Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913_3_pae_tpiA	1,978,503	Δ776 bp		insB1–insA	insB1, insA

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913_3_pae_tpiA	1978503	1979278	776	31 [0]	[0] 31	insB1–insA	insB1,insA

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	= 1978502	0 (0.000)	27 (0.900)	24/268	0.3	100%	intergenic (‑305/+16)	flhD/insB1	flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B
	?	NC_000913_3_pae_tpiA	1979279 =	0 (0.000)					intergenic (‑64/‑474)	insA/uspC	IS1 repressor TnpA/universal stress protein

CTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAAT  >  NC_000913_3_pae_tpiA/1978377‑1978649                                                                                                                              |                                                                                                                                                    cTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAACCACTCAATTACTTAACATAAATGtataagtcatacttttgttttgg                                                                                                                              <  2:422021‑M1/149‑24 (MQ=255) cTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgg                                                                                                                              <  1:111849‑M1/149‑24 (MQ=255)  tAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttggg                                                                                                                             >  1:73441‑M1/1‑125 (MQ=255)  tAAGATTTTTCCTAAATCGACGCAACTGTACTCCTCGTAACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttggg                                                                                                                             >  1:422021‑M1/1‑125 (MQ=255)              tAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataa                                                                                                                                                >  2:61208‑M1/1‑113 (MQ=255)              tAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataa                                                                                                                                                <  1:61208‑M1/118‑6 (MQ=255)                       gCAACTGTACTCGTCCCTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAACGCGTGATGCAGATCACACAAAACACTTCATTACTTAACAGAAATTtataagtcatacttttgttttgggtgtatttcaatctgttaaaaa                                                                                                        <  2:316424‑M1/149‑46 (MQ=255)                             gTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGCTTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtaaaagtcatacttttgttttaggtgtatttcaatcttttaaaaagttttt                                                                                                  >  2:111896‑M1/1‑98 (MQ=255)                                     tacTACACGCACATACAACGGAGGGGGGCTGCGATTTTTAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataaggcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgc                                                                                          <  2:338531‑M1/148‑60 (MQ=255)                                             gCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgtttcgggtggatttcaatctgttaaaaagtttttcgctacgctagcaagc                                                                                  >  1:105998‑M1/1‑82 (MQ=255)                                                  tACAACGGAGGGCTGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAAGGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaa                                                                             <  2:70691‑M1/149‑73 (MQ=255)                                                  tACAACGAAGGGGGGCTGAGATTGTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtgtaagtcatacttttgttctgggtgtatttcatgctgttaaaaagtctttcgcgacgctagcaagcaaaaa                                                                             >  1:525703‑M1/1‑77 (MQ=255)                                                   aCAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGATAAATGtataagtcatacttttgtttttggtgtatttcaatctgttaaaaagtttttcgctaggctacaaagcaaaaat                                                                            >  2:542296‑M1/1‑76 (MQ=255)                                                   aCAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGAGCACACAAAACACTCAATTACTTAACCTAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaat                                                                            <  2:194209‑M1/149‑74 (MQ=255)                                                             ggggCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaa                                                                  <  1:44695‑M1/149‑84 (MQ=255)                                                                  tGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagaaagcaaaaatgaaaaaggaataatc                                                             >  1:514700‑M1/1‑61 (MQ=255)                                                                    cGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctggcaagcaaaaatgatacaggactaagcga                                                           >  2:512975‑M1/1‑59 (MQ=255)                                                                       ttttCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgcta                                                                                        <  1:551784‑M1/117‑62 (MQ=255)                                                                       ttttCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgcta                                                                                        >  2:551784‑M1/1‑56 (MQ=255)                                                                              taatGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgt                                                 >  1:391971‑M1/1‑49 (MQ=255)                                                                                        tGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagt                                       >  1:519271‑M1/1‑39 (MQ=255)                                                                                            gaccacacaaaaCACTCAATTAATTAACATACATTtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttacgcacagtcaaa                                   <  2:182853‑M1/146‑115 (MQ=255)                                                                                                  acaAACCACTCAATTACTTAACATAAAGGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataact                             <  1:358187‑M1/149‑121 (MQ=255)                                                                                                  acaAAACACTCAATTCCTTAACATAAATGtataagtcatacttttggtgtgggtggagttcaatctgtgaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatcggatgtttagcacactcaaaaaaact                             >  2:335747‑M1/1‑29 (MQ=255)                                                                                                          cTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaa                     <  1:146011‑M1/149‑129 (MQ=255)                                                                                                             aaTTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaat                                                                            <  2:499597‑M1/91‑74 (MQ=255)                                                                                                             aaTTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaat                                                                            >  1:499597‑M1/1‑18 (MQ=255)                                                                                                                   gctgcataaATGtataagtcatacttttgttttgggtgtatttgaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatc            >  1:541324‑M1/5‑12 (MQ=255)                                                                                                                         tAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgctat      >  1:459158‑M1/1‑6 (MQ=255)                                                                                                                         tAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatatgctat      >  1:459162‑M1/1‑6 (MQ=255)                                                                                                                             tGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgctataaat  <  1:505521‑M1/149‑148 (MQ=255)                                                                                                                              |                                                                                                                                                    CTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAAT  >  NC_000913_3_pae_tpiA/1978377‑1978649

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: ‑