Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913_3_pae_pgi	3,440,077	Δ11 bp	coding (943‑953/990 nt)	rpoA ←	RNA polymerase, alpha subunit

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913_3_pae_pgi	3440077	3440087	11	38 [0]	[0] 38	rpoA	RNA polymerase, alpha subunit

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	= 3440076	0 (0.000)	37 (0.840)	35/274	0.3	100%	coding (954/990 nt)	rpoA	RNA polymerase, alpha subunit
	?	NC_000913_3_pae_pgi	3440088 =	0 (0.000)					coding (942/990 nt)	rpoA	RNA polymerase, alpha subunit

AGCCTGGCGATGGCTGCTGTTGCGGTTCAGTTGACGACCACTCTTACGATGGCGCATGACCTTATCCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAG  >  NC_000913_3_pae_pgi/3439943‑3440235                                                                                                                                                  |                                                                                                                                                    ttgcggaacatagcctggcgatggctgctgttgcggttcagttgacgaccactcttacgatggcgcatgaccttatccttctcagtaaaaccttaacctgtgatccggttactcgtcagcgatgcttgccggtggccagttttccCaga                                                                                                                                                  <  1:247421‑M2/4‑1 (MQ=255)   gcggaacatagcctggcgatggctgctgtagcggttcagttgacgaccactcttccgatggcgcatgaccttatccttctcagtaaaaccttaacctgtgatccggttactcgtcagcgatgcttgccggtggccagttttccCAgaga                                                                                                                                                <  1:677057‑M2/6‑1 (MQ=255)               ctggcgatggctgctgttgcggttcagttgacgaccactcttacgatggcgcatgaccttatccttctcagtaaaaccttaacctgtgatccggttactcgtcagcgatgcttgccggtggccagttttccCAGAGACAGTCCACGGGa                                                                                                                                    >  1:531694‑M2/132‑149 (MQ=255)                     atggctgctgttgcggttcagttgacgaccactcttacgatggcgcatgaccttatccttctcagtaaaaccttaacctgtgatccggttactcgtcagcgatgcttgccggtggccagttttccCAGAGACAGTCCACGGGAAGCCAg                                                                                                                              >  1:230237‑M2/126‑149 (MQ=255)                     atggctgctgttgcggttcagttgacgaccactcttacgatggcgcatgaccttatccttctcagtaaaaccttaacctgtgatccggttactcgtcagcgatgcttgccggtggccagttttccCAGAGACAGTCCACGGGAAGCCAg                                                                                                                              <  1:384157‑M2/24‑1 (MQ=255)                                 gcggttcagttgacaacttctcttacgatggcgcatgacctcatacttttcagtaaaaccttaacctgtgatccggttactcgtcagcgatgcttgccggtggccagttttccCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAAt                                                                                                                  <  1:457785‑M2/36‑1 (MQ=255)                                   ggttcagttgacgaccactcttacgatggcgcatgaccttatccttctcagtaaaaccttaacctgtgatccggttactcgtcagcgatgcttgccggtggccagttttccCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAAtct                                                                                                                >  1:595922‑M2/112‑149 (MQ=255)                                          ttgacgaccactcttacgatggcgcatgaccttatccttctcagtaaaaccttaacctgtgatccggttactcgtcagcgatgcttgccggtggccagttttccCAGAGACAGTCCACGGGAAGCCAGCCCGTCTTTAATCTCCGTCag                                                                                                         >  1:686996‑M2/105‑149 (MQ=255)                                                    ttcttacgatggcgcatgacctcatccttctcagtaaaaccttaacctgtgatccggttactcgtcagcgatgcttgccggtggccagttttccCAGAGACAGTCCACGGGACAACAGATCCTGTTGAATCTCAGTAAGAGATTTTTTa                                                                                               <  2:759185‑M2/55‑1 (MQ=255)                                                    ctcttacgatggcgcatgaccttatccttctcagtaaaaccttaacctgtgatccggttactcgtcagcgatgcttgccggtggccagttttccCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCGCAGTAAGAGATTGTTTa                                                                                               >  1:249045‑M2/95‑149 (MQ=255)                                                         acgatggcgcatgaccttatccttctcagtaaaaccttaacctgtgatccggttactcgtcagcgatgcttgccggtggccagttttccCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAg                                                                                          >  2:626533‑M2/90‑149 (MQ=255)                                                                 gcatgaccttatccttctcagtaaaaccttaacctgtgatccggttactcgtcagcgatgcttgccggtagccagttttccCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGCTTTTTTAccaaggtccgccg                                                                                  >  1:729477‑M2/82‑143 (MQ=255)                                                                   atgaccttatccttctcagtaaaaccttaacctgtgatccggttactcgtcagcgatgcttgccggtggccagttttccCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGtt                                                                                <  2:230237‑M2/70‑1 (MQ=255)                                                                     gaccttatccttctcagtaaaaccttaacctgtgatccggttactcgtcagcgatgcttgccggtggccagttttccCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAg                                                                                          >  2:782928‑M2/78‑137 (MQ=255)                                                                     gaccttatccttctcagtaaaaccttaacctgtgatccggttactcgtcagcgatgcttgccggtggccagttttccCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAg                                                                                          <  1:782928‑M2/60‑1 (MQ=255)                                                                        cttatccttctcagtaaaaccttaacctgtgatccggttactcgtcagcgatgcttgccggtggccagttttccCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAATGTTAGGCGTTTTAAg                                                                           <  1:626533‑M2/75‑1 (MQ=255)                                                                          gatccttgccagtaaaaccttaacctgtgatccggttactcgtcagcgatgcttgccggtggccagttttccCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGa                                                                         <  1:36387‑M2/77‑1 (MQ=255)                                                                            tccttctcagtaaaaccttaacctgtgatccggttactcgtcagcgatgcttgccggtggccagttttccCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGc                                                                       >  1:125478‑M2/71‑149 (MQ=255)                                                                              cttctcagtaaaaccttaacctgtgatccggttactcgtcagcgatgcttgccggtggccagttttccCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTATCAAGTTTAGGCGTTTTAAGGagccc                                                                     >  2:654293‑M2/69‑147 (MQ=255)                                                                              cttctcagtaaaaccttaacctgtgatccggttactcgtcagcgatgcttgccggtggccagttttccCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTaa                                                                            <  1:49731‑M2/74‑1 (MQ=255)                                                                              cttctcagtaaaaccttaacctgtgatccggttactcgtcagcgatgcttgccggtggccagttttccCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTaa                                                                            >  2:49731‑M2/69‑142 (MQ=255)                                                                              cttctcagtaaaaccttaacctgtgatccggttactcgtcagcgatgcttgccggtggccagttttccCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTc                                                                     >  2:778579‑M2/69‑149 (MQ=255)                                                                                 cgcagtaaaaccttaacctgtgatccggttactcgtcagcgatgcttgccggtggccagttttccCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAAc                                                                  <  1:90722‑M2/84‑1 (MQ=255)                                                                                           ccttaacctgtgatccggttactcgtcagcgatgcttgccggtggccagttttccCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGGTTTAAGGAGCTCAACCTCGGTACGc                                                        >  1:192031‑M2/56‑149 (MQ=255)                                                                                             ttaacctgtgatccggttactcgtcagcgatgcttgccggtggccagttttccCAGAGACAGTGCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTg                                                      >  1:669157‑M2/54‑149 (MQ=255)                                                                                                   tgtgatccggttactcgtcagcgatgcttgccggtggccagttttccCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAg                                                >  2:608986‑M2/48‑149 (MQ=255)                                                                                                      gatccggttactcgtcagcgatgcttgccggtggccagttttccCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCGGTACCAGATc                                             >  2:68636‑M2/45‑149 (MQ=255)                                                                                                                ctcgtcagcgatgcttgccggtggccagttttccCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAg                                   <  2:125478‑M2/115‑1 (MQ=255)                                                                                                                     cagcgacgcttgccggtggccagtttcccCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCACGGTTATTCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGAt                              <  1:68636‑M2/120‑1 (MQ=255)                                                                                                                      agcgatgcttgccggtggccagttttccCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGAACGCTGTACCACATCACCGGTATAGGGGATa                             >  1:161877‑M2/29‑149 (MQ=255)                                                                                                                              ttgccggtggccagttttccCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGc                     >  2:26888‑M2/21‑149 (MQ=255)                                                                                                                                gccggtggccagttttccCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGGTAGCTTCTGCtt                   >  1:466288‑M2/19‑149 (MQ=255)                                                                                                                                   ggtggccagttttccCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCCGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAACGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTaa                <  2:595922‑M2/134‑1 (MQ=255)                                                                                                                                     tggccagttttccCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAgg              <  2:476798‑M2/136‑1 (MQ=255)                                                                                                                                        ccagttttccCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAggccg           >  2:393565‑M2/11‑147 (MQ=255)                                                                                                                                        ccagttttccCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAg           <  2:531694‑M2/139‑1 (MQ=255)                                                                                                                                         cagttttccCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGt          >  1:85625‑M2/10‑149 (MQ=255)                                                                                                                                                 cCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTGAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCCGATCACCTCTCTAGTGGATGGCTTCTGCATTAAGGCCATTAGCagag  >  1:600585‑M2/2‑149 (MQ=255)                                                                                                                                                  |                                                                                                                                                    AGCCTGGCGATGGCTGCTGTTGCGGTTCAGTTGACGACCACTCTTACGATGGCGCATGACCTTATCCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAG  >  NC_000913_3_pae_pgi/3439943‑3440235

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑