New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	AM260479	342083 =	5 (0.180)	4 (0.160)	4/200	2.0	40.7%	coding (214/1548 nt)	amtB	ammonium transporter
	?	AM260479	342103 =	7 (0.270)					coding (234/1548 nt)	amtB	ammonium transporter

GCATCTGCCCCGGCCGCCTCCGCCGCCCCCGCTGCAGCCGCTGCCGAAGCTTCGGCGCCGGCTGCCGCCGCGGCCGCACCGGCCGCCGCCCCCGCGGAAGCGGCCGCCGCGCCGGCCGCACCGGTGCCCAACAAGGGCGACACCGCCTGGCTGCTGGTCTCGACCGCCTTCGTGATCCTGATGACGCTGCCCGGCCTGGCGCTGTTCTACGGCGGCCTGGTGCGCTCCAAGA  >  AM260479/341984‑342215                                                                                                                        |                                                                                                                 aggccgccgtagaacagcgccaggccgggcagcgtcatcaggatcacgaaggcggtcgagaccagcagccaggcggtgtcgcccttgttgggcaccggtgcggccggcgcggcggccgcACCGGTGCCcaac                                                                                                      >  2:688011‑M2/120‑132 (MQ=255)               cgccTCCGCCGCCCCCGCTGCAGCCGCTGCCGAAGCTTCGGCGCCGGCTGCCGCCGCGGCCGCACCGGCCGCCGCCCCCGCGGAAGCGGCCGCCGCGCCGGCCGCACCGGTGCCCAACAAGGGCGACACCGCCt                                                                                      >  2:47243/1‑134 (MQ=255)                                          gatcacgaaggcggtcgagaccagcagccaggcggtgtcgcccttgttgggcaccggtGCGGCCGCCGCGCCGGCCGCACCGGTGCCCAACAAGGGCGACACCGCCTGGCTGCTGGTCTCGACCGCCTTCGTGa                                                           <  1:688011‑M1/76‑1 (MQ=255)                                            tcacgaaggcggtcgagaccagcagccaggcggtgtcgcccttgttgggcaccggtgcggccggcgcggcggccgcACCGGTGCCCAACAAGGGCGACACCGCCTGGCTGCTGGTCTCGACCGCCTTCGTGATc                                                         <  1:688011‑M2/58‑1 (MQ=255)                                                   ggcggtcgagaccagcagccaggcggtgtcgcccttgttgggcaccggtgcggccggcgcggcggccgcACCGGTGCCCAACAAGGGCGACAcc                                                                                          <  1:70417‑M2/25‑1 (MQ=255)                                                   ggcggtcgagaccagcagccaggcggtgtcgcccttgttgggcaccggtgcggccggcgcggcggccgcACCGGTGCCCAACAAGGGCGACAcc                                                                                          >  2:70417‑M2/70‑94 (MQ=255)                                                              cTGCCGCCGCGGTCGCACCGGCCGCCGCCCCCGCGGAAGCGGCCGCCGCGCCGGCCGCACCGGTGCCCAACAAGGGCGACACCGCCTGGCTGCTGGTCTCGACCGCCTTCGTGATCCTGATGACGCTGCCCGGc                                       >  1:824612/1‑134 (MQ=255)                                                                      gcgGCCGCACCGGCCGCCGCCCCCGCGGAAGCGGCCGCCGCGCCGGCCGCACCGGTGCCCAACAAGGGCGACACCGCCTGGCTGCTGGTCTCGACCGCCTTCGTGATCCTGATGACGCTGCCCGGCCt                                     <  1:586496/128‑1 (MQ=255)                                                                      gcgGCCGCACCGGCCGCCGCCCCCGCGGAAGCGGCCGCCGCGCCGGCCGCACCGGTGCCCAACAAGGGCGACACCGCCTGGCTGCTGGTCTCGACCGCCTTCGTGATCCTGATGACGCTGCCCGGCCt                                     >  2:586496/1‑128 (MQ=255)                                                                           ggtgtcgcccttgttgggcaccggtGCGGCCGCCGCGCCGGCCGCACCGGTGCCCAACAAGGGCGACACCGCCTGGCTGCTGGTCTCGACCGcc                                                                  <  1:70417‑M1/69‑1 (MQ=255)                                                                           ggtgtcgcccttgttgggcaccggtGCGGCCGCCGCGCCGGCCGCACCGGTGCCCAACAAGGGCGACACCGCCTGGCTGCTGGTCTCGACCGcc                                                                  >  2:70417‑M1/26‑94 (MQ=255)                                                                                       gttgggcaccggtGCGGCCGCCGCGCCGGCCGCACCGGTGCCCAACAAGGGCGACACCGCCTGGCTGCTGGTCTCGACCGCCTTCGTGATCCTGATGACGCTGCCCGGCCTGGCGCTGTTCTACGGCGGCCt                >  2:688011‑M1/14‑132 (MQ=255)                                                                                                   aGCGGCCGCCGCGCCGGCCGCACCGGTGCCCAACAAGGGCGACACCGCCTGGCTGCTGGTCTCGACCGCCTTCGTGATCCTGATGACGCTGCCCGGCCTGGCGCTGTTCTACGGCGGCCTGGTGCGCTCCAAGa  <  2:265580/134‑1 (MQ=255)                                                                                                           ccgcgccgGCCGCACCGGTGCCCAACAAGGGCGACACCGCCTGGCTGCTGGTCTCGACCGCCTTCGTGATCCTGATGACGCTGCCCGGCCTGGCGCTGTTCTACGGCGGCCt                >  2:138051/1‑112 (MQ=255)                                                                                                           ccgcgccgGCCGCACCGGTGCCCAACAAGGGCGACACCGCCTGGCTGCTGGTCTCGACCGCCTTCGTGATCCTGATGACGCTGCCCGGCCTGGCGCTGTTCTACGGCGGCCt                <  1:138051/112‑1 (MQ=255)                                                                                                                  ggccgcACCGGTGCCCAACAAGGGCGACACCGCCTGGCTGCTGGTCTCGACCGCCTTCGTGATCCTGATGACGCTGCCCGGCCTGGCGCTGTTCTACGGCGGCCTgg              <  1:754834‑M2/101‑1 (MQ=255)                                                                                                                  ggccgcACCGGTGCCCAACAAGGGCGACACCGCCTGGCTGCTGGTCTCGACCGCCTTCGTGATCCTGATGACGCTGCCCGGCCTGGCGCTGTTCTACGGCGGCCTgg              >  2:754834‑M2/7‑107 (MQ=255)                                                                                                                        |                                                                                                                 GCATCTGCCCCGGCCGCCTCCGCCGCCCCCGCTGCAGCCGCTGCCGAAGCTTCGGCGCCGGCTGCCGCCGCGGCCGCACCGGCCGCCGCCCCCGCGGAAGCGGCCGCCGCGCCGGCCGCACCGGTGCCCAACAAGGGCGACACCGCCTGGCTGCTGGTCTCGACCGCCTTCGTGATCCTGATGACGCTGCCCGGCCTGGCGCTGTTCTACGGCGGCCTGGTGCGCTCCAAGA  >  AM260479/341984‑342215

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ 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.