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

CTTGTGTTAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAATT  >  NC_000913_3_vch_tpiA/257762‑258055                                                                                                                                                  |                                                                                                                                                     ctcgtattaaaaatTTTCTAAATTGTGCCAATTGGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagt                                                                                                                                                   <  2:283542‑M1/143‑4 (MQ=255) cTTGTGTTAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGATTGGACATCTGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagt                                                                                                                                                   <  2:219429‑M1/149‑4 (MQ=255) cTTGTGTTAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagt                                                                                                                                                   <  1:472193‑M1/149‑4 (MQ=255)            aaTTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataat                                                                                                                                        <  2:424260‑M1/149‑15 (MQ=255)            aaTTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataat                                                                                                                                        <  2:299501‑M1/149‑15 (MQ=255)               ttGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcga                                                                                                                                     <  1:32346‑M1/149‑18 (MQ=255)               ttGCTAAATTTTGCCAATTTGGTAAAACAGTTGAATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGTTCAAAAAATTTACCGCACTAGGCCCGTATAATCGTGAAGGTAagtgcaaagataatcga                                                                                                                                     <  1:139050‑M1/149‑18 (MQ=255)                   tAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattct                                                                                                                                 >  2:276608‑M1/1‑128 (MQ=255)                                          cAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgc                                                                                                          >  2:258486‑M1/1‑105 (MQ=255)                                            gTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgt                                                                                                        <  1:234336‑M1/149‑47 (MQ=255)                                                 aTCACAACAGAAGCTAAAAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacg                                                                                                   >  2:341156‑M1/1‑98 (MQ=255)                                                                        cGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgt                                                                            <  1:290155‑M1/149‑75 (MQ=255)                                                                         gTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaacctgcaccggaagtgcgtg                                                                           >  2:461436‑M1/1‑74 (MQ=255)                                                                              cGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgagtgtctggctgtatgcgtgaacgtgaaaccggcaccggaagtgcgtgcattc                                                                      >  2:379263‑M1/1‑69 (MQ=255)                                                                               gAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATAATCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgggtgaattct                                                                     >  1:305479‑M1/1‑68 (MQ=255)                                                                                       acCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctgg                                                             <  1:389581‑M1/149‑90 (MQ=255)                                                                                         tggaaGGGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGCTAagtgctaagataatcgatcctgtttctattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtg                                                           <  1:490825‑M1/147‑92 (MQ=255)                                                                                            aaGAGCAGATTGATCAAAAAATTTACCCGACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggat                                                        <  2:270926‑M1/149‑95 (MQ=255)                                                                                               agcagcTTTAGCAAAAAATTTACCCCACTAGGTCTCTATTTTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatgga                                                     <  2:281679‑M1/149‑98 (MQ=255)                                                                                                gCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataaacgattatttttagattgtctgtctgtatcgttctgcttgaaaccggcaccggaagtgcgtgaattctggggctggtggatggag                                                    >  1:152473‑M1/1‑51 (MQ=255)                                                                                                  aGATTGATCAAAAAATTTACCGCCCTAGGCCCGTATATTCGTGCAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagct                                                  >  1:74011‑M1/1‑49 (MQ=255)                                                                                                    aTTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctgg                                                >  1:176525‑M1/1‑47 (MQ=255)                                                                                                      ttataaaaaaatttacCGCACTAGGCCCGTATATTCGTGAAGGTAagtttaaagataatctattctttttcgattgtctggctgtatgcgttaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaa                                              <  1:258879‑M1/144‑105 (MQ=255)                                                                                                            aaaaaTTTACCGCTCTAGGCTCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggttgtatgcgttaatgtgaaatcggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcag                                        <  1:188870‑M1/149‑111 (MQ=255)                                                                                                            aaaaaTTTACCACACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattcttttttgattgtctggctgtatgtgtcaacgtgaatccggcaccggaagtgcgtgaatgctggggctggtggatggagctggaagcgcag                                        <  1:157183‑M1/149‑111 (MQ=255)                                                                                                                              gCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttttacctac                      <  2:176525‑M1/149‑129 (MQ=255)                                                                                                                                ccGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttttacctacag                    >  2:23032‑M1/1‑19 (MQ=255)                                                                                                                                          gTGAAGGTAagtgcaaagataatcgattctttttcgattgtttggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttttacctacagttaccagttt          <  1:258486‑M1/149‑141 (MQ=255)                                                                                                                                           tGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgccggactcccgtcttaccttacattaccagctct         >  2:101114‑M1/1‑8 (MQ=255)                                                                                                                                             aaGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttttacctacagttaccagtttggt       <  1:341156‑M1/149‑144 (MQ=255)                                                                                                                                                  aagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttttacctacagttaccagtttggtctgtt  <  1:280815‑M1/149‑149 (MQ=255)                                                                                                                                                  |                                                                                                                                                     CTTGTGTTAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAATT  >  NC_000913_3_vch_tpiA/257762‑258055

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: ‑