New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_007779	= 4019417	131 (0.780)	4 (0.030)	4/412	NT	5.4%	coding (1807/4236 nt)	Y75_RS19860	rhs element protein RhsB
	?	NC_007779	= 4019535	17 (0.110)					coding (1689/4236 nt)	Y75_RS19860	rhs element protein RhsB

CCGTCCGGCAGCATCGTATTCCATACTGCGCGTCAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTC‑AGCCCTTCCTCG‑CGGTGCACCGCCGTCATCTGCCCGAAGCGGTCATGGTCATAACGGGTTACATAACCGGAACAGTCGGTGAAGCTCAGCAACTGACCGTAACGGCTCCACGTCATGGTTTTCCGGCTGCCGGTGGCATCTTCCGTTGCGCAGGGTAAGTCACTGT  >  NC_007779/4019298‑4019683                                                                                                                                                                                                                                                |                                                                                                                                                     cgttctggcggcATCTTATTCCATCCTGCGGGTCAGCCCGCCCTGCGTGGTATGGGCGGCCTTTCCCCACGTGTCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTAACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTCCACGGCAATTAACTGTCCCCGGCTGTCGTATGCGCGGTACTGACTC‑AGCCCTTCCTCG‑CGGGGCa                                                                                                                                                     <  2:1564804/233‑1 (MQ=11) cctcccggcgGCACCGTATTCCATCTTGCGCGTCAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCGCGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGCCAATGCCGGCGGGCAGGTCACCGGCGATGTGGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTCCTGACTC‑AGCCCTTCCTCG‑CGGTGCa                                                                                                                                                     >  2:1864750‑M2/5‑238 (MQ=255) ccGTCCGGCAGCATCGTATTCCATACTGCGCGTCAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTC‑AGCCCTTCCTCG‑CGGTGCa                                                                                                                                                     >  1:1573380‑M2/1‑238 (MQ=255)  cGTCCGGCAGCATCGTATTCCATACTGCGCGTCAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTC‑AGCCCTTCCTCG‑CGGTGCa                                                                                                                                                     <  1:325584‑M2/238‑2 (MQ=255)  cGTCCGGCAGCATCGTATTCCATACTGCGCGTCAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTC‑AGCCCTTCCTCG‑CGGGGCa                                                                                                                                                     <  1:955873‑M2/238‑2 (MQ=255)    tCCGGCAGCATCGTATTCCATACTGCGCGTCAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTC‑AGCCCTTCCTCG‑CGGTGCacc                                                                                                                                                   <  1:822625‑M2/238‑4 (MQ=255)    tCCGGCAGCATCGTATTCCATACTGCGCGTCAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCCTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGGATGCGCGGTACTGACTC‑AGCCCTTCCTCG‑CGGTGCacc                                                                                                                                                   <  1:1538492‑M2/238‑4 (MQ=255)      cGGCAGCTTCTTATCCCTTACTGGGCGTCACCCACCGTTGCGTGGACCGGGTGCACTTCCCCCACGCTGCGTACTGTGCCCCTTTTCTGCTGCCGTCCGGGGCATTGCCGGCGGTCAGGTCCCCGGCGATGTTGTATTCACACCGCGTTTCAGGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTC‑AGCCCTTCCTCG‑CGGTGCCccgcc                                                                                                                                                <  2:1132119/239‑1 (MQ=11)             aTCGTATTCCATACTGCGCGTCAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTC‑AGCCCTTCCTCG‑CGGTGCaccgccgtcat                                                                                                                                           >  1:1795222‑M2/1‑226 (MQ=255)             aTCGTATTCCATACTGCGCGTCAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTC‑AGCCCTTCCTCG‑CGGTGCaccgccgtca                                                                                                                                            >  1:1308377‑M2/1‑226 (MQ=255)              tCGTATTCCATACTGCGCGTCAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACCGCTGTCGTATGCGCGGTACTTCCTC‑CGCCCCTCCCCG‑CCGTGcccccgcggcattc                                                                                                                                         >  2:529323/1‑228 (MQ=11)                    tCCATACTGCGCGTCAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTC‑AGCCCTTCCTCG‑CGGTGCACCGCCGTCATCTGCCCGaa                                                                                                                                  <  1:345948/239‑1 (MQ=31)                     ccATACTGCGCGTCCGCCCCCCCTGCGTGGTCCGGGCGGGCTTTCCCCACGCTTCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGAGGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTC‑AGCCCTTCCTCG‑CGGTGCACCGCCGTCATCTGCCCGAAg                                                                                                                                 <  2:1321962/239‑1 (MQ=255)                     ccATACTGCGCGTCAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTC‑AGCCCTTCCTCG‑CGGTGCACCGCCGTCATCTGCCCGAAg                                                                                                                                 <  1:753449/239‑1 (MQ=31)                        tACTGCGCGTCAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCCGCGTGGCTTTCACGGCCATTAACTGTCCACGGCTGTCGGTTGCGCCGTCCTGACCC‑AGCCCCTCCCCC‑CGGTGCCCCCCCCTCCTCTGCCCGAACCgg                                                                                                                              >  2:976994/1‑239 (MQ=11)                        tACTGCGCGTCAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGGCCGGTCACCCGCCGTGTTGTATTCTTACCTCTATTCATGGCCCTGCGTGGCCTTCCCGGCAATTAACTGTCCACGGCTGTCCTATGCGGCGTAATGACTCAAGCCTTCCCTGG‑CGGTCCA‑CGCCCGCCTCCGCCCGGAGCgg                                                                                                                              >  2:753449/1‑239 (MQ=11)                         aCTGCGCGTCAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTC‑AGCCCTTCCTCG‑CGGTGCACCGCCGTCATCTGCCCGAAGCggt                                                                                                                             <  1:1096220/239‑1 (MQ=31)                          cTGCGCGTCAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTC‑AGCCCTTCCTCG‑CGGTGCACCGCCGTCATCTGCCCGAAGCggtc                                                                                                                            <  1:1505835/239‑1 (MQ=31)                           tGCGCGTCAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTC‑AGCCCTTCCTCG‑CGGTGCACCGCCGTCATCTGCCCGAAGCggtca                                                                                                                           <  1:275079/239‑1 (MQ=31)                           tGCGCGTCAGCCCGCCCTGCGGGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCACTGACGGCGGTCCGGTCACCGGGGATGTTGTATTCATCCCGCGTTTCATATCCCTGCGGGTCTTTCACGGCCCTTAACTTTCCACGGCTGTCGTCTGCGCGGTAACGACTC‑AGGTCTTTCTCG‑CGGCGCCCCCCCGGCCTCTGccacaaccgcgcc                                                                                                                           >  2:1263998/1‑228 (MQ=11)                           tGCGCGTCACCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGGCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAGCTGTCCACGGCTGTCGTATGCGCGGTACTGACTC‑AGCCCTTCCTCG‑CGGTGCACCGCCGTCATCTGCCCGAAGCggtca                                                                                                                           <  1:1776950/239‑1 (MQ=14)                             cgcgTCAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCCGGTCCCCGGCGCTGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTAGTTCACGGCAATTTACTGGCCACGGCTGTCGGAGGCGCGGTACTGACTC‑AGCCCTTCCTCG‑CGGTTGACGCCCCTCATCCGCCCGaaaccggcgtg                                                                                                                         >  2:657045/1‑230 (MQ=11)                             cgcgTCAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCCGGTCACCGGCGATGTTGTAATCATACCGCGTTTCATGGCCCTGTGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTCTGCGCGGTACTGACGC‑AGCCCTTCCCCC‑CGGTGCACCCACGGCATTTGGCCGAAGCggtcatg                                                                                                                         >  2:928881/1‑239 (MQ=11)                             cgcgTCAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCCTACCGCGTTTCATGGCCCCGCGTGTCCTTCACGGCAATTAACTGTCCACGGCTGTCGGATGCGCGGTTCTGACTC‑AGCCCTTCCCCC‑CCCGGCCCCCCCGGCATCCGCCCCACGCgggcatg                                                                                                                         >  2:345948/1‑239 (MQ=11)                             cgcgTCAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTC‑AGCCCTTCCTCG‑CGGTGCACCGCCGTCATCTGCCCGAAGCggtcatg                                                                                                                         >  1:308022/1‑239 (MQ=31)                             cgcgTCAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTC‑AGCCCTTCCTCG‑CGGTGCACCGCCGTCATCTGCCCGAAGCggtcatg                                                                                                                         >  1:1771852/1‑239 (MQ=31)                             cgcgTCAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTC‑AGCCCTTCCTCG‑CGGTGCACCGCCGTCATCTGCCCGAAGCggtcatg                                                                                                                         >  1:717137/1‑239 (MQ=31)                             cgcgTCAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCCGCGAAGTTTTATTCATACCCCGTTTCATGGCCCTGCGTGTTTTTCCCGTCAATTCACTGTCCACTGCCTGCCTATGCTCGGTACTGACTC‑AGCCCTTCCTCGTCGGTGC‑CCCCCCTCAACTGCCCGAACCggctctc                                                                                                                         >  2:1774207/1‑234 (MQ=11)                               cgTCAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGGGGTACTGACTC‑AGCCCTTCCTCG‑CGGGCCCCCGCCGTCCTCTGCCCGAAGGgggcaatg                                                                                                                        >  2:721608/1‑235 (MQ=11)                                                                                                                                ccGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTC‑AGCCCTTCCTCG‑CGGTGCaccgccgtcattgccccggacggcagcagaaacgggacacagtacgatgcg                                                                                                   >  2:103285‑M2/1‑111 (MQ=255)                                                                                                                                ccGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTC‑AGCCCTTCCTCG‑CGGTGCaccgccgtcattgccccggacggcagcagaaacgggacacagtacgatgcg                                                                                                   <  1:103285‑M2/162‑52 (MQ=255)                                                                                                                                 cGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTC‑AGCCCTTCCTCG‑CGGTGCaccgccgtcattgccccggacggcagcagaaacgggacacagtacgatgcgtggggaaaggccgtccgtaccacgcagggcgggctgacgcgcagtatggaatacgatgctgccggacgggtcatccg                      <  2:11587‑M2/238‑129 (MQ=255)                                                                                                                                                    ccGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTC‑AGCCCTTCCTCG‑CGGTGCaccgccgtcattgccccggacggcagcagaaacgggacacagtacgatgcgtggggaaaggccgtccgtaccacgcagggcgggctgacgcgcagtatggaatacgatgctgccggacgggtcatccgcctgaccagtgaaaacggca  >  1:11587‑M2/1‑91 (MQ=255)                                                                                                                                                                                                                                                |                                                                                                                                                     CCGTCCGGCAGCATCGTATTCCATACTGCGCGTCAGCCCGCCCTGCGTGGTACGGACGGCCTTTCCCCACGCATCGTACTGTGTCCCGTTTCTGCTGCCGTCCGGGGCAATGACGGCGGTCAGGTCACCGGCGATGTTGTATTCATACCGCGTTTCATGGCCCTGCGTGTCTTTCACGGCAATTAACTGTCCACGGCTGTCGTATGCGCGGTACTGACTC‑AGCCCTTCCTCG‑CGGTGCACCGCCGTCATCTGCCCGAAGCGGTCATGGTCATAACGGGTTACATAACCGGAACAGTCGGTGAAGCTCAGCAACTGACCGTAACGGCTCCACGTCATGGTTTTCCGGCTGCCGGTGGCATCTTCCGTTGCGCAGGGTAAGTCACTGT  >  NC_007779/4019298‑4019683

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 29 ≤ 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.