New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	AM260479	= 3984523	25 (0.910)	4 (0.160)	4/194	2.0	14.9%	coding (1860/2433 nt)	ntrY	signal transduction histidine kinase, nitrogen metabolism regulator NtrY
	?	AM260479	= 3984534	23 (0.930)					coding (1849/2433 nt)	ntrY	signal transduction histidine kinase, nitrogen metabolism regulator NtrY
Rejected: Frequency below/above cutoff threshold.

TACAGGTGCAGCACTTCCGCCACCAGGCTGTTGAGCTGCAGCGACTGCAGCACCGCGGGCGGTGTGCGCGCGTAGTCGCGGAAGTCATCGACCATGCGCTTCATCGCGGCCACCTGGTTGACGATGGTGGCCGCGCCACGCTTGAGCACATCGGCGTCGGTGCCTTCGAGCTTGGGCGAGAGCTTCATCTGCAGGCGCTCGGCCGAGAGCTGGATCGGCGTCAGCGGGTTCTTGATCTCGTGCGCAAGGCGCCGT  >  AM260479/3984410‑3984664                                                                                                                             |                                                                                                                                   tACAGGTGCAGCACTTCCGCCACCAGGCTGTTGAGCTGCAGCGACTGCAGCACCGCGGGCGGTGTGCGCGCGTAGTCGCGGAAGTCATCGACCATGCGCTTCATCGCGGCCACCTGGTTGACGATggtggccgc                                                                                                                           >  2:666858‑M2/1‑125 (MQ=255) tACAGGTGCAGCACTTCCGCCACCAGGCTGTTGAGCTGCAGCGACTGCAGCACCGCGGGCGGTGTGCGCGCGTAGTCGCGGAAGTCATCGACCATGCGCTTCATCGCGGCCACCTGGTTGACGATggtggccgc                                                                                                                           >  2:278348‑M2/1‑125 (MQ=255)      gTGCAGCACTTCCGCCACCAGGCTGTTGAGCTGCAGCGACTGCAGCACCGCGGGCGGTGTGCGCGCGTAGTCGCGGAAGTCATCGACCATGCGCTTCATCGCGGCCACCTGGTTGACGATggtggcc                                                                                                                             <  1:103998‑M2/127‑8 (MQ=255)      gTGCAGCACTTCCGCCACCAGGCTGTTGAGCTGCAGCGACTGCAGCACCGCGGGCGGTGTGCGCGCGTAGTCGCGGAAGTCATCGACCATGCGCTTCATCGCGGCCACCTGGTTGACGATggtggcc                                                                                                                             >  2:103998‑M2/1‑120 (MQ=255)             aCTTCCGCCACCAGGCTGTTGAGCTGCAGCGACTGCAGCACCGCGGGCGGTGTGCGCGCGTAGTCGCGGAAGTCATCGACCATGCGCTTCATCGCGGCCACCTGGTTGACGATGGTGGCCGCGCCACGCTTGAg                                                                                                               >  2:239676/1‑134 (MQ=255)                  cGCCACCAGGCTGTTGAGCTGCAGCGACTGCAGCACCGCGGGCGGTGTGCGCGCGTAGTCGCGGAAGTCATCGACCATGCGCTTCATCGCGGCCACCTGGTTGACGATGGTGGCCGCGCCACGCTTGAGcaca                                                                                                           <  2:384866/133‑1 (MQ=255)                     caccaGGCTGTTGAGCTGCAGCGACTGCAGCACCGCGGGCGGTGTGCGCGCGTAGTCGCGGAAGTCATCGACCATGCGCTTCATCGCGGCCACCTGGTTGACGATGGTGGCCGCGCCACGCTTGAGCACATCgg                                                                                                       >  1:528572/1‑134 (MQ=255)                       ccaGGCTGTTGAGCTGCAGCGACTGCAGCACCGCGGGCGGTGTGCGCGCGTAGTCGCGGAAGTCATCGACCATGCGCTTCATCGCGGCCACCTGGTTGACGATGGTGGCCGCGCCACGCTTGAGCACATCGGCg                                                                                                     <  2:842487/134‑1 (MQ=255)                        caGGCTGTTGAGCTGCAGCGACTGCAGCACCGCGGGCGGTGTGCGCGCGTAGTCGCGGAAGTCATCGACCATGCGCTTCATCGCGGCCACCTGGTTGACGATggtggccgcgatgaagcgcatggtcgatgact                                                                                                    >  2:87270‑M2/1‑102 (MQ=255)                        caGGCTGTTGAGCTGCAGCGACTGCAGCACCGCGGGCGGTGTGCGCGCGTAGTCGCGGAAGTCATCGACCATGCGCTTCATCGCGGCCACCTGGTTGACGATGGTGGCCGCGCCACGCTTGAGCACATCGGCGt                                                                                                    <  2:282135/134‑1 (MQ=255)                               ttGAGCTGCAGCGACTGCAGCACCGCGGGCGGTGTGCGCGCGTAGTCGCGGAAGTCATCGACCATGCGCTTCATCGCGGCCACCTGGTTGACGATGGTGGCCGCGCCACGCTTGAGCACATCGGCGTCGGTg                                                                                               <  1:432652/132‑1 (MQ=255)                                         gCGACTGCAGCACCGCGGGCGGTGTGCGCGCGTAGTCGCGGAAGTCATCGACCATGCGCTTCATCGCGGCCACCTGGTTGACGATGGTGGCCGCGCCACGCTTGAGCACATCGGCGTCGGTGCCTTCGAGCTTg                                                                                   <  2:654877/134‑1 (MQ=255)                                                cagcaCCGCGGGCGGTGTGCGCGCGTAGTCGCGGAAGTCATCGACCATGCGCTTCATCGCGGCCACCTGGTTGACGATggtggccgcgatgaagcgcatggtcgatgacttccgcgactacgcgcgcacaccgc                                                                            <  1:373478‑M2/134‑57 (MQ=255)                                                         gggcggTGTGCGCGCGTAGTCGCGGAAGTCATCGACCATGCGCTTCATCGCGGCCACCTGGTTGACGATGGTGGCCGCGCCACGCTTGAGCACATCGGCGTCGGTGCCTTCGAGCTTGGGCGAGAGCTTCATCt                                                                   <  1:239676/134‑1 (MQ=255)                                                              gtgtGCGCGCGTAGTCGCGGAAGTCATCGACCATGCGCTTCATCGCGGCCACCTGGTTGACGATGGTGGCCGCGCCACGCTTGAGCACATCGGCGTCGGTGCCTTCGAGCTTGGGCGAGAGCTTCATCTGCAgg                                                              <  2:1063486/134‑1 (MQ=255)                                                                   cgcgcgTAGTCGCGGAAGTCATCGACCATGCGCTTCATCGCGGCCACCTGGTTGACGATgg                                                                                                                                  <  2:741476‑M2/61‑3 (MQ=255)                                                                   cgcgcgTAGTCGCGGAAGTCATCGACCATGCGCTTCATCGCGGCCACCTGGTTGACGATgg                                                                                                                                  >  1:741476‑M2/1‑59 (MQ=255)                                                                    gcgcgTAGTCGCGGAAGTCATCGACCATGCGCTTCATCGCGGCCACCTGGTTGACGATGGTGGCCGCGCCACGCTTGAGCACATCGGCGTCGGTGCCTTCGAGCTTGGGCGAGAGCTTCATCTGCAGGCGCTCg                                                        >  2:568996/1‑134 (MQ=255)                                                                         tAGTCGCGGAAGTCATCGACCATGCGCTTCATCGCGGCCACCTGGTTGACGATGGTGGCCGCGCCACGCTTGAGCACATCGGCGTCGGTGCCTTCGAGCTTGGGCGAGAGCTTCATCt                                                                   <  1:272131/118‑1 (MQ=255)                                                                         tAGTCGCGGAAGTCATCGACCATGCGCTTCATCGCGGCCACCTGGTTGACGATGGTGGCCGCGCCACGCTTGAGCACATCGGCGTCGGTGCCTTCGAGCTTGGGCGAGAGCTTCATCt                                                                   >  2:272131/1‑118 (MQ=255)                                                                             cgcgGAAGTCATCGACCATGCGCTTCATCGCGGCCACCTGGTTGACGATGGTGGCCGCGCCACGCt                                                                                                                   <  1:477975/66‑1 (MQ=255)                                                                             cgcgGAAGTCATCGACCATGCGCTTCATCGCGGCCACCTGGTTGACGATGGTGGCCGCGCCACGCt                                                                                                                   >  2:477975/1‑66 (MQ=255)                                                                                          gACCATGCGCTTCATCGCGGCCACCTGGTTGACGATGGTGGCCGCGCCACGCTTGAGCACATCGGCGTCGGTGCCTTCGAGCTTGGGCGAGAGCTTCATCTGCAGGCGCTCGGCCGAGAGCTGGATCGGCGTc                                   <  2:528572/133‑1 (MQ=255)                                                                                           aCCATGCGCTTCATCGCGGCCACCTGGTTGACGATGGTGGCCGCGCCACGCTTGAGCACATCGGCGTCGGTGCCTTCGAGCTTGGGCgag                                                                             >  2:28104/1‑90 (MQ=255)                                                                                           aCCATGCGCTTCATCGCGGCCACCTGGTTGACGATGGTGGCCGCGCCACGCTTGAGCACATCGGCGTCGGTGCCTTCGAGCTTGGGCgag                                                                             <  1:28104/90‑1 (MQ=255)                                                                                                   cTTCATCGCGGCCACCTGGTTGACGATGGTGGCCGCGCCACGCTTGAGCACATCGGCGTCGGTGCCTTCGAGCTTGGGCGAGAGCTTCATCTGCAgg                                                              <  1:776261/97‑1 (MQ=255)                                                                                                   cTTCATCGCGGCCACCTGGTTGACGATGGTGGCCGCGCCACGCTTGAGCACATCGGCGTCGGTGCCTTCGAGCTTGGGCGAGAGCTTCATCTGCAgg                                                              >  2:776261/1‑97 (MQ=255)                                                                                                          gcgGCCACCTGGTTGACGATggtggccgcgatgaagcgcatggtcgatgacttccgcgactacgcgcgcacaccg                                                                             >  1:544895‑M2/1‑20 (MQ=255)                                                                                                          gcgGCCACCTGGTTGACGATggtggccgcgatgaagcgcatggtcgatgacttccgcgactacgcgcgcacaccg                                                                             <  2:544895‑M2/75‑56 (MQ=255)                                                                                                            ggCCACCTGGTTGACGATGGTGGCCGCGCCACGCTTGAGCACATCGGCGTCGGTGCCTTCGAGCTTGGGCGAGAGCTTCATCTGCAGGCGCTCGGCCGAGAGCTGGATCGGCGTCAGCGGGTTCTTGATCTCGt                >  2:699431/1‑134 (MQ=255)                                                                                                                 ccTGGTTGACGATGGTGGCCGCGCCACGCTTGAGCACATCGGCGTCGGTGCCTTCGAGCTTGGGCGAGAGCTTCATCTGCAGGCGCTCGGCCGAGAGCTGGATCGGCGTCAGCGGGTTCTTGATCTCGTgcgc            <  2:291529/133‑1 (MQ=255)                                                                                                                 ccTGGTTGACGATGGTGGCCGCGCCACGCTTGAGCACATCGGCGTCGGTGCCTTCGAGCTTGGGCGAGAGCTTCATCTGCAGGCGCTCGGCCGAGAGCTGGATCGGCGTCAGCGGGTTCTTGATCTCGTgcgc            >  1:291529/1‑133 (MQ=255)                                                                                                                          cGATGGTGGCCGCGCCACGCTTGAGCACATCGGCGTCGGTGCCTTCGAGCTTGGGCGAGAGCTTCATCTGCAGGCGCTCGGCCGAGAGCTGGATCGGCGTCAGCGGGTTCTTGATCTCGTGCGCAAGGCGCCGt  >  2:1026794/1‑134 (MQ=255)                                                                                                                             |                                                                                                                                   TACAGGTGCAGCACTTCCGCCACCAGGCTGTTGAGCTGCAGCGACTGCAGCACCGCGGGCGGTGTGCGCGCGTAGTCGCGGAAGTCATCGACCATGCGCTTCATCGCGGCCACCTGGTTGACGATGGTGGCCGCGCCACGCTTGAGCACATCGGCGTCGGTGCCTTCGAGCTTGGGCGAGAGCTTCATCTGCAGGCGCTCGGCCGAGAGCTGGATCGGCGTCAGCGGGTTCTTGATCTCGTGCGCAAGGCGCCGT  >  AM260479/3984410‑3984664

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ 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.