New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1207790 =	18 (0.380)	26 (0.590)	24/454	0.8	67.7%	coding (290/630 nt)	ycfK	protein StfP
	?	NC_000913	1209619 =	8 (0.180)					intergenic (‑500/‑66)	tfaE/pinE	putative tail fiber assembly protein TfaE/site‑specific DNA recombinase

TCCTCCGTTGCATACCCCTGAATACTTAAAATAGAGCGACCTGTATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTCACCACGTAAATCAGGCAATTTATTTGTCGGATAAGCCTTTGCCAGTTCCGGGTATTCTTCAGCAGAAAAAGCGGCACCATTGCATTTCAGCCAGCCTGTTGGCGGAGTGGCTGAAGGCCACGGAACCGGGACACCAACAGGTAATGCAGAGCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAACATGCTTATTGGCTATGTACGCGTATCAACAAATGACCAGAACACAGATCTACAACGTAATGCGCTGAACTGTGCAGGATGCGAGCTGATTTTTGAAGACAAGATAAGCGGCACAAAGTCCGAAAGGCCGGGACTGAAAAAACTGCTCAGGACATTATCGGCAGGTGACACTCTGGTTGT  >  NC_000913/1209369‑1209863                                                                                                                                                                                                                                                           |                                                                                                                                                                                                                                                     tcctccGTTGCATACCCCTGAATACTTAAAATAGAACGACCTGTATCAGTCCCCCGCCCGTCATCCCAGCCACGAATAAACTCACCACGTAAATCAGGCAATTTATTTGTCGGATAAGCCTTTGCCAGTTCCGGGTATTCTTCAGCAGAGAAAGCGGCACCATTGCATTTCAGCCAGCCTGTTGGCGGAGTGGCTGAAGGCCACGGAACCGGGACACCAACAGGTAATGCAGAGCCTTCTCCCAAACCAAc                                                                                                                                                                                                                                                      >  2:372467/1‑251 (MQ=255)         attgataggtgcgctgacattgtcataatttgcaacaacggcaacacaggcattattaaacgcaaccgggaatacaactgtatttccatccgccccagaggcagatgcttttgcggcattccacccccactgaatgattactgattgctcaataccaccaatcataaccggtatagctatgaaaccggtgcgtcctaatgtagccgttgctgcattgagttttgctccttctcccaaaccaaCGTTTATg                                                                                                                                                                                                                                               >  1:324370‑M2/243‑250 (MQ=255)         attgataggtgcgctgacattgtcataatttgcaaaaacggcaacacaggcattattaaacgcaaccgggaatacaactgtatttcaatcccccccagaggcagatgcttttgcggcattccacccccactgaatgattactgattgctcaataccaccaatcctaaccggtatagctatgaaaccggtgcgtcctaatgtagccgttgctgaattgagttttgctccttctcccaaaccaaCGTTTATg                                                                                                                                                                                                                                               >  1:387282‑M2/243‑250 (MQ=255)                    cgctgacattgtcataatttgcaacaacggcaacacaggcattattaaacgcaaccgggaatacaactgtatttccatcccccccagaggcagatgcttttgcggcattccacccccactgaatgattactgattgctcaataccaccaatcataaccggtatagctatgaaaccggtgcgtcctaatttagccgttgctgcattgagttttgctccttctcccaaaccaaCGTTTATGAAAATGAAGaaa                                                                                                                                                                                                                                   <  1:50047‑M2/20‑1 (MQ=255)                        aCTTAAAATAGATCGACCTGGATCAATTCCCCGCCCGTAATCCCAGCCACGAATAAACTCACCACGTAAATCAGGCAATTTATTTGTCGGATAAGCCTTTGCCAGTTCCGGGTATTCTTCAGCAGAAAAAGCGGCACCATTGCATTTCAGCCAGCCTGTTGGCGGAGTGGCTGAAGGCCACGGAACCGGGACACCAACAGGTAATGCAGAGCCGGCTCCCAAACCAACGTTTATGAAAATGAAGaaagaa                                                                                                                                                                                                                                <  2:248811/250‑4 (MQ=255)                               tcataatttgcaacaacggcaacacaggcattattaaacgcaaccgggaatacaactgtatttccatcccccccagaggcagatgcttttgcggcattccacccccactgaatgattactgattgctcaataccaccaatcataaccggtatagctatgaaaccggtgcgtcctaatgtagccgttgctgcattgagttttgctccttctcccaaaccaaCGTTTATGAAAATGAAGAAATAACATGCaa                                                                                                                                                                                                                         >  1:378585‑M2/221‑250 (MQ=255)                                       tgcaacaacggcaacacaggcattattaaacgcaaccgggaatacaactgtatttccatcccccccagaggcagatgcttttgcggcattccacccccactgaatgattactgattgctcaataccaccaatcataaccggtatagctttgaaacaggtgcgtcctaatgtagccgttgctgcattgagttttgatccttctcccaaaccaaCGTTTATGAAAATGAAGAAATAACAAGCAAATGGcatc                                                                                                                                                                                                                 >  2:321474‑M2/213‑250 (MQ=255)                                        ccTGTATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTCACCACGTAAATCAGGCAATTTATTTGTCGGATAAGCCTTTGCCAGTTCCGGGTATTCTTCAGCAGAAAAAGCGGCACCATTGCATTTCAGCCAGCCTGTTGGCGGAGTGGCTGAAGGCCACGGAACCGGGACACCAACAGGTAATGCAGAGCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGcatcat                                                                                                                                                                                                               <  1:257692/251‑1 (MQ=255)                                           gTATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTCACCACGTAAATCAGGCAATTTATTTGTCGGATAAGCCTTTGCCAGTTCCGGGTATTCTTCAGCAGAAAAAGCGGCACCATTGCATTTCAGCCAGCCGGTTGGCGGAGTGGCGGAAGGCCACGGAACCGGGACGCCAACAGGTAATGCAGAGCCTGCTCTCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTcc                                                                                                                                                                                                            <  1:323427/251‑1 (MQ=255)                                                   agcacaggcattattaaacgcaaccgggaatacaactgtatttccatcccccccagaggcagatgcttttgcggcattccacccccactgaatgattactgattgctcaataccaccaatcataaccggtatagctatgaaaccggtgcgtcctaatgtagccgttgctgcattgagttttgctccttctcccaaaccaaCGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCt                                                                                                                                                                                                        <  1:184942‑M2/47‑1 (MQ=255)                                                   aacacaggcattattaaacgcaaccgggaatacaactgtatttccatcccccccagaggcagatgcttttgcggcattccacccccactgcatgattactgattgctcaataccaccaatcataaccggtatagctatgaaaccggtgcgtcctaatgtagccgttgctgcattgagttttgctccttctcccaaaccaaCGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCt                                                                                                                                                                                                        >  2:184942‑M2/201‑247 (MQ=255)                                                       gaggcattattaaacgcaaccgggaatacaactgtatttccatcacccccagaggcagatgcttttgcggcattccacccccactgaatgattactgattgctcaataccaccaatcataaccggtatagctatgaaaccggtgcgtcctaatgtagccgttgctgcattgagttttgctccttctcccaacccacCGTTTATCAAATTCAAGAAATAACAAGAAAATGGCATCATTCATGCTTTTaca                                                                                                                                                                                                  >  2:144730‑M2/197‑248 (MQ=255)                                                       cgcccgTCATCCCAGCCACGAATAAACTCACCACGTAAATCAGGCAATTTATTTGTCGGATAAGCCTTTGCCAGTTCCGGGTATTCTTCAGCAGAAAAAGCGGCACCATTGCATTTCAGCCAGCCTGTTGGCGGAGTGGCTGAAGGCCACGGAACCGGGACACCAACAGGTAATGCAGAGCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAg                                                                                                                                                                                                <  1:114759/251‑1 (MQ=255)                                                                   aacgcaaccgggaatacaactgtatttccatcccccccagaggcagatgcttttgcggcattccacccccactgaatgattactgattgctcaataccaccaatcataaccggtatagctatgaaaccggtgcgtcctaatgtagccgttgctgcattgagttttgctccttctcccaaaccaaCGt                                                                                                                                                                                                                                                    >  1:307566‑M2/185‑187 (MQ=255)                                                                   aacgcaaccgggaatacaactgtatttccatcccccccagaggcagatgcttttgcggcattccacccccactgaatgattactgattgctcaataccaccaatcataaccggtatagctatgaaaccggtgcgtcctaatgtagccgttgctgcattgagttttgctccttctcccaaaccaaCGt                                                                                                                                                                                                                                                    <  2:307566‑M2/3‑1 (MQ=255)                                                                       cACGAATAAACTCACCACGTAAATCAGTCAATTTATTTGTCGGATAAGCCTTTGCCAGTTCCGGGTATTCTTCAGCAGAAAAAGCGGCTCCATTGCATGTCAGCCAGCCTGTTGGCGGAGTGGCTGAAGGCCACGGAACCGGGACACCAACAGGTAATGCAGAGCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAACATGCt                                                                                                                                                                                <  1:290742/251‑1 (MQ=255)                                                                          ccgggaatacaactgtatttccatcccccccagaggcagatgcttttgcggcattccacccccactgaatgattactgattgctcaataccaccaatcataaccggtatagctatgaaaccggtgcgtcctaatgtagccgttgctgcattgagttttgctccttctcccaaaccaaCGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAACATGCTTAt                                                                                                                                                                             >  1:444465‑M2/178‑251 (MQ=255)                                                                           cgggaatacaactgtatttccatcccccccagaggcagatgcttttgcggcattccacccccactgaatgattactgattgctcaataccaccaatcataaccggtatagctatgaaaccggtgcgtcctaatgtagccgttgctgcattgagttttgctccttctcccaaaccaaCGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAACATGCTTAtt                                                                                                                                                                            >  2:30946‑M2/177‑251 (MQ=255)                                                                                  acaactgtatttccatcccccccagaggcagatgcttttgcggcattccacccccactgaatgattactgagtgctcaataccaccaatcataaccggtatagctatgaaaccggtgcgtcctaatgtagccgttgctgcattgagttttgctccttctcccaaaccaaCGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAACATGCTTATTGGCTATg                                                                                                                                                                     <  2:497193‑M2/82‑1 (MQ=255)                                                                                   caccacGTAAATCAGGCAATTTATTTGTCGGATAAGCCTTTGCCAGTTCCGGGTATTCTTCAGCAGAAAAAGCGGCACCATTGCATTTCAGCCAGCCTGTTGGCGGAGTGGCTGAAGGCCACGGAACCGGGACACCAACAGGTAATGCAGAGCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAACATGCTTATTGGCTAt                                                                                                                                                                      <  1:214365/249‑1 (MQ=255)                                                                                              ccaacccccccagaggcagatgcttttgcggcattccacccccactgaatgattactgattgctcaataccaccaatcataaccggtatagctatgaaaccggtgcgtcctaatgtagccgttgctgcattgagttttgctccttctcccaaaccaaCGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAACATGCTTATTGGCTATGTACGCGTATcaa                                                                                                                                                         <  2:172351‑M2/94‑1 (MQ=255)                                                                                                  cccccccagagtcagatgcttttgcgtcattccacccccactgaatgattactgattgctcaataccaccaatcataaccgggatagctatgaagccggtgcgtcctaatgtagccgttgctgcattgagttttgctccttctcccaaaccaaCGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATGTAACATGCTTATCGGCTATGTACGCGTATcaacaa                                                                                                                                                      <  2:324370‑M2/97‑1 (MQ=255)                                                                                                       ttatttGTCGGATAAGCCTTTGCCAGTTCCGGGTATTCTTCAGCAGAAAAAGCGGCACCATTGCATTTCAGCCAGCCTGTTGGCGGAGTGGCTGAAGGCCACGGAACCGGGACACCAACAGGTAATGCAGAGCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAACATGCTTATTGGCTATGTAAGCGTATCAACAAATGAcc                                                                                                                                                >  1:266054/1‑251 (MQ=255)                                                                                                         agaggcagatgctgttgcggcattccacccccactgaatgattactgattgctcaataccaccaatcataaccggtatagctatgaaaccggtgcgtcctaatgtagccgttgctgcattgagttttgctccttctcccaaaccaaCGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAACATGCTTATTGGCTATGTACGCGTATCAACAAATGACCAg                                                                                                                                              <  2:397310‑M2/105‑1 (MQ=255)                                                                                                          gaggcagatgcttttgcggcattccacccccactgaatgattactgattgctcaataccaccaatcataaccggtatagctttgaaaccggtgcgtcctaatgtagccgttgctgcattgagttttgctccttctcccaaaccaaCGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAACATGCTTATTGGCTATGTACGCGTATCAACAAATGACCAGa                                                                                                                                             <  1:321474‑M2/106‑1 (MQ=255)                                                                                                                   gcttttgaggcattccacccccactgaatgattactgattgctcaataccaccaatcataaccggtatagctatgaaaccggtgcgtcctaatgtagccgttgctgcattgagttttgctcattctcccaaaccaaCGTTTATGAAACTGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGTATTTACCATGCTTATTGGCTATGTACGCGTATCAACAACTGACCAGAACACCGATc                                                                                                                                    >  2:416349‑M2/137‑251 (MQ=255)                                                                                                                    cttttgcggcattccacccccactgaatgattactgattgctcaataccaccaatcataaccggtatagctatgaaaccggtgcgtcctaatgtagccgttgctgcattgagttttgctccttctcccaaaccaaCGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAACATGCTTATTGGCTATGTACGCGTATCAACAAATGACCAGAACACAGATCt                                                                                                                                   >  2:148864‑M2/136‑251 (MQ=255)                                                                                                                                                       gattgctcaataccaccaatcataaccggtatagctatgaaaccggtgcgtcctaatgtagccgttgctgcattgagttttgctccttctcccaaaccaaCGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAACATGCTTATTGGCTATGTACGCGTATCAACAAATGACCAGAACACAGATCTACAACGTAATGCGCTGAACTGTGCAGGATGCGa                                                                                                  <  1:46258‑M2/149‑1 (MQ=255)                                                                                                                                                                                ccggtatagctatgaaaccggtgcgtcctaatgtagccgttgctgcattgagttttgctccttctcccaaaccaaCGTTTATGAACATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAACATGCTTATTGGCTATGTACGCGTATCAACAAATGCCCAGAACACAGATCTACAACGTAATGCGCTGAACTGTGCAGGATGCGAGCTGATTTTTGAAGCCAAGATAGGCgg                                                                       >  2:98167‑M2/76‑251 (MQ=255)                                                                                                                                                                                  ggtatagctatgaaaccggtgcgtcctaatgtagccgttgctgcattgagttttgctccttctcccaaaccaaCGTTTATGACAATGAAGAAATCACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAACATGCTTATTGGCTATGTACGCGTATCAACAAATGACCAGAACACAGATCTACAACGTAATGCGCTGAACTGTGCAGGATGCGAGCTGATTTTTGAAGACAAGATAAGCGGc                                                                      >  2:411196‑M2/74‑250 (MQ=255)                                                                                                                                                                                   gtatagctatgaaaccggtgcgtcctaatgtagccgttgctgcattgagttttgctccttctcccaaaccaaCGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAACATGCTTATTGGCTATGTACGCGTATCAACAAATGACCAGAACACAGATCTACAACGTAATGCGCTGAACTGTGCAGGATGCGAGCTGCTTTTTGAAGACAAGATAAGCGGcac                                                                    >  1:455402‑M2/73‑251 (MQ=255)                                                                                                                                                                                                        gtcctcatgtagccgttgctgcattgagttttgctccttctcccaaaccaaCGTTTATGAAAATGAAGAGATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAACATGCTTATTGGCTATGTACGCGTATCAACAAATGACCAGAACACAGATCTACACCGTACTGCGCTGCACTGTGCAGGATGCGAGCTGATTTTTGAAGACAAGATAAGCGGCCCACAGTCCGACAGGCCGGGACt                                               >  2:182403‑M2/52‑251 (MQ=255)                                                                                                                                                                                                              atgtagccgttgctgcattgagttttgctccttctcccaaaccaaCGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAACATGCTTATTGGCTATGTACGCGTATCAACAAATGACCAGAACACAGATCTACAACGTAATGCGCTGAACTGTGCAGGATGCGAGCTGATTTTTGAAGACAAGATAAGCGGCACAAAGTCCGAAAGGCCGGGACTGaaaaa                                         <  1:148864‑M2/206‑1 (MQ=255)                                                                                                                                                                                                                                tgagttttgctccttctcccaaaccaaCGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAACATGCTTATTGGCTATGTACGCGTATCAACAAATGACCAGAACACAGATCTACAACGTAATGCGCTGAACTGTGCAGGATGCGAGCTGATTTTTGAAGACAAGATAAGCGGCACAAAGTCCGAAAGGCCGGGACTGAAAAAACTGCTCAGGACATTAt                        <  1:59819‑M2/223‑1 (MQ=255)                                                                                                                                                                                                                                                     aaCCAACGTTTATGACAATGAAGAAATAACAAGCCAATGGCATCATTCCTGCTTTTACCAGGGAGATTTAACATGCTTATTGGCTATGTACGCGTATCAACAAATGTCCAGAACACAGATCTACAACGTAATGCGCTGAACTGTGCAGGATGCGAGCTGATTTTTTCAGACAAGATAAGCGGCACAAAGTCCGAAAGGCCGGGACTGAAAAAACTCCTAAGAACATTAACGGCAGGGGACAATCTGGttat  >  2:75121/1‑249 (MQ=255)                                                                                                                                                                                                                                                           |                                                                                                                                                                                                                                                     TCCTCCGTTGCATACCCCTGAATACTTAAAATAGAGCGACCTGTATCAATCCCCCGCCCGTCATCCCAGCCACGAATAAACTCACCACGTAAATCAGGCAATTTATTTGTCGGATAAGCCTTTGCCAGTTCCGGGTATTCTTCAGCAGAAAAAGCGGCACCATTGCATTTCAGCCAGCCTGTTGGCGGAGTGGCTGAAGGCCACGGAACCGGGACACCAACAGGTAATGCAGAGCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAACATGCTTATTGGCTATGTACGCGTATCAACAAATGACCAGAACACAGATCTACAACGTAATGCGCTGAACTGTGCAGGATGCGAGCTGATTTTTGAAGACAAGATAAGCGGCACAAAGTCCGAAAGGCCGGGACTGAAAAAACTGCTCAGGACATTATCGGCAGGTGACACTCTGGTTGT  >  NC_000913/1209369‑1209863

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.