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	258683	776	55 [0]	[0] 55	[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)	53 (1.250)	45/274	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

CTTGTGTTAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAATT  >  NC_000913_3_vch_tpiA/257762‑258055                                                                                                                                                  |                                                                                                                                                     cTTGTGTTAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagt                                                                                                                                                   <  1:639048‑M1/149‑4 (MQ=255)    gtgtTAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACGGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCAGAAGAGCAGATTGATCAAAAAATTTACCGCACTACGCCCGGATATTCGTGAAGGTAagtgca                                                                                                                                                >  2:556010‑M1/1‑143 (MQ=255)        gaaaaatTAGATAAATATTGACAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAAAATGAAAAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaaga                                                                                                                                            <  2:11333‑M1/148‑11 (MQ=255)                       ttttGCCAATTTGGTAAAACAGGTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattcttttt                                                                                                                             <  1:16972‑M1/149‑26 (MQ=255)                             cAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaggataatagattctttttcgtttg                                                                                                                       >  1:240707‑M1/1‑118 (MQ=255)                              aaTTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgt                                                                                                                      >  1:402081‑M1/1‑117 (MQ=255)                                        aaCAGTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtat                                                                                                            <  1:767321‑M1/149‑43 (MQ=255)                                            gTTGCATCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCACACGTGTGCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgt                                                                                                        <  1:701007‑M1/149‑47 (MQ=255)                                                caaaaccacaagagataGCAAAGACGAGACCAACACGAAACCCCAAGAGCAGATTGATCAAAAAAATTACCGCACTAGGCCCGGATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaac                                                                                                    <  1:5711‑M1/142‑51 (MQ=255)                                                cATGACAACAGGATATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGTCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaac                                                                                                    <  1:324625‑M1/149‑51 (MQ=255)                                                 aTCACAACATGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctctatgcgtccacg                                                                                                   >  2:8837‑M1/1‑98 (MQ=255)                                                 aTCACAACAGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaccg                                                                                                   >  2:288420‑M1/1‑98 (MQ=255)                                                    acaacaGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtga                                                                                                >  1:400660‑M1/1‑95 (MQ=255)                                                      aacaGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaa                                                                                              >  2:238644‑M1/1‑93 (MQ=255)                                                      aacaGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaa                                                                                              >  1:249466‑M1/1‑93 (MQ=255)                                                        caGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaaggtgaaacc                                                                                            >  1:202046‑M1/1‑91 (MQ=255)                                                         aGGAGATAGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccg                                                                                           >  1:315679‑M1/1‑90 (MQ=255)                                                                aGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgt                                                                                                  >  1:365268‑M1/1‑83 (MQ=255)                                                                aGCAATGACGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgt                                                                                                  <  2:365268‑M1/135‑53 (MQ=255)                                                                       aCGTTACCGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcg                                                                             <  2:249466‑M1/149‑74 (MQ=255)                                                                        cGTTAACGAGTGGACACTTGATAATCAGATTCATCAAAAAATTTACTGCTCTAGTCCCGTATATTCGTGAAGCTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgt                                                                            <  2:648953‑M1/149‑75 (MQ=255)                                                                              cGAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgcaaccggcaccggaagtgcgggaattc                                                                      >  2:489303‑M1/1‑69 (MQ=255)                                                                               gAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaa                                                                                                                                              <  2:436178‑M1/76‑9 (MQ=255)                                                                               gAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaa                                                                                                                                              >  1:436178‑M1/1‑68 (MQ=255)                                                                               gAGTGGACACCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTAGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtaaaaccagcaccggaagttcgtgaattct                                                                     >  2:133243‑M1/1‑68 (MQ=255)                                                                                 ggggacACCCGAAGAGCGCATTGATCAAAAAATTTCCCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgatgctttttcgattgtcttgctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctgg                                                                   <  1:437778‑M1/147‑84 (MQ=255)                                                                                       acCCGAAGAGCAGATTGATCAAAAAATTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctgg                                                             >  1:136338‑M1/1‑60 (MQ=255)                                                                                        ctcgaAGAGCAGATTGATCAAAATATGTACCGCATTAGGCCCGTATTTTCGTGAAGGTAagtgcaaagataatcgattccttgtcgattggctggctgtatgcgtcaacgtgaaaccggcaccggaagtgctggaattctggggctggt                                                            <  2:378043‑M1/147‑91 (MQ=255)                                                                                            gagagcCGGTTGATCAAAAAATTCTCCGCACTAGGCCCGTATTTTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggat                                                        <  1:581181‑M1/148‑95 (MQ=255)                                                                                            aaGAGCAGATTGACTAAAAAATTTAGCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagctaatcgattctttttctgttgtctggttgtatgcgtcgacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggat                                                        <  1:708791‑M1/149‑95 (MQ=255)                                                                                                    ccgatctaaaaaatttaacgCACGAGGGCCGTATATTCGTGAAGGTAagtggaaagatattcgattgtttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctgg                                                <  2:377139‑M1/142‑103 (MQ=255)                                                                                                          cAAAAAAATTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagagaatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgc                                          <  1:692934‑M1/149‑109 (MQ=255)                                                                                                           aaaaaaTTTACCGCACTAGGCCCGTATATTTGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgca                                         <  2:380275‑M1/149‑110 (MQ=255)                                                                                                           aaaaaaTTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgcttgtctggctgtctgcgtcaacgtgaaaccggcaccggaagtccgggaattctggggcgggtggatagcgctcggagcgca                                         >  2:300755‑M1/1‑40 (MQ=255)                                                                                                            aaaaaTTTACCGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaaatgcgtgaattctggggcgggaggagagagcgggaagatcgg                                        >  1:377139‑M1/1‑39 (MQ=255)                                                                                                            aaaaaTGTAACGCACTAGGCCCGTATATTCGAGAAGGAAagtacaaagataatcgattctttttcgattgtctggcggtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcag                                        <  2:240707‑M1/149‑111 (MQ=255)                                                                                                                     ccGCACTAGGCCCTGATATTCGTGAAGGTAagtgcaaacataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgt                               <  2:56063‑M1/149‑120 (MQ=255)                                                                                                                      cGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaatccggtgccttgattgaacaagttgtggggctggtggatggagctggaatcgcaggaatcccgtt                              <  1:382864‑M1/149‑121 (MQ=255)                                                                                                                      cGCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgtt                              <  1:246099‑M1/149‑121 (MQ=255)                                                                                                                       gCACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcactggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttt                             >  1:743174‑M1/1‑28 (MQ=255)                                                                                                                       gCACTAGGCCCGTATATTCGTCAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgaaagaatccctttt                             <  2:402081‑M1/149‑122 (MQ=255)                                                                                                                        cACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgt                                                                            >  2:107095‑M1/1‑27 (MQ=255)                                                                                                                        cACTAGGCCCGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgt                                                                            <  1:107095‑M1/101‑75 (MQ=255)                                                                                                                               cccGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaaccccgttttacctaca                     <  2:641220‑M1/149‑130 (MQ=255)                                                                                                                                ccGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctg                                                                    >  1:622254‑M1/1‑19 (MQ=255)                                                                                                                                ccGTATATTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctg                                                                    <  2:622254‑M1/101‑83 (MQ=255)                                                                                                                                   tataTTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttttacctacagtta                 >  1:578257‑M1/1‑16 (MQ=255)                                                                                                                                   tataTTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttttacctacagtta                 <  1:301390‑M1/149‑134 (MQ=255)                                                                                                                                   tataTTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttttacctacagtta                 >  2:533613‑M1/1‑16 (MQ=255)                                                                                                                                     tatTCGTGAAGGTAagtgcaaagataatcgattcttttttttttttttttctgtatgcgtcaacgtgaaaccgtcaccggaagtgcgtggattctggggctggtggttggcgctggaagtgccggaatgccgttttacctacagttatc               >  2:260140‑M1/1‑14 (MQ=255)                                                                                                                                      atTCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttttacctacagttacca              <  1:238644‑M1/149‑137 (MQ=255)                                                                                                                                        tCGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttttacctacagttaccagt            >  1:512738‑M1/1‑11 (MQ=255)                                                                                                                                         cGTGAAGGTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttttacctacagttaccagtt           <  2:400660‑M1/149‑140 (MQ=255)                                                                                                                                                gTAagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttttacctacagttaccagtttggtctg    >  1:368868‑M1/1‑3 (MQ=255)                                                                                                                                                  aagtgcaaagataatcgattctttttcgattgtctggctgtatgcgtcaacgtgaaaccggcaccggaagtgcgtgaattctggggctggtggatggagctggaagcgcaggaatcccgttttacctacagttaccagtttggtctgtt  <  2:572143‑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 < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑