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	60 [0]	[0] 59	[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)	55 (1.520)	46/268	0.0	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

ACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCG‑CACTAGGCCCGTATATTCGTGAAGGTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAA  >  NC_000913_3_vch_tpiA/257759‑258053                                                                                                                                                      |                                                                                                                                                   aCGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGGTCAAAAAATTTACCG‑CACTAGGCCCGTATATTCGTGAAGGTA                                                                                                                                                    <  2:451374‑M1/149‑1 (MQ=255)  cGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCG‑CACTAGGCCCGTATATTCGTGAAGGTAa                                                                                                                                                   <  1:455162‑M1/149‑2 (MQ=255)       gtgtTAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCG‑AACTAGGCCCGTATATTCGTGAAGGTAagtgca                                                                                                                                              >  2:378643‑M1/1‑143 (MQ=255)         gtTAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCG‑CACTAGGCCCGTATATTCGTGAAGGTAagtgcaaa                                                                                                                                            <  1:205015‑M1/149‑9 (MQ=255)         gtTAAAAATTTGCTAAATTTGGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCG‑CACTAGGCCCGTATATTCGTGAAGGTAagtgcaaa                                                                                                                                            <  1:148689‑M1/149‑9 (MQ=255)          ttAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCG‑CACTAGGCCCGTATATTCGTGAAGGTAagtgcaaag                                                                                                                                           >  2:240589‑M1/1‑140 (MQ=255)           tAAAAATTTGCTAAATTTTGCCAAGTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCG‑CACTAGGCCCGTATATTCGTGAAGGTAagtgcaaaga                                                                                                                                          <  2:200821‑M1/149‑11 (MQ=255)               aaTTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGAAACCATTCCCG‑ATATTCGTGAAGGTAagtgcaaagataat                                                                                                                                      <  1:332861‑M1/149‑15 (MQ=255)                     cTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCG‑CACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattc                                                                                                                                <  1:243682‑M1/149‑21 (MQ=255)                      tAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACTCGAAGAGCAGATTGATCAAAAAATTTACCG‑CACTATGCCCGTATATTCGTGAAGGTAagttcaaggatactcggttcg                                                                                                                               >  2:345214‑M1/1‑128 (MQ=255)                      tAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCG‑CACTACGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattct                                                                                                                               >  2:73052‑M1/1‑128 (MQ=255)                      tAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTAGACACCCGAAGAGCAGATTGATCAAAAAATTTACCG‑CACTAGGCCCGTAGATTCGTGAAGGTAagtgaaaagatcatggattct                                                                                                                               >  2:603654‑M1/1‑128 (MQ=255)                          ttttGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCG‑CACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattcttttt                                                                                                                           <  1:240589‑M1/149‑26 (MQ=255)                          ttttGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCG‑CACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattcttttt                                                                                                                           >  1:38069‑M1/1‑124 (MQ=255)                          ttttGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCG‑CACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattcttttt                                                                                                                           <  2:631853‑M1/149‑26 (MQ=255)                           tttGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCG‑CACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttc                                                                                                                          <  1:25764‑M1/149‑27 (MQ=255)                            ttGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCG‑CACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcg                                                                                                                         <  1:385556‑M1/149‑28 (MQ=255)                               ccAATTTGGTAAAACAGTTGCATCACAACAGCAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCG‑CACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgatt                                                                                                                      >  1:514569‑M1/1‑119 (MQ=255)                                   tttGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCG‑CACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtct                                                                                                                  >  1:596880‑M1/1‑115 (MQ=255)                                    ttGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCG‑CACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctg                                                                                                                 >  1:388613‑M1/1‑114 (MQ=255)                                       gTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCG‑CACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgaatctttttagattgcttggat                                                                                                              >  2:124443‑M1/1‑111 (MQ=255)                                         aaaaCAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCG‑CACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgt                                                                                                            <  2:388613‑M1/149‑41 (MQ=255)                                                ttGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCG‑CACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctgtctgtatgcgtc                                                                                                     >  1:289775‑M1/1‑102 (MQ=255)                                                   cATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCG‑CACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaac                                                                                                  <  2:596880‑M1/149‑51 (MQ=255)                                                     tCAAAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCG‑CACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagctaatcgattctttttcgattgtctggctgtatgcgtcaacgt                                                                                                <  2:63780‑M1/149‑53 (MQ=255)                                                        caacaGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCG‑CACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaa                                                                                             >  1:2201‑M1/1‑94 (MQ=255)                                                              gagaTAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCG‑CACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggc                                                                                       >  1:189101‑M1/1‑88 (MQ=255)                                                                       aTGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCG‑CACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagt                                                                              <  2:69239‑M1/149‑71 (MQ=255)                                                                             ttACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCG‑CACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttt                                                                                                                            <  1:624604‑M1/97‑25 (MQ=255)                                                                             ttACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCG‑CACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttt                                                                                                                            >  2:624604‑M1/1‑73 (MQ=255)                                                                                 cGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCG‑CACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattc                                                                    >  1:117201‑M1/1‑69 (MQ=255)                                                                                    gTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCG‑CACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctgg                                                                 <  1:585727‑M1/149‑84 (MQ=255)                                                                                    cgggcccccctaagagcAGAGTGATCAAAAAATTTACCT‑CACGAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctgg                                                                 <  1:202182‑M1/142‑84 (MQ=255)                                                                                     tGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCG‑CACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggg                                                                <  1:546876‑M1/149‑85 (MQ=255)                                                                                         cacCCGAAGGGCAGATTGATCAAAAAATTTACCG‑CACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctg                                                            <  2:299129‑M1/149‑89 (MQ=255)                                                                                                agagCAGATTGATCAATAGATTTACCG‑CACTAGGCCTGGATATTCGTGAAGGTAagtggaatgagaatcgattcttgtttgattgtctggctgtatgcgtcaacgtgaaaccggctccggaagtgcgtgaattctggggctggtggatg                                                     <  2:632690‑M1/149‑96 (MQ=255)                                                                                                   gCAGATTGATCAAAAAATTTCCCG‑CACTAGGCCCGTATAAAAGCGAAAGTAtgtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggag                                                  <  1:53295‑M1/149‑99 (MQ=255)                                                                                                      gATTGATCAAAAAATTTACCG‑CACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctgg                                                                                                                <  1:570430‑M1/84‑37 (MQ=255)                                                                                                      gATTGATCAAAAAATTTACCG‑CACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctgg                                                                                                                >  2:570430‑M1/1‑48 (MQ=255)                                                                                                         tGATCAAAAAATTGACCG‑CACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaa                                            <  2:563692‑M1/149‑105 (MQ=255)                                                                                                              aaaaaaTTTACCG‑GACGAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcggcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgca                                       <  2:113123‑M1/149‑110 (MQ=255)                                                                                                              aaaaaaTTTACCG‑CACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgca                                       >  2:350896‑M1/1‑40 (MQ=255)                                                                                                              aaaaaaTTTACCG‑CACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctgcggctggtgtatggagctgtgagcgca                                       >  2:382419‑M1/1‑40 (MQ=255)                                                                                                              aaaaaaTTTACCG‑CACTAGGCCCGTAGATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaacggaagtgcgtgaattctggggctggtggatagagctggaagcgcc                                       >  2:8939‑M1/1‑40 (MQ=255)                                                                                                              aaaaaaGTTACCG‑CACTAGGCCCGTATATTCGTGAAGGTAagggcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggacgttcgttaattctggggctggtggatggagctggaagcgca                                       <  2:286421‑M1/149‑110 (MQ=255)                                                                                                               aaaaaTTTACCG‑CACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcag                                      >  1:545789‑M1/1‑39 (MQ=255)                                                                                                                         cG‑CACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgtt                            <  1:489068‑M1/149‑121 (MQ=255)                                                                                                                         cG‑CACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaacaggcaccggaaatgcgtgatttcagggggtggtggatgcagctggaaccgcggggaccccgtt                            >  2:634366‑M1/1‑29 (MQ=255)                                                                                                                                 ggCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttttaccta                     >  1:63887‑M1/1‑22 (MQ=255)                                                                                                                                  gCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttttacctac                    >  1:98758‑M1/1‑21 (MQ=255)                                                                                                                                   cccGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttttacctaca                   >  1:574905‑M1/1‑20 (MQ=255)                                                                                                                                   cccGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctgggggctggagctggaagcgcaggaatcccgttttacctaca                   >  1:574924‑M1/1‑20 (MQ=255)                                                                                                                                      gTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttttacctacagtt                >  1:562987‑M1/1‑17 (MQ=255)                                                                                                                                       tataTTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttttacctacagtta               >  2:12159‑M1/1‑16 (MQ=255)                                                                                                                                        atatTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttttacctacagttac              <  2:562987‑M1/149‑135 (MQ=255)                                                                                                                                              gTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttttacctacagttaccagttt        <  1:12159‑M1/149‑141 (MQ=255)                                                                                                                                               tGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttttacctacagttaccagtttg       <  1:566853‑M1/149‑142 (MQ=255)                                                                                                                                               tGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctgaggctggtggatggagctggaagagcaggaatcccgttttacctacagttaccagtttg       >  2:213336‑M1/1‑8 (MQ=255)                                                                                                                                               ggaAGGTAagcgcaaagataatcgattccttttcgattgactggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttttacctacagttaccagtttg       <  2:554958‑M1/148‑142 (MQ=255)                                                                                                                                                    gTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgctttacctacagttaccagttttgtctg  >  1:14077‑M1/1‑3 (MQ=255)                                                                                                                                                      |                                                                                                                                                   ACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCG‑CACTAGGCCCGTATATTCGTGAAGGTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAA  >  NC_000913_3_vch_tpiA/257759‑258053

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑