Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913_3_vch_tpiA	257,908	Δ776 bp		[crl]	[crl]

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913_3_vch_tpiA	257908–258675	258683	9–776	31 [0]	[0] 31	[crl]	[crl]

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_vch_tpiA	= 257907	0 (0.000)	28 (0.940)	23/272	0.4	100%	noncoding (257907/4641682 nt)	repeat_region	repeat region
	?	NC_000913_3_vch_tpiA	258684 =	0 (0.000)					noncoding (258684/4641682 nt)	repeat_region	repeat region

TGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCAGGAATCCCGTTTTACC‑TACAGTTACCAGTTTGGTCTGTT  >  NC_000913_3_vch_tpiA/258538‑258831                                                                                                                                                   |                                                                                                                                                     cttgtgttaaaaatttgctaaattttgccaatttggtaaaacagttgcatcacaacaggagatagcaatgacgttaccgattggacatctgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGt                                                                                                                                                    <  2:219429‑M2/3‑1 (MQ=255) cttgtgttaaaaatttgctaaattttgccaatttggtaaaacagttgcatcacaacaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGt                                                                                                                                                    <  1:472193‑M2/3‑1 (MQ=255) ctcgtattaaaaattttctaaattgtgccaattgggtaaaacagttgcatcacaacaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGt                                                                                                                                                    <  2:283542‑M2/3‑1 (MQ=255)            aatttgctaaattttgccaatttggtaaaacagttgcatcacaacaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAAt                                                                                                                                         <  2:424260‑M2/14‑1 (MQ=255)            aatttgctaaattttgccaatttggtaaaacagttgcatcacaacaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAAt                                                                                                                                         <  2:299501‑M2/14‑1 (MQ=255)               ttgctaaattttgccaatttggtaaaacagttgcatcacaacaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGa                                                                                                                                      <  1:32346‑M2/17‑1 (MQ=255)               ttgctaaattttgccaatttggtaaaacagttgaatcacaacaggagatagcaatgacgttaccgagtggacacccgaagagcagattgttcaaaaaatttaccgcactaggcccgtataatcgtgaaggtaAGTGCAAAGATAATCGa                                                                                                                                      <  1:139050‑M2/17‑1 (MQ=255)                   taaattttgccaatttggtaaaacagttgcatcacaacaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCt                                                                                                                                  >  2:276608‑M2/129‑149 (MQ=255)                                          cagttgcatcacaacaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGc                                                                                                           >  2:258486‑M2/106‑149 (MQ=255)                                            gttgcatcacaacaggagatagcaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGt                                                                                                         <  1:234336‑M2/46‑1 (MQ=255)                                                 atcacaacagaagctaaaaatgacgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACg                                                                                                    >  2:341156‑M2/99‑149 (MQ=255)                                                                        cgttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGt                                                                             <  1:290155‑M2/74‑1 (MQ=255)                                                                         gttaccgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCTGCACCGGAAGTGCGTg                                                                            >  2:461436‑M2/75‑149 (MQ=255)                                                                              cgagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGAGTGTCTGGCTGTATGCGTGAACGTGAAACCGGCACCGGAAGTGCGTGCATTc                                                                       >  2:379263‑M2/70‑149 (MQ=255)                                                                               gagtggacacccgaagagcagattgatcaaaaaatttaccgcactaggcccgtataatcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGGGTGAATTCt                                                                      >  1:305479‑M2/69‑149 (MQ=255)                                                                                       acccgaagagcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCtgg                                                              <  1:389581‑M2/89‑1 (MQ=255)                                                                                         tggaagggcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaagctaAGTGCTAAGATAATCGATCCTGTTTCTATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCtggtg                                                            <  1:490825‑M2/91‑1 (MQ=255)                                                                                            aagagcagattgatcaaaaaatttacccgactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGtggat                                                         <  2:270926‑M2/94‑1 (MQ=255)                                                                                               agcagctttagcaaaaaatttaccccactaggtctctattttcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGtggatgga                                                      <  2:281679‑M2/97‑1 (MQ=255)                                                                                                gcagattgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAAACGATTATTTTTAGATTGTCTGTCTGTATCGTTCTGCTTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAg                                                     >  1:152473‑M2/52‑149 (MQ=255)                                                                                                  agattgatcaaaaaatttaccgccctaggcccgtatattcgtgcaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCt                                                   >  1:74011‑M2/50‑149 (MQ=255)                                                                                                    attgatcaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTgg                                                 >  1:176525‑M2/48‑149 (MQ=255)                                                                                                      ttataaaaaaatttaccgcactaggcccgtatattcgtgaaggtaAGTTTAAAGATAATCTATTCTTTTTCGATTGTCTGGCTGTATGCGTTAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGaa                                               <  1:258879‑M2/104‑1 (MQ=255)                                                                                                            aaaaatttaccgctctaggctcgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGTTGTATGCGTTAATGTGAAATCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCAg                                         <  1:188870‑M2/110‑1 (MQ=255)                                                                                                            aaaaatttaccacactaggcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTTGATTGTCTGGCTGTATGTGTCAACGTGAATCCGGCACCGGAAGTGCGTGAATGCTGGGGCTGGTGGATGGAGCTGGAAGCGCAg                                         <  1:157183‑M2/110‑1 (MQ=255)                                                                                                                              gcccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCAGGAATCCCGTTTTACC‑TAc                      <  2:176525‑M2/128‑1 (MQ=255)                                                                                                                                ccgtatattcgtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCAGGAATCCCGTTTTACC‑TACAg                    >  2:23032‑M2/20‑149 (MQ=255)                                                                                                                                          gtgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTTTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCAGGAATCCCGTTTTACC‑TACAGTTACCAGttt          <  1:258486‑M2/140‑1 (MQ=255)                                                                                                                                           tgaaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCCGGACTCCCGTCTTACCTTACA‑TTaccagctct         >  2:101114‑M2/9‑145 (MQ=255)                                                                                                                                             aaggtaAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCAGGAATCCCGTTTTACC‑TACAGTTACCAGTTTGGt       <  1:341156‑M2/143‑1 (MQ=255)                                                                                                                                                  aAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCAGGAATCCCGTTTTACC‑TACAGTTACCAGTTTGGTCTGtt  <  1:280815‑M2/148‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                                     TGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTGAAGGTAAGTGCAAAGATAATCGATTCTTTTTCGATTGTCTGGCTGTATGCGTCAACGTGAAACCGGCACCGGAAGTGCGTGAATTCTGGGGCTGGTGGATGGAGCTGGAAGCGCAGGAATCCCGTTTTACC‑TACAGTTACCAGTTTGGTCTGTT  >  NC_000913_3_vch_tpiA/258538‑258831

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑