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

TTCGAAAATCAAACAAAAAATGAGCAATACCCGACATTTGGGCAGAAAATTGGATGATAGTTTACCAGATTTTGCGACCATTGTGGTGAGTCGATGCCGGAAATGGGGAAAAAGAGATGCGCTTTAGTCTGAAATAGTTGACTTAGTCCCTTATTGGCGATGTGGTTTTTGTTTTACCTGTCTGTCAGGTGGCAGCAAAAAGCAACTTTCCAGTTTTTACGCTGATTCAGATTTTAGCTATAAAAAAACCCGCCGAAGCGGGTTTTTTCGAAAA  >  CP009273/3370874‑3371147                                                                                                                                      |                                                                                                                                             tcttttctggtctgacggcgcttactgctgaattcactgtcggcgaaggtaagttgatgactcatgatgaaccctgttctatggctccagatgacaaacatgatctcatatcagggacttgttcgcaccttccATAGTTGACt                                                                                                                                     >  2:63386‑M2/134‑143 (MQ=255)       aaTGAAACAAAAAATGAGCAAGACCCGACATTTGGGCAGAAAATTGGATGATAGTTTACCAGATTTTGCGACCATTGTGGTGAGTCGATGCCGGAAATGGGGAAAAACAGATGCGCTTTAGTCTGAAATAGTTGACTTAGTCCCTTAtt                                                                                                                         <  1:153123/149‑1 (MQ=255)        agcaaacaaaAAATGAGCAATACCCGACATTTGGGCAGAAAATTGGATGATAGTTTACCAGATTTTGCGACCATTGTGGTGAGTCGATGCCGGAAATGGGGAAAAAGAGATGCGCTTTAGTCTGAAATAGTTGACTTAGTccc                                                                                                                              <  2:394176/141‑1 (MQ=255)           aaacaaaAAATGAGCAATACCCGACATTTGGGCAGAAAATTGGATGATAGTTAACCAGATTTTGCGACCATTGGGGTGAGTCGATGCCGGAAATGGGGAAAAGGAGATGCGCTTTAGTCTGAAATAGTTGAcacgagactacc                                                                                                                           >  2:211365/1‑132 (MQ=255)            aacaaaAAATGAGCAATACCCGACATTTGGGCAGGAAATTGGATGATAGTTTACCAGATTTTGCGACCATTGTGGTGAGTCGATGCCGGAAATGGGGAAAAAGAGATGCGCGTTAGTCTGAAATAGTTGACTTAGTCCCTTATTAGCGa                                                                                                                    >  1:12422/1‑149 (MQ=255)                aaaaaTGAGCAATACCCGACATTTGGGCAGAAAATTGGATGATAGTTTACCAGATTTTGCGACCATTGTGGTGAGTCGATGCCGGAAATGGGGAAAAAGAGATGCGCTTTAGTCTGAAATAGTTGACTTAGTCCCTTATTGGCGAtgtg                                                                                                                >  1:394897/1‑149 (MQ=255)                             aCCCGACATTTGGGCAGAAAATTGGATGATAGTTTACCAGATTTTGCGACCATTGTGGTGAGTCGATGCCGGAAATGGGGAAAAAGAGATGCGCTTTAGTCTGAAATAGTTGACTTAGTCCCTTATTGGCGATGTGGTTTTTGTTTTAc                                                                                                   <  1:373246/149‑1 (MQ=255)                                   ccctgtcggcgaaggtaagttgatgactcatgatgacccctgttctatggctccagatgacaaacatgatctcatatcagggacttgttcgcaccttccATAGTTGACTTAGTCCCTTATTGGCGATGTGGTTTTTGTTTTACctgtct                                                                                             <  1:71182‑M2/50‑1 (MQ=255)                                   cATTTGGGCAGAAAATTGGATGATAGTTTACCAGATTTTGACGCCATTGTGGTGAGTCGATGCCGGAAATGGGGAAAAAGAGATGCGCTTTAGTCTGAAATAGTTGACTTAGTCCCTTATTGGCGATGTGGTTTTTGTTTTACctgtct                                                                                             <  1:146485/149‑1 (MQ=255)                                     ctgtcggcgaaggtaagttgatgactcatgatgaaccctgttctatggctccagatgacaaacatgatctcatatcagggacttgttcgcaccttccATAGTTGACTTAGTCCCTTATTGGCGATGTGGTTTTTGTTTTACctgtctgt                                                                                           <  1:177611‑M2/52‑1 (MQ=255)                                       tGGGCAGAAAATTGGATGATAGTTTACCAGATTTTGCGACCATTGTGGTGAGTCGATGCCGGAAATGGGGAAAAAGAGATGCGCTTTAGTCTGAAATAGTTGACTTAGTCCCTTATTGGCGATGTGGTTTTTGTTTTACCTGTCTGTCa                                                                                         <  1:159387/149‑1 (MQ=255)                                            aGAAAATTGGATGATAGTTTACCAGATTTTGCGACCATTGTGGTGAGTCGATGCCGGAAATGGGGAAAAAGAGATGCGCTTTAGTCTGAAATAGTTGACTTAGTCCCTTATTGGCGATGTGGTTTTTGTTTTACCTGTCTGTCAGGTgg                                                                                    <  1:260134/149‑1 (MQ=255)                                             gaaggtaagtcgatgcctcaggatgaaccctgttctatggctccagatgacaaacatgatcgcatatcagggacctgttcgcaccttccATAGTTGACTTAGTCCCTTATTGGCGATGTGGTTTTTGTTTTACCTGTCTGTCa                                                                                         <  2:316204‑M2/54‑1 (MQ=255)                                             gaaggtaagtagatgactcatgatgaaccctgttctatggctccagatgacaaacatgatctcatatcagggacatgttcgcaccttccATAGTTGACTTTGTCCCTTATTGGCGATGTGGTTTTTGTTTTACCTGTCTGTCa                                                                                         <  2:316200‑M2/54‑1 (MQ=255)                                                     gttgatgactcatgatgaaccctgttctatggctccagatgacaaacatgatctcatatcagggacttgttcgcaccttccATAGTTGACTTAGTCCCTTATTGGCGATGTGGTTTTTGTTTTACCTGTCTGTCAGGtggccg                                                                                 >  2:400227‑M2/82‑141 (MQ=255)                                                           aGTTTACCAGATTTTGCGACCATTGTGGTGAGTCGATGCCGGAAATGGGGAAAAAGAGATGCGCTTTAGTCTGAAATAGTTGACTTAGTCCCTTATTGGCGATGTGGTTTTTGTTTTACCTGTCTGTCAGGTGGCAGCaaaaa                                                                           <  2:187658/143‑1 (MQ=255)                                                             tttACCAGATTTTGCGACCATTGTGGTGAGTCGATGCCGGAAATGGGGAAAAAGAGATGCGCTTTAGTCTGAAATAGTTGACTTAGTCCCTTATTGGCGATGTGGTTTTTGTTTTACCTGTCTGTCAGGTGGCAGCAAAAAGc                                                                         >  2:215054/1‑143 (MQ=255)                                                                aCCAGATTTTGCGACCATTGTGGTGAGTCGATGCCGGAAATGGGGAAAAAGAGATGCGCTTTAGTCTGAAATAGTTGACTTAGTCCCTTATTGGCGATGTGGTTTTTGTTTTACCTGTCTGTCAGGTGGCAGCAAAAAGTAACTTTCCa                                                                <  1:41428/149‑1 (MQ=255)                                                                                        gAGGCGATGCCGGAAATGGGGAAAAAGAGATGCGCTTTAGTCTGAAATAGTTGACTTAGTCCCTTATTGGCGATGTGGTTTTTGTTTTACCTGTCTGTCAGGTGGCAGCAAAAAGCAACTTTCTAGTTTTTACGCTGATTCAGATTTTa                                        <  1:314766/149‑1 (MQ=255)                                                                                          gTCGATGCCGGAAATGGGGAAAAAGAGATGCGCTTTAGTCTGAAATAGTTGACTTAGTCCCTTATTGGCGATGTGGTTTTTGTTTTACCTGTCTGTCAGGTGGCAGCCAAAAGCAACTTTCCAGTTTTTACGCTGATTCAGAt                                            >  2:362768/1‑143 (MQ=255)                                                                                                     aaaTGGGGAAAAAGAGATGCGCTTAAGTCTGAAATAGTTGACTTAGTCCCTTATTGGCGATGTGGTTTTTGTTCTACCTGTCTGTCAGGTGGCAGCAAAAAGCAACTTTCCAGTTTTTACGCTGATTCAGATTTTAGCTATaa                                 <  2:254111/143‑1 (MQ=255)                                                                                                           catatcagggacttgttcgcaccttccATAGTTGACTTAGTCCCTTATTGGCGATGTGGTTTTTGTTTTACCTGTCTGTCAGGTGGCAGCAAAAAGCAACTTTCCAGTATTTACGCTGATTCAGAGTTTAGCTATAAAAAAACccgccg                     >  1:434875‑M2/28‑149 (MQ=255)                                                                                                                     attctcTTTAGTCTGAAATAGTTGACTTAGTCCCTTATTGGCGATGTGGTTTTTGTTTTACCTGTCTGTCAGGTGGCAGCAAAAAGCAACTTTCCAGTTTTTACGCTGATTCAGATTTTAGCTATAAAAAAACCCGCCGAAGc                 >  2:360910/6‑143 (MQ=255)                                                                                                                        cgcTTTAGTCTGAAATAGTTGACTTAGTCCCTTATTGGCGATGTGGTTTTTGTTTTACCTGTCTGTCAGGTGGCAGCAAAAAGCAACTTTCCAGTTTTTACGCTGATTCAGATTTTAGCTATAAAAAAACCCGCCGAAGCGGGtttttt        <  1:435577/149‑1 (MQ=255)                                                                                                                        cgcCTTAGTCTCAACTAGTTTTCGTAGTCCCTTATTCGAGCTGTGGTTTCTGTTCTACCTGTCCGTCAGGTGGCAGCAAAAAGCAACTTTCCAGTTTTTACGCTGATTCAGATTTTAGCTATAAAAAAACCCGCCGAAGCGGGtttttt        <  1:241710/149‑1 (MQ=255)                                                                                                                                    aaaTAGTTGACTTAGTCCCTTATTGGCGATGTGGTTTTTGTTTTACCTGTCTGTCAGGTGGCAGCAAAAAGCAACTTTCCAGTTTTTACGCTGATTCAGATTTTAGCTATGAAAAAACCCGCCGAAGCAGGTTGTTTCGaaaa  >  2:377599/1‑143 (MQ=255)                                                                                                                                      |                                                                                                                                             TTCGAAAATCAAACAAAAAATGAGCAATACCCGACATTTGGGCAGAAAATTGGATGATAGTTTACCAGATTTTGCGACCATTGTGGTGAGTCGATGCCGGAAATGGGGAAAAAGAGATGCGCTTTAGTCTGAAATAGTTGACTTAGTCCCTTATTGGCGATGTGGTTTTTGTTTTACCTGTCTGTCAGGTGGCAGCAAAAAGCAACTTTCCAGTTTTTACGCTGATTCAGATTTTAGCTATAAAAAAACCCGCCGAAGCGGGTTTTTTCGAAAA  >  CP009273/3370874‑3371147

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.