New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	= 3360109	NA (NA)	7 (0.240)	6/270	NT	28.0%	noncoding (1/1195 nt)	IS5	repeat region
	?	CP009273	3371007 =	18 (0.630)					intergenic (‑228/+167)	sspA/rpsI	stringent starvation protein A, phage P1 late gene activator, RNAP‑associated acid‑resistance protein, inactive glutathione S‑transferase homolog/30S ribosomal subunit protein S9

GCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGTACTTCCCCCAATAATTGGCTGGTGTTTATGCAAAATGGTCAAGAAGTGGTAATTGATAGCGGTAAAAGCGTTAGCCTCACACTGACAATGGCTCCAGCTTTTAAGGATGAAGGGGAACTAACCGACATGACAGATATTACAG  >  CP009273/3359996‑3360256                                                                                                                  |                                                                                                                                                    gcgtACTGCTGACTTCACTGCCGGCGTGGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGTACTTGTTCGCACCTTCCTTAGTACTTCCCCCAATAATTTGCTGGTGTTTATg                                                                                                                  <  1:273982/146‑1 (MQ=17)         ctgAATTCCCTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGTACTTCCCCCAATAATTGGCTGGTGTTTATGCAAAATgg                                                                                                          <  1:506599/149‑1 (MQ=255)              ttCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGTACTTCCCCCAATAATTGGCTGGTGTTTATGCAAAATGGTCaag                                                                                                     >  1:350783/1‑149 (MQ=255)               tCACTATCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGCACTTGTTCGCACCCTCCGTAGTACTTCCCCCAATAATTGGCTGGTGTTTATGCAAAATggcaaagg                                                                                                    >  1:203162/1‑143 (MQ=18)                   tGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGTACTTCCCCCAATAATTGGCTGGTGTTTATGCAAAATGGTCaa                                                                                                      >  2:9022/1‑143 (MQ=255)                          gAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGTACTTCCCCCAATAATTGGCTGGTGTTTATGCAAAATGGTCAAGAAGTGGTAATTg                                                                                         <  1:429258/149‑1 (MQ=255)                            aGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCGGGGACTTGTTCGCACCGTCCTTAGTACTTCCCCCGATAATTGGCTGGTGTTTATGCCAAATGGTGAAGAAGTGGTAATTGAt                                                                                       >  1:17669/1‑149 (MQ=21)                              gTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGTACTTCCCCCAATAATTGGCTGGTGTTTATGCAAAATGGTCAAGAAGTGGTAATTGATAg                                                                                     >  1:69775/1‑149 (MQ=255)                                           tCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGAGACTTGTTCGCACCTTCCTTAGTACTTCCCCCAATAATTGGCTGGTGTTTATGCAAAATGGTCAAGAAGTGGTAATTGGTAGCGGTaaa                                                                              >  2:256528/1‑143 (MQ=255)                                                 tgaACCCTGTCCTATGGCTCCAGATGACAAACACGAGCTCATATCAGGGACTTGTTCGCACCTTCCTTAGTACTTCCCCCAATAATTGGCTGGTGTTTATGCAAAATGGTCAAGAAGTGGTAATTGATAGCGGTAAAAGCGTTAGCCTc                                                                  <  1:164312/149‑1 (MQ=255)                                                  gaACCCTTTTTTATGTCTCCAGATTCCAAACCTGATCTTATATCAGGGACTTGTTCGCACCTTCCTTAGTACTTCCCCCAATAATTGGTTGGTGTTTATGCAAAATGGTCAAGAAGTGGTAATTGATAGCGGTAAAAGCGTTa                                                                       <  2:57090/143‑1 (MQ=37)                                                               tGGCTCCAGAGGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGTACTTCCCCCAATAATTGGCTGGTGTTTATGCAAAATGGTCAAGAAGTGGTAATTGATAGCGGTAAAAGCGTTAGCCTCACACTGAc                                                          <  2:285118/143‑1 (MQ=255)                                                                    ccAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGTACTTCCCCCAATAATTGGCTGGTGTTTATGCAAAATGGTCAAGAAGTGGTAATTGATAGCGGTAAAAGCGTTAGCCTCACGCTGACAATGCCTCGAg                                               >  1:197424/1‑149 (MQ=255)                                                                    ccAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGTACTTCCCCCAAGAATTGACTGGTGTTTATGCAAAATGGTCAAGAAATGGTAATTGATAGCGGTAAAAGCGTTAGCCTCACACTGACGATGGCTGCAg                                               >  1:126315/1‑149 (MQ=38)                                                                        aTGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGTACTTCCCCCAATAATTGGCTGGTGTTTATGCAAAATGGTCAAGAAGTGGTAATTGATAGCGGTAAAAGCGTTAGCCTCACACTGACAATGGCTCCAGCttt                                           <  1:446613/149‑1 (MQ=255)                                                                           aCAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGTACTTCCCCCAATAATTGGCTGGTGTTTATGCAAAATGGTCAAGAAGTGGTAATTGATAGCGGTAAAAGCGTTAGCCTCACACTGACAATGGCTCCAGCTTTTaa                                        <  1:252317/149‑1 (MQ=255)                                                                             aaaCATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGTACTTCCCCCAATAATTGGCTGGTGTTTATGCAAAATGGTCAAGAAGTGGTAATTGATAGCGGTAAAAGCGTTAGCCTCACACTGACAATGGCTCCAGCtt                                            >  2:409197/1‑143 (MQ=255)                                                                             aaaCATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGTACTTCCCCCAATAATTGGCTGGTGTTTATGCAAAATGGTCAAGAAGTGGTAATTGATAGCGGTAAAAGCGTTAGCCTCACACTGACAATGGCTCCAGCTTTTAAgg                                      >  1:379858/1‑149 (MQ=255)                                                                             aaaCATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGTACTTCCCCCAATAATTGGCTGGTGTTTATGCAAAATGGTCAAGAAGTGGTAATTGATAGCGGTAAAAGCGTTAGCCTCACACTGACAATGGCTCCAGCTTTTAAgg                                      >  1:236427/1‑149 (MQ=255)                                                                              aaCAGGAGCTCATATCAGGGACTTGTTCGCACCTTCCTTAGTACTTCCCCCAATAATTGGCTGGTGTTTATGCAAAATGGTCAAGAAGTGGTAATTGATAGCGGTAAAAGCGTTAGCCTCACACTGACAATGGCTCCAGCTTTTAAGGa                                     <  1:195791/149‑1 (MQ=255)                                                                               aCATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGTACTTCCCCCAATAATTGGCTGGTGTTTATGCAAAATGGTCAAGAAGTGGTAAGTGATAGCGGTAAAAGCGTTAGCCTCACACTGACAATGGCTCCAGcctgt                                          >  2:354991/1‑139 (MQ=255)                                                                                   gATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGTACTTCCCCCAATAATTGGCTGGTGTTTATGCAAAATGGTCAAGAAGTGGTAATTGATAGCGGTAAAAGCGTTAGCCTCACACTGACAATGGCTCCAGCTTTTAAgg                                      <  2:62132/143‑1 (MQ=255)                                                                                   gATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGTACTTCCCCCAATAATTGGCTGGTGTTTATGCAAAATGGTCAAGAAGTGGTAATTGATAGCGGTAAAAGCGTTAGCCTCACACTGACAATGGCTCCAGCTTTTAAGGATGAAg                                <  1:91508/149‑1 (MQ=255)                                                                                     tctcATATCAGGGACTTGTTCGCACCTTCCTTAGTACTTCCCCCAATAATTGGCTGGTGTTTATGCAAAATGGTCAAGAAGTGGTAATTGATAGCGGTAAAAGCGTTAGCCTCACACTGACAATGGCTCCAGCTTTTAAGGATGAAggg                              >  1:433339/1‑149 (MQ=255)                                                                                     tctcATATCAGGGACTTGTTCGCACCTTCCTTAGTACTTCCCCCAATAATTGGCTGGTGTTTATGCAAAATGGTCAAGAAGTGGTAATTGATAGCGGTAAAAGCGTTAGCCTCACACTGACAATGGCTCCAGCTTTTAAGGATGAAggg                              <  1:526200/149‑1 (MQ=255)                                                                                           agcAGGGACTTGTTCGCACCTTCCTTAGTACTTCCCCCAATAATTGGCTGGTGTTTATGCAAAATGGTCAAGAAGTGGTAATTGATAGCGGTAAAAGCGTTAGCCTCACACTGACAATGGCTCCAGCTTTTAAGGATGAAGGGGAACTa                        <  1:7365/147‑1 (MQ=255)                                                                                             cAGGGACTTGTTCGCACCTTCCTTAGTACTTCCCCCAATAATTGGCTGGTGTTTATGCAAAATGGTCAAGAAGTGGTAATTGATAGCGGTAAAAGCGTTAGCCTCACACTGACAATGGCTCCAGCTTTTAAGGATGAAGGGGAACTAAc                      <  1:417103/149‑1 (MQ=255)                                                                                                       ttCGCACCTTCCTTAGTACTTCCCCCAATAATTGGCTGGTGTTTATGCAAAATGGCCCAGAAGTGGTAATTGGTAGCGGTAAAAGCGTTAGCCTCACACTGACCATGGCGCCCGCGTTTAAGGCTGAAGCGGCACAAAACggc                  >  2:47481/1‑141 (MQ=255)                                                                                                           cACCTTCCTTAGTACTTCCCCCAATAATTGGCTGGTGTTTATGCAAAATGGTCAAGAAGTGGTAATTGATAGCGGTAAAAGCGTTAGCCTCACACTGACAATGGCTCCAGCTTTTAAGGATGAAGGGGAACTAACCGACATGACAGata        <  1:262274/149‑1 (MQ=255)                                                                                                           cACCTTCCTTAGTACGTCCCCCAATAATGGGCTGGTGTTTATGCAAAATGGTCAAGAAGTGGTAATTGATAGCGGTAAAAGCGTTAGCCTCACACTGACAATGGCTCCAGCTTTTAAGGATGAAGGGGAACTAACCGACATGa              <  2:227854/143‑1 (MQ=255)                                                                                                                 ccttAGTACTTCCCCCAACAATTGGCCGGTGTTTATGCAAAATGGTCAAGAAGTGGTAATTGATAGCGGTAAAAGCGTTAGCCTCACACTGACAATGGCTCCAGCTTTTAAGGATGAAGGGGAACTAACCGACATGACAGATATTACAg  <  1:303736/149‑1 (MQ=255)                                                                                                                  |                                                                                                                                                    GCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGTACTTCCCCCAATAATTGGCTGGTGTTTATGCAAAATGGTCAAGAAGTGGTAATTGATAGCGGTAAAAGCGTTAGCCTCACACTGACAATGGCTCCAGCTTTTAAGGATGAAGGGGAACTAACCGACATGACAGATATTACAG  >  CP009273/3359996‑3360256

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: ‑
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.