New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	= 3360109	NA (NA)	6 (0.290)	5/276	NT	40.0%	noncoding (1/1195 nt)	IS5	repeat region
	?	CP009273	3370794 =	9 (0.440)					intergenic (‑15/+380)	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

TGTCCTTTTCCACGTGTTCGATCTCGAAACTTACACCTTTCTCAGCCAGCACAATGCGGACCTGATGGCTATAGATGTCAGTAGGACCGGAAAACAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCTCCAGGTATAGTCAGAATTTTTACTGCTACCAGC‑CACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAAAATCAAACAAAAAATGAGCAATACCCGACATTTGGGCAGAAAATTGGATGATAGTTTACC  >  CP009273/3370647‑3370939                                                                                                                                                    |                                                                                                                                                   gggacaagaaaatctcgtttctggtctgacggcgcttactgctgaattcactgtcggcgaaggtaagttgatgactcatgatgaaccctgttctatggctccagatgacaaacatgatctcatatcagggacttgttcgcaccttccAt                                                                                                                                                   >  2:224122‑M2/148‑149 (MQ=255)         aacatctcctttctggtcctactgcgctgactgctgaatgcactgtcggcgaagggaagtggatgactcatgatgaaccctgttctatggctccagatgacaaacatgatctcatatcagggacttgttcgcaccttccATAGTCAGaa                                                                                                                                           <  1:279271‑M2/10‑1 (MQ=255)            atctctttgctggtctgacggcgcttactgctgaattcactgtcggcgaaggtaagttgatgactcatgatgaaccctgttctatggctccagatgacaaacatgatctcatatcagggacttgttcgcaccttccATAGTCAGAAttt                                                                                                                                        <  2:6971‑M2/13‑1 (MQ=255)                     aTCTCGAACCTAACACAAATCGCAGCCAGCACAATGCGGACCTGATAGCTATAGATGTGAGTAGGACCGAGAAAAAGAGTGATTAGCGAACGTTTGTGGGCAGCAACAGGCAGTAAAACCTCCAGGTAGCGTCAAGAGATTTACTgtca                                                                                                                               >  1:132049/1‑146 (MQ=255)                                                        gCGGACCTGATGGCTATAGATGTCAGTAGGACCGGAAAACAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCTCCAGGTATAGTCAGAATTTTTACTGCTACCAGC‑CACCAGGTGGCCAGTCAGAAGTTGTGTTAc                                                                                           <  1:229308/149‑1 (MQ=255)                                                            aCCTGATGGCTATAGATGTCAGTAGGACCGGAAAACAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCTCCAGGTATAGTCAGAATTTTTACTGCTACCCGC‑CACCAGGTGGCCAGTCAGAAGTTGTGTTACCCaa                                                                                       >  1:157527/1‑149 (MQ=255)                                                                     tgatgactcatgatgaaccctgttctatggctccagatgacaaacatgatctcatatcagggacttgttcgcaccttccATAGTCAGAATTTTTCCTGCTACCAGG‑CACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACg                                                                              >  1:185153‑M2/80‑149 (MQ=255)                                                                                        cGGAAAACAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCTCCAGGTATAGTCAGAATTTTTACTGCTACCAGC‑CACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAAAAt                                                           >  2:173888/1‑149 (MQ=255)                                                                                            aaaCAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCTCCAGGTATAGTCAGAATTTTTACTGCTACCAGC‑CACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTTTTCGAAAATcaaa                                                       >  1:229456/1‑149 (MQ=255)                                                                                                      tattgcggatcttttttGGCAGCGACAGGCATCAAAACCTCCTGGGATAGTCATAATTTTTGCTTCTACCATC‑CACTAGGTGTCCAGTCCGTTGTTGTTTGACCCAATATGGAATGACTCTCTTTGTTTGAAAATCAAACAAAAAATGa                                             <  1:171325/138‑1 (MQ=255)                                                                                                      cagatgacaaacatgatctcatatcagggacttgttcgcaccttccATAGTTAGAATTTTTACTGCTACCAGC‑CACTAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAAAATCAAACAAAAAATGa                                             <  2:13059‑M2/103‑1 (MQ=255)                                                                                                                       ggCAGCGACAGCCATGAAAACCTCCAGGTATAGTCAGAATTTTTACTGCTACCAGC‑CACCAGGTGGCAAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAAAATCAAACAAAAAATGAGCAATACCCGACAttta                            >  1:83448/1‑148 (MQ=255)                                                                                                                          aGCGACAGCCATGAAAACCTCCAGGTATAGTCAGAATTTTTACTGCTACCAGCACTTCAAGT‑TCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAAAATCAAACAAAAAATGAGCAATACCCGACATTTGGGc                         <  2:83916/149‑1 (MQ=255)                                                                                                                                  ccATGAAAACCTCCAGGTATAGTCAGAATTTTTACTGCTACCAGC‑CACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAAAATCAAACAAAAAATGAGCAATACCCGACATTTGGGCAGAAAAtt                 <  2:132187/149‑1 (MQ=255)                                                                                                                                     ttgttcgcaccttccATAGTCAGAATTTTTACTGCTACCAGC‑CACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAAAATCAAACAAAAAATGAGCAATACCCGACATTTGGGCAGAAAATTGga              <  2:110994‑M2/134‑1 (MQ=255)                                                                                                                                     ttgttcgcaccttccATAGACAGAATATTTACTGCTAACAGC‑CACCAGGTGGGCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTACGAAAATCAAACAAAAAATGAGCAATACCCGACATTTGGGCAGAAAATTGga              <  2:299207‑M2/134‑1 (MQ=255)                                                                                                                                               cAGGTATAGTCAGAATTTTTACTGCTACCAGC‑CACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAAAATCAAACAAAAAATGAGCAATAGCCGACATTGCGGCAGAAAATTGGATGATAGTTTa    <  2:180419/149‑1 (MQ=255)                                                                                                                                                 cccATAGTCAGAATTTTTACTGCTACCAGC‑CACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAAAATCAAACAAAAAATGAGCAATACCCGACATTTGGGCAGAAAATTGGATGATAGTTTAcc  <  2:92741‑M2/146‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                   TGTCCTTTTCCACGTGTTCGATCTCGAAACTTACACCTTTCTCAGCCAGCACAATGCGGACCTGATGGCTATAGATGTCAGTAGGACCGGAAAACAGCGTCATTACCGAACGTTTGTTGGCAGCGACAGCCATGAAAACCTCCAGGTATAGTCAGAATTTTTACTGCTACCAGC‑CACCAGGTGGCCAGTCAGAAGTTGTGTTACCCAATAAGGAACGACTCTCTTTGTTCGAAAATCAAACAAAAAATGAGCAATACCCGACATTTGGGCAGAAAATTGGATGATAGTTTACC  >  CP009273/3370647‑3370939

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ 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.