New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1207790 =	4 (0.070)	55 (1.350)	27/102	0.1	87.3%	coding (290/630 nt)	ycfK	e14 prophage; protein StfP
	?	NC_000913	1209619 =	13 (0.320)					pseudogene (37/537 nt)	stfE	e14 prophage; putative side tail fiber protein fragment

ATAACCGGTATAGCTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/1207868‑1207790 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ccttctcccaaaccaaCGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAA  >  NC_000913/1209619‑1209683                                                                                                                                                  ATAACCGGTATAGCTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTC                                                                              >  1:3791617/1‑68   acCCGGTATAGCTATGAACCCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTC                                                                            <  1:486233/66‑1   AACCGGTATAGCTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTC                                                                            <  1:3544331/68‑1     CCGGTATAGCTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCC                                                                          >  1:126988/1‑68     CCGGTATAGCTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCC                                                                          >  1:2775708/1‑68      CGGTATAGCTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCA                                                                         >  1:2836674/1‑68       GGTATAGCTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAA                                                                        <  1:3381640/68‑1       GGTATAACTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAA                                                                        <  1:2668777/68‑1        GTATAGCTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAA                                                                       <  1:658534/68‑1        GTATAGCTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAA                                                                       <  1:3655031/68‑1        GTATAGCTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAA                                                                       <  1:2767754/68‑1            AGCTATGAAACCGGTGCGTCCTCATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAA                                                                   >  1:2714212/1‑68            AGCTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAA                                                                   >  1:747150/1‑68            AGCTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAA                                                                   >  1:2938310/1‑68             GCTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAAC                                                                  >  1:1046344/1‑68             GCTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAAC                                                                  >  1:3355872/1‑68             GCTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAAC                                                                  >  1:1037512/1‑68               TATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGT                                                                >  1:2149948/1‑68               TATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGT                                                                >  1:3980267/1‑68               TATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGT                                                                >  1:3839197/1‑68               TATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGT                                                                >  1:2591264/1‑68               TATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGT                                                                <  1:919591/68‑1                    AACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATG                                                           >  1:3731590/1‑68                     ACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGA                                                          >  1:3127921/1‑68                     ACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGA                                                          >  1:1996742/1‑68                          TGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATG                                                     >  1:2557016/1‑68                          TGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATG                                                     >  1:3802502/1‑68                           GCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGA                                                    >  1:144280/1‑68                                  AATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATA                                             <  1:1915019/68‑1                                    TGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAAC                                           >  1:1801060/1‑68                                    TGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAAC                                           >  1:3683489/1‑68                                    TGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAAC                                           >  1:320743/1‑68                                    TGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAAC                                           >  1:3359702/1‑68                                    TGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAAC                                           >  1:1658983/1‑68                                    TGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAAC                                           >  1:1066096/1‑68                                    TGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAAC                                           >  1:1995675/1‑68                                     GTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACA                                          >  1:2513766/1‑68                                     GTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACA                                          >  1:2271468/1‑68                                     GTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACA                                          >  1:95339/1‑68                                     GTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACA                                          >  1:135801/1‑68                                      TAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAA                                         >  1:2971706/1‑68                                       AGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAG                                        >  1:3655048/1‑68                                         CCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACTCTTATGAAAATGAAGAAATAACAAGCA                                      >  1:2628535/1‑68                                         CCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCA                                      >  1:267459/1‑68                                         CCGTTGCTGCATTGAGTTTTGCTCCTTCGCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCA                                      <  1:127001/68‑1                                          CGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAA                                     >  1:2839621/1‑68                                           GTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAA                                    <  1:2745267/68‑1                                               CTGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGC                                <  1:1466313/68‑1                                                TGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCA                               <  1:565405/68‑1                                                TGCATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCA                               <  1:1133027/68‑1                                                   ATTGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCA                            >  1:3914044/1‑68                                                     TGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATT                          >  1:3372880/1‑68                                                     TGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATT                          <  1:4000669/68‑1                                                     TGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATT                          <  1:693096/68‑1                                                     TGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATT                          <  1:3681593/68‑1                                                     TGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATT                          <  1:1843225/68‑1                                                     TGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATT                          <  1:3400735/68‑1                                                     TGAGTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATT                          <  1:1717633/68‑1                                                        GTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCT                       >  1:1062916/1‑68                                                        GTTTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCT                       >  1:3996998/1‑68                                                          TTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGt                     >  1:1617805/1‑67                                                          TTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGC                     <  1:2044012/68‑1                                                          TTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGC                     <  1:185343/68‑1                                                          TTTGCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGC                     >  1:1687272/1‑68                                                             GCTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTT                  >  1:3708749/1‑68                                                              CTCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTT                 <  1:1155907/68‑1                                                               TCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTA                >  1:710335/1‑68                                                               TCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTA                >  1:1484754/1‑68                                                               TCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTA                >  1:340896/1‑68                                                                 CTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACC              >  1:3741702/1‑68                                                                 CTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACC              <  1:1253096/68‑1                                                                 CTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACC              >  1:3489868/1‑68                                                                       CCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGG        <  1:282641/68‑1                                                                       CCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGG        <  1:3522062/68‑1                                                                       CCAAACCAACGTTTATGAAAAGGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGG        <  1:605279/68‑1                                                                        CAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGA       <  1:958502/68‑1                                                                        CAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATCGCATCATTCCTGCTTTTACCAGGGGGA       <  1:333687/68‑1                                                                             CAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAA  >  1:826600/1‑68                                                                                                                                                  ATAACCGGTATAGCTATGAAACCGGTGCGTCCTAATGTAGCCGTTGCTGCATTGAGTTTTGCTCCTTCTCCCAAACCAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/1207868‑1207790 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ccttctcccaaaccaaCGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAA  >  NC_000913/1209619‑1209683

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ 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.