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

TTGCGGAACATAGCCTGGCGATGGCTGCTGTTGCGGTTCAGTTGACGACCACTCTTACGATGGCGCATGACCTTATCCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGC  >  NC_000913_3_pae_pgi/3439932‑3440224                                                                                                                                                 |                                                                                                                                                     ttGCGGAACATAGCCTGGCGATGGCTGCTGTTGCGGTTCAGTTGACGACCACTCTTACGATGGCGCATGACCTTATCCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCcaga                                                                                                                                                  <  1:247421‑M1/149‑5 (MQ=255)   gCGGAACATAGCCTGGCGATGGCTGCTGTAGCGGTTCAGTTGACGACCACTCTTCCGATGGCGCATGACCTTATCCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCcagaga                                                                                                                                                <  1:677057‑M1/149‑7 (MQ=255)               cTGGCGATGGCTGCTGTTGCGGTTCAGTTGACGACCACTCTTACGATGGCGCATGACCTTATCCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCcagagacagtccacggga                                                                                                                                    >  1:531694‑M1/1‑131 (MQ=255)                     aTGGCTGCTGTTGCGGTTCAGTTGACGACCACTCTTACGATGGCGCATGACCTTATCCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCcagagacagtccacgggaagccag                                                                                                                              >  1:230237‑M1/1‑125 (MQ=255)                     aTGGCTGCTGTTGCGGTTCAGTTGACGACCACTCTTACGATGGCGCATGACCTTATCCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCcagagacagtccacgggaagccag                                                                                                                              <  1:384157‑M1/149‑25 (MQ=255)                                 gCGGTTCAGTTGACAACTTCTCTTACGATGGCGCATGACCTCATACTTTTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCcagagacagtccacgggaagccagcacgtctttaat                                                                                                                  <  1:457785‑M1/149‑37 (MQ=255)                                   ggTTCAGTTGACGACCACTCTTACGATGGCGCATGACCTTATCCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCcagagacagtccacgggaagccagcacgtctttaatct                                                                                                                >  1:595922‑M1/1‑111 (MQ=255)                                          ttGACGACCACTCTTACGATGGCGCATGACCTTATCCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCcagagacagtccacgggaagccagcccgtctttaatctccgtcag                                                                                                         >  1:686996‑M1/1‑104 (MQ=255)                                                    ttcttACGATGGCGCATGACCTCATCCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCcagagacagtccacgggacaacagatcctgttgaatctcagtaagagatttttta                                                                                               <  2:759185‑M1/148‑56 (MQ=255)                                                    ctctTACGATGGCGCATGACCTTATCCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCcagagacagtccacgggaagccagcacgtctttaatcgcagtaagagattgttta                                                                                               >  1:249045‑M1/1‑94 (MQ=255)                                                         aCGATGGCGCATGACCTTATCCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCcagagacagtccacgggaagccagcacgtctttaatctcagtaagagattttttaccaag                                                                                          >  2:626533‑M1/1‑89 (MQ=255)                                                                 gcATGACCTTATCCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTAGCCAGTTTTCCcagagacagtccacgggaagccagcacgtctttaatctcagtaagagcttttttaccaaggtccgccg                                                                                  >  1:729477‑M1/1‑81 (MQ=255)                                                                   aTGACCTTATCCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCcagagacagtccacgggaagccagcacgtctttaatctcagtaagagattttttaccaaggttaggcgtt                                                                                <  2:230237‑M1/149‑71 (MQ=255)                                                                     gACCTTATCCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCcagagacagtccacgggaagccagcacgtctttaatctcagtaagagattttttaccaag                                                                                          >  2:782928‑M1/1‑77 (MQ=255)                                                                     gACCTTATCCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCcagagacagtccacgggaagccagcacgtctttaatctcagtaagagattttttaccaag                                                                                          <  1:782928‑M1/137‑61 (MQ=255)                                                                        cTTATCCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCcagagacagtccacgggaagccagcacgtctttaatctcagtaagagattttttaccaatgttaggcgttttaag                                                                           <  1:626533‑M1/149‑76 (MQ=255)                                                                          gatCCTTGCCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCcagagacagtccacgggaagccagcacgtctttaatctcagtaagagattttttaccaaggttaggcgttttaagga                                                                         <  1:36387‑M1/148‑78 (MQ=255)                                                                            tCCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCcagagacagtccacgggaagccagcacgtctttaatctcagtaagagattttttaccaaggttaggcgttttaaggagc                                                                       >  1:125478‑M1/1‑70 (MQ=255)                                                                              cTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCcagagacagtccacgggaagccagcacgtctttaatctcagtaagagattttttatcaagtttaggcgttttaaggagccc                                                                     >  2:654293‑M1/1‑68 (MQ=255)                                                                              cTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCcagagacagtccacgggaagccagcacgtctttaatctcagtaagagattttttaccaaggttaggcgttttaaggagctc                                                                     >  2:778579‑M1/1‑68 (MQ=255)                                                                              cTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCcagagacagtccacgggaagccagcacgtctttaatctcagtaagagattttttaccaaggttaggcgttttaa                                                                            <  1:49731‑M1/142‑75 (MQ=255)                                                                              cTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCcagagacagtccacgggaagccagcacgtctttaatctcagtaagagattttttaccaaggttaggcgttttaa                                                                            >  2:49731‑M1/1‑68 (MQ=255)                                                                                 cgcagTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCcagagacagtccacgggaagccagcacgtctttaatctcagtaagagattttttaccaaggttaggcgttttaaggagctcaac                                                                  <  1:90722‑M1/147‑85 (MQ=255)                                                                                           ccTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCcagagacagtccacgggaagccagcacgtctttaatctcagtaagagattttttaccaaggttaggcggtttaaggagctcaacctcggtacgc                                                        >  1:192031‑M1/1‑55 (MQ=255)                                                                                             ttAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCcagagacagtgcacgggaagccagcacgtctttaatctcagtaagagattttttaccaaggttaggcgttttaaggagctcaacctcggtacgctg                                                      >  1:669157‑M1/1‑53 (MQ=255)                                                                                                   tgtgATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCcagagacagtccacgggaagccagcacgtctttaatctcagtaagagattttttaccaaggttaggcgttttaaggagctcaacctcggtacgctgtaccag                                                >  2:608986‑M1/1‑47 (MQ=255)                                                                                                      gATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCcagagacagtccacgggaagccagcacgtctttaatctcagtaagagattttttaccaaggttaggcgttttaaggagctcaacctcggtacgcggtaccagatc                                             >  2:68636‑M1/1‑44 (MQ=255)                                                                                                                cTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCcagagacagtccacgggaagccagcacgtctttaatctcagtaagagattttttaccaaggttaggcgttttaaggagctcaacctcggtacgctgtaccagatcaccgatatag                                   <  2:125478‑M1/149‑116 (MQ=255)                                                                                                                     cAGCGACGCTTGCCGGTGGCCAGTTTCCCcagagacagtccacgggaagccagcacgtctttaatctcagtaagagattttttaccacggttattcgttttaaggagctcaacctcggtacgctgtaccagatcaccgatatagtggat                              <  1:68636‑M1/149‑121 (MQ=255)                                                                                                                      aGCGATGCTTGCCGGTGGCCAGTTTTCCcagagacagtccacgggaagccagcacgtctttaatctcagtaagagattttttaccaaggttaggcgttttaaggagctcaacctcggaacgctgtaccacatcaccggtataggggata                             >  1:161877‑M1/1‑28 (MQ=255)                                                                                                                              ttGCCGGTGGCCAGTTTTCCcagagacagtccacgggaagccagcacgtctttaatctcagtaagagattttttaccaaggttaggcgttttaaggagctcaacctcggtacgctgtaccagatcaccgatatagtggatagcttctgc                     >  2:26888‑M1/1‑20 (MQ=255)                                                                                                                                gCCGGTGGCCAGTTTTCCcagagacagtccacgggaagccagcacgtctttaatctcagtaagagattttttaccaaggttaggcgttttaaggagctcaacctcggtacgctgtaccagatcaccgatatagtgggtagcttctgctt                   >  1:466288‑M1/1‑18 (MQ=255)                                                                                                                                   ggTGGCCAGTTTTCCcagagacagtccacgggaagccagcacgtctttaatctccgtaagagattttttaccaaggttaggcgttttaacgagctcaacctcggtacgctgtaccagatcaccgatatagtggatagcttctgctttaa                <  2:595922‑M1/149‑135 (MQ=255)                                                                                                                                     tGGCCAGTTTTCCcagagacagtccacgggaagccagcacgtctttaatctcagtaagagattttttaccaaggttaggcgttttaaggagctcaacctcggtacgctgtaccagatcaccgatatagtggatagcttctgctttaagg              <  2:476798‑M1/149‑137 (MQ=255)                                                                                                                                        ccAGTTTTCCcagagacagtccacgggaagccagcacgtctttaatctcagtaagagattttttaccaaggttaggcgttttaaggagctcaacctcggtacgctgtaccagatcaccgatatagtggatagcttctgctttaaggccg           >  2:393565‑M1/1‑10 (MQ=255)                                                                                                                                        ccAGTTTTCCcagagacagtccacgggaagccagcacgtctttaatctcagtaagagattttttaccaaggttaggcgttttaaggagctcaacctcggtacgctgtaccagatcaccgatatagtggatagcttctgctttaaggcag           <  2:531694‑M1/149‑140 (MQ=255)                                                                                                                                         cAGTTTTCCcagagacagtccacgggaagccagcacgtctttaatctcagtaagagattttttaccaaggttaggcgttttaaggagctcaacctcggtacgctgtaccagatcaccgatatagtggatagcttctgctttaaggcagt          >  1:85625‑M1/1‑9 (MQ=255)                                                                                                                                                 ccagagacagtccacgggaagccagcacgtctttaatctcagtgagagattttttaccaaggttaggcgttttaaggagctcaacctcggtacgctgtacccgatcacctctctagtggatggcttctgcattaaggccattagcagag  >  1:600585‑M1/1‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                     TTGCGGAACATAGCCTGGCGATGGCTGCTGTTGCGGTTCAGTTGACGACCACTCTTACGATGGCGCATGACCTTATCCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGC  >  NC_000913_3_pae_pgi/3439932‑3440224

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: ‑