                                                                                                            >  2:254712‑M1/1‑171 (MQ=255)                                                                                aaaGGCGCATGTCTGGCGACCGGGATCGTTTCTACCGCAGAGGTGCAGGTTGCCACGGCCGCTGTGCTGGTG‑GCACTTGTGACCTCGCGCAAATGATACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATGGATTACCGAccagtccgatctcttctacaccatgaaagccgctctggggctgaaataaaaccgcgcccggcagtgaattttcgctgctgg                                                                                                                                                          <  2:261032‑M1/251‑82 (MQ=255)                                                                                                         aCGTTTCTACCGCAGAGTTGCAGGATGCCACGCCCGCTGCGCTGGTG‑GCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgctctcttctacaccatgaaagccgctctggggctgaaataaaaccgcgcccggcagtgaattttcgctgccgggtggttttttagctgttagcaacc                                                                                                                                  >  2:562541‑M1/1‑145 (MQ=255)                                                                                                                      agagTTGCAGGATGCCACGCCCGCTGCGCTGGTG‑GCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGCAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgctctcttctacaccatgaaagccgctctggggctgaaataaaaccgcgccc                                                                                                                                                                                >  1:41081‑M1/1‑132 (MQ=255)                                                                                                                      agagTTGCAGGATGACACGCCCGCTGCGCT‑GTGTGCACATGTGACCTCGCGCAAAGGCTACGGTCCGCGCGCGACCAGTGAAAAATGCCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgacctctgctacgccatgaaagccgctctggggctgaaataaaccctcgccc                                                                                                                                                                                <  2:41081‑M1/191‑60 (MQ=255)                                                                                                                           tGCAGGATGCCACGCCCGCTGCGAAGGTG‑GCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGTTCGATTACCGAccagaccgatctcttctacaccatgaaagccgctctggggctgaaatacaaccgcgcccggcagtgaattttcgctgccgggtggtttttttgctgttagcaaccagacttaatagcagatcac                                                                                                               >  2:224126‑M1/1‑127 (MQ=255)                                                                                                                                            gccgatctgggg‑gcaCATGTGCCCTCTCGCTAAGGCTACGGTCCGAGCGGGACCTGTGAAAAATGTCCGGGGAACGCTCTGGAAAAAGGCTGAAAAGGATCGATTACCGAccagaccgagctcgtctactccatgaacgccgctctggggctgaaataaaaccgcgcccggcagtgaattttcgctgccgggtggttttgttgctgttagcatccagacttaatggcagatcacgggctcatacgttcatg                                                                                              <  2:564452‑M1/245‑142 (MQ=255)                                                                                                                                                cgctgGTG‑GCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaaagccgctctggggctgaaataaaaccgcgcccggcagtgaattttcgctgccgggtggtttttttgctgttagcaaccagacttaatggcagatcacgggcgcatacgctcatggtta                                                                                          <  1:562541‑M1/251‑146 (MQ=255)                                                                                                                                                             aTGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaaagccgctctggggctgaaataaaaccgcgcccggcagtgaattttcgctgccgggtggtttttttgctgttagcaaccagacttaatggcagatcacgggcgcatacgctcatggttaaaacatgaagag                                                                              <  1:305031‑M1/251‑158 (MQ=255)                                                                                                                                                                     ccgagcaactGCTACGGGCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCTAccaggccgatctcttctacaccatgaaagccgctctggggctgaaataaatccgcgcccggcagtgaattttcgctgccgggtggtttttttgctgttagcaaccagactgaatggcagatcacggtcgcatacgctcatggttaaaacatgaagagggatggtg                                                                      <  2:96286‑M1/247‑166 (MQ=255)                                                                                                                                                                       gcgcAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaaagccgctctggggctgaaataaaaccgcgcccggcagtgaattttcgctgccgggtggtttttttgctgttagcaaccagacttaatggcagatcacgggcgcattcgctcatggttaaaacatgaaaagggatggtgct                                                                    >  2:254636‑M1/1‑84 (MQ=255)                                                                                                                                                                                                        aaaaggttcgggttacgCTCTGGAAAAAGGTGGAAATGGATCCATTACCGAccagaccgatctcttctacactctgaaagtcgctctggggctggaataaaaccgcgcctggcagtgatttttcgctgccgggtggtttttttgctgttagcaaccagactgaatgggagatcactggcgcatacgcttatggttaaaacatgaagagggatggtgctatgaaaataacatttctggttaccttgcttttc                                   <  2:62045‑M1/243‑201 (MQ=255)                                                                                                                                                                                                         aaaTGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaaagccgctctggggctgaaataaaaccgcgcccggcagtgaattttcgctgccgggtggtttttttgctgttagcaaccagacttaatggcagatcacgggcgcatacgctcatggttaaaacatgaagagggatggtgctatgaaaataacattactggttaccttgcttttcg                                  >  1:509037‑M1/1‑50 (MQ=255)                                                                                                                                                                                                               ccGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaaagccgctctggggctgaaataaaaccgcgcccggcagtgaattttcgctgccgggtggtttttttgctgttagcaaccagacttaatggcagatcacgggcgcatacgctcatggttaaaacatgaagagggatggtgctatgaaaataacattactggttaccttgcttttcggtctgg                            >  1:224982‑M1/1‑44 (MQ=255)                                                                                                                                                                                                                  ggTAACGCTCTGGAAGAAGGCGGAAAAGGATCGATTACCGAccagaccgatctctgctacaccatgaaagccgctctggggttgaaataaaaccgcgcccggcagtgaattttcgctgccgggtggtttttttgctgttagcaaccagacttaatggcagatcacgggcgcatacgctcatggttaaatcatgaagagggatggtgctatgaaaataacattactggttaccttgcttt                                     <  2:396422‑M1/239‑199 (MQ=255)                                                                                                                                                                                                                  ggTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaaagccgctctggggctgaaataaaaccgcgcccggcagtgaattttcgctgccgggtggtttttttgctgttagcaaccagacttaatggcagatcacgggcgcatacgctcatggttaaaacatgaagagggatggtgctatgaaaataacattactggttaccttgcttt                                     >  1:396422‑M1/1‑41 (MQ=255)                                                                                                                                                                                                                  ggTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAccagaccgatctcttctacaccatgaaagccgctctggggctgaaataaaaccgcgcccggcagtgaattttcgctgccgggtggtttttttgctgttagcaaccagacttaatggcagatcacgggcgcatacgctcatggttaaaacatgaagagggatggtgctatgaaaataacattactggttaccttgcttgtcggtctggttt                         <  1:138529‑M1/251‑211 (MQ=255)                                                                                                                                                                                                                               aaaacGGCGGAAACGGATCGATTAACGAacagaccgatatcttctacaccatgaaagccgctctggggctgaactaacaccgcgcccggcagtgaattttcgctgacgggtggttattttgctgttagagaccaggcttaatggcagataacgggcgcataagctcatggttaaaacctgaagtgggatggtgctatgaaaataacattactggttaccttgcttttcggtctggtttttttacccacctt            >  2:36495‑M1/1‑28 (MQ=255)                                                                                                                                                                                                                                aaaaGGCGGAAAAGGAGCGATTACCGCccagaccgatctcttctacaccatgaaagccgctctggggctgaaataaacccgcgcccggcagtgaattttcgctgccgggtggtttttttgctgttagcaaccagacttaatggcagatcacgggcgcatacgctcatggttaaaacatgaagagggatggtgctatgaaaataacattactggttaccttgcttttcggtctggtttttttaaccaccgtc           <  2:479777‑M1/251‑225 (MQ=255)                                                                                                                                                                                                                                       ggAAAAGGAGCGCTTACCGAccagaacgatctcttctacaccatgaaagccgctctggggctgaaataaaaccgcgcccggaagtgaagtttcgctgccgggtggtttttttgctgttagcaaccagtcttaatggaagatcacgggcgcataagcccatggttaaaacatgaagagggatggaaatttgaaaataacattcctggttaccttgcttttcggtctgttttttttaaccaccgtcgacggtg    >  2:556202‑M1/1‑20 (MQ=255)                                                                                                                                                                                                                                         aaaaGGATCGATTACCGAccagaccgatctcttctacaccatgaaagccgctctggggctgaaataaaaccgcgcccggcagtgaattttcgctgccgggtggtttttttgctgttagcaaccagacttaatggcagatcacgggcgcatacgctcatggttaaaacatgaagagggatggtgctatgaaaataacattactggttaccttgcttttcggtctggtttttttaaccaccgtcggcgctgcc  >  1:244312‑M1/1‑18 (MQ=255)                                                                                                                                                                                                                                                          |                                                                                                                                                                                                                                          AACCGGTGTCAAAACCTATAACGGCGCGCTGGGCGTCGATATTCACGAAAAAGATCACCCAACGATTCTGGAAATGGCAAAAGCCGCAGGTCTGGCGACCGGTAACGTTTCTACCGCAGAGTTGCAGGATGCCACGCCCGCTGCGCTGGTG‑GCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAACAGCTGCTTAACGCTCGTGCCGACGTTACGCTTGGCGGCGGCGCAAAAACCTTTGCTGAAACGGCAACCGCTGGTGAATGGCAGGGAAAAACGCTGCGTGAACAGGCACAGGCGCGTGGTTATCAGTTGGTGAGCGATGCTGCCTCACTGAATTCGGTGACGGAAGCGAATCAGCAAAAACCCCTGCTTGGCCTGTTTGCTGACGGCAATATGCCAGTGCGCTGGCTAGGAC  >  NC_000913/402142‑402623

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑