New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1978503 =	NA (NA)	46 (0.510)	35/274	NT	34.6%	noncoding (768/768 nt)	IS1	repeat region
	?	NC_000913	2380552 =	87 (0.960)					coding (92/1296 nt)	menF	isochorismate synthase 2

AATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/1978650‑1978503 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAATCTCTTGCGACAAATGGCGCAGTAGATTTTCCAGCGCCGTAGTAAGTGATTGCACGCGGACCTCTCCCTGTTAAAAGCCTCACATTATACGGGGTACTACAAAAAAAATG  >  NC_000913/2380552‑2380698                                                                                                                                                                                                                                                                                                         AATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCG                                                                                                                                                    <  1:1442575/149‑1    TGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTGTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGGAA                                                                                                                                                 <  2:131674/149‑1          GCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTAGCTGATCATAAACCACGATCAAGAAGTTGGAGTCATTACCGGATTATCGA                                                                                                                                           >  2:791773/1‑149               ACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGGAATATCGATAACC                                                                                                                                      <  2:1311985/149‑1                   GAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGGAATATCGATAACCCGAA                                                                                                                                  <  1:203014/149‑1                       CTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGGAATATCGATAACCCGAATGCC                                                                                                                              >  2:781219/1‑149                         GAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGGAATATCGATAACCCGAATGCCGG                                                                                                                            <  2:1596542/149‑1                            GCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGGAATATCGATAACCCGAATGCCGGGTG                                                                                                                         >  2:1358016/1‑149                                     GGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAA                                                                                                                <  2:1168105/149‑1                                     GGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAA                                                                                                                >  1:1570887/1‑149                                      GCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAAT                                                                                                               <  2:994778/149‑1                                            CTGGGACGGAAGTCGCTGGCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAATCTCTTG                                                                                                         <  2:591050/149‑1                                                  CGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAATCTCTTGCGACAA                                                                                                   >  1:669173/1‑149                                                              TCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAATCTCTTGCGACAAATGGCGCAGTAG                                                                                       <  1:1226518/149‑1                                                                aTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAATCTCTTGCGACAAATGGCGCAGTAGAT                                                                                     >  2:1226820/2‑149                                                                GTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAATCTCTTGCGACAAATGGCGCAGTAGAT                                                                                     >  1:1553592/1‑149                                                                 TTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAAT                                                                                                               >  2:744008/1‑122                                                                 TTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAAT                                                                                                               <  1:744008/122‑1                                                                    TCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAATCTCTTGCGACAAATGGCGCAGTAGATTTTC                                                                                 <  1:18442/149‑1                                                                    TCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAATCTCTTGCGACAAATGGCGCAGTAGATTTTC                                                                                 <  1:793277/149‑1                                                                            GGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGGAATATCTATAACCCGAATGCCGGTTGTCGCAGGAATCTCTTGAGACAAATGGCGCAGTGGATTTTCCAGCGCCG                                                                         >  1:1420539/1‑149                                                                            GGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACAATCAATAAGTTGGAGTCATTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAATCTCTTGCGACAAATGGCGCAGTAGATTTTCCAGCGCCG                                                                         <  1:781219/149‑1                                                                             GTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAAT                                                                                                               <  2:901583/110‑1                                                                             GTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAAT                                                                                                               >  1:901583/1‑110                                                                                 AGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAATCTCTTGCGACAAATGGCGCAGTAGATTTTCCAGCGCCGTAGTA                                                                    >  2:1124073/1‑149                                                                                     GCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAATCTCTTGCGACAAATGGCGCAGTAGATTTTCCAGCGCCGTAGTAAGTG                                                                >  1:1260055/1‑149                                                                                      CATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAATCTCTTGCGACAAATGGCGCAGTAGATTTTCCAGCGCCGTAGTAAGTGA                                                               >  2:1428125/1‑149                                                                                               GTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAATCTCTAGCGACAAATCGCGCAGTAGATATTCCAGCGCCGTAGTAAGTGATTGCACGCG                                                      >  1:1307131/1‑149                                                                                                TCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAATCTCTTGCGACAAATGGCGCAGTAGATTTTCCAGCGCCGTAGTAAGTGATTGCACGCGG                                                     >  2:493549/1‑149                                                                                                TCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAATCTCTTGCGACAAATGGCGCAGTAGATTTTCCAGCGCCGTAGTAAGTGATTGCACGCGG                                                     >  2:22672/1‑149                                                                                                TCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAATCTCTTGCGACAAATGGCGCAGTAGATTTTCCAGCGCCGTAGTAAGTGATTGCACGCGG                                                     <  1:965127/149‑1                                                                                                 CATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAATCTCTTGCGACAAATGGCGCAGTAGATTTTCCAGCGTCGTAGTAAGTGATTGCACGCGGA                                                    >  1:435748/1‑149                                                                                                  ATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAATCTCTTGCGACAAATGGCGCAGTAGATTTTCCAGCGCCGTAGTAAGTGATTGCACGCGGAC                                                   <  1:163831/149‑1                                                                                                  ATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAATCTCTTGCGACAAATGGCGCAGTAGATTTTCCAGCGCCGTAGTAAGTGATTGCACGCGGAC                                                   <  2:158083/149‑1                                                                                                      GGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTAATTACCGGAATATCGATAAACAGAATGCCGGGTGTCGCAGGAATCTCTTGCGACAAATTTATCCGTAGATTTTCCAGCGCCGAAGTAAGTGATTGCACGCGGACCTCT                                               >  1:809531/1‑149                                                                                                                GAACATAAAACACTATCAATAAGTTGGAGTCATTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAATCTCTTGCGACAAATGGCGCAGTAGATTTTCCAGCGCCGTAGTAAGTGATTGCACGCGGACCTCTCCCTGTTAAA                                     >  2:546031/1‑149                                                                                                                GAACACAAAACACTATCAATAAGTTGGAGTCATTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAATCTCTTGCGACAAATGGCGCAGTAGATTTTCCAGCGCCGTAGTAAGTGATTGCACGCGGACCTCTCCCTGTTAAA                                     >  2:728351/1‑149                                                                                                                              ATCAATAAGTTGGAGTCATTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAATCTCTTGCGACAAATGGCGCAGTAGATTTTCCAGCGCCGTAGTAAGTGATTGCACGCGGACCTCTCCCTGTTAAAAGCCTCACATTATA                       >  1:190794/1‑149                                                                                                                               TCAATAAGTTGGAGTCATTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAATCTCTTGCGACAAATGGCGCAGTAGATTTTCCAGCGCCGTAGTAAGTGATTGCACGCGGACCTCTCCCTGTTAAAAGCCTCACATTATAC                      >  1:818379/1‑149                                                                                                                                 AATAAGTTGGAGTCATTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAATCTCTTGCGACAAATGGCGCAGTAGATTTTCCAGCGCCGTAGTAAGTGATTGCACGCGGACCTCTCCCTGTTAAAAGCCTCACATTATACGG                    >  2:138555/1‑149                                                                                                                                 AATAAGTTGGAGTCATTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAATCTCTTGCGACAAATGGCGCAGTAGATTTTCCAGCGCCGTAGTAAGTGATTGCACGCGGACCTCTCCCTGTTAAAAGCCTCACATTATACGG                    >  1:1258398/1‑149                                                                                                                                      GTTGGAGTCATTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAATCTCTTGCGACAAATGGCGCAGTAGATTTTCCAGCGCCGTAGTAAGTCATTGCACGCGGACCTCTCCCTGTTAAAAGCCTCACATTATACGGatcgg               >  2:780430/1‑144                                                                                                                                          GAGTCATTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAATCTCTTGCGACAAATGGCGCAGTAGATTTTCCAGCGCCGTAGTAAGTGATTGCACGCGGACCTCTCCCTGTTAAAAGCCTCACATTATACGGGGTACTACA           >  1:605749/1‑149                                                                                                                                          GAGTCATTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAATCTCTTGCGACAAATGGCGCAGTAGATTTTCCAGCGCCGTAGTAAGTGATTGCACGCGGACCTCTCCCTGTTAAAAGCCTCACATTATACGGGGTACTACA           >  1:656161/1‑149                                                                                                                                          GAGTCATTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAATCTCTTGCGACAAATGGCGCAGTAGATTTTCCAGCGCCGTAGTAAGTGATTGCACGCGGACATCTCCATTTTAAAACCATCCAATTATACGGGGTACTAaa           >  1:390545/1‑147                                                                                                                                               ATTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAATCTCTTGCGACAAATGGCGCAGTAGATTTTCCAGCGCCGTAGTAAGTGATTGCACGCGGACCTCTCCCTGTTAAAAGCCTCACATTATACGGGGTACTACAAAAAA      >  2:187528/1‑149                                                                                                                                               ATTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAATCTCTTGCGACAAATGGCGCAGTAGATTTTCCAGCGCCGTAGTAAGTGATTGCACGCGGACCTCTCCCTGTTAAAAGCCTCACATTATACGGGGTACTACAAAAAA      <  1:493549/149‑1                                                                                                                                               ATTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAATCTCTTGCGACAAATGGCGCAGTAGATTTTCCAGCGCCGTAGTAAGTGATTGCACGCGGACCTCTCCCTGTTAAAAGCCTCACATTATACGGGGTACTACAAAAAA      <  1:22672/149‑1                                                                                                                                                TTACCGGAATATCGATAACCCGAATTCCGGGTGTAGCCGGAATCTCTTGGGACAATTGGCGCAGTATATTTTCCAGCGCCGTAGTAAGTGATTGCACGCGGACCTCTCCCTGTTAAAAGCCTCACATTATACGGGGTACTACAAAAAAA     <  2:101631/149‑1                                                                                                                                                TTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAATCTCTTGCGACAAATGGCGCAGTATATTTTCCAGCGCCGTAGTAAGTGATTGCACGCGGACCTCTCCCTGTTAAAAGCCTCACATTATACGGGGTACTACAAAAAAA     <  2:669173/149‑1                                                                                                                                                TTACCGGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAATCTCTTGCGACAAATGGCGCAGTAGATTTTCCAGCGCCGTAGTAAGTGATTGCACGCGGACCTCTCCCTGTTAAAAGCCTCACATTATACGGGCTACTACAAAAAAA     >  1:324201/1‑149                                                                                                                                                   CCGGAATATCGATAACCCTAATGCCGGGTGTCGCCGGAATCTCTTGCGACAAATGGCGCAGTGGATTTTCCAGCGCCGTAGTAAGTGATTGCACGCGGACCTCTCCCTGTTAAAATCCTCACATTATACGGGGTACTACAAAAAAAATG  <  2:1420539/149‑1                                                                                                                                                                                                                                                                                                         AATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/1978650‑1978503 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGAATATCGATAACCCGAATGCCGGGTGTCGCCGGAATCTCTTGCGACAAATGGCGCAGTAGATTTTCCAGCGCCGTAGTAAGTGATTGCACGCGGACCTCTCCCTGTTAAAAGCCTCACATTATACGGGGTACTACAAAAAAAATG  >  NC_000913/2380552‑2380698

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ 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.