New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 1103374	312 (0.720)	51 (0.120)	17/190	29.7	0.18	intergenic (‑374/+44)	ugpB/regA2	sn‑glycerol‑3‑phosphate‑binding periplasmic protein ugpB/photosynthetic apparatus regulatory protein RegA
	?	NC_014034	2330184 =	161 (0.350)					intergenic (+159/+153)	RCAP_rcc02161/mrcA	hypothetical protein/penicillin‑binding protein 1A
Rejected: Position hash score below cutoff.

AGGCAGGCGGACCGGCGCCGCGACGGAGAGGTCCGAACGCGGGGGGCGCCTCGGGGCGATTTCGCCGCGCGGCCGCGCGGCGATCCGCCGGGGGCTCCGCCCCCG....................................................................................................  >  NC_014034/1103270‑1103374 ....................................................................................................CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCG  >  NC_014034/2330184‑2330283                                                                                                                                                                                                                                              TCCGAACGCGGGGGGCGCCTCGGGGCGATTTCGCCGCGCGGCCGCGCGGCGATCCGCCGGGGGCTCCGCCCCCGGACCCCCGGCGCATTTGCGCCCAGAAA                                                                           >  1:4619091/1‑101 (MQ=255)                                                                                cgacccgggCGGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGG                           <  2:3396608/92‑1 (MQ=32)                                                                                 gacccgggCGGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGGGGC                          >  1:1550653/9‑101 (MQ=17)                                                                                 gacccgggCGGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGC                          >  1:7300841/9‑101 (MQ=32)                                                                                 gacccgggCGGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGC                          <  1:4857334/93‑1 (MQ=32)                                                                                  gcccgggCGGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCT                         <  1:1339415/94‑1 (MQ=17)                                                                                  acccgggCGGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCT                         <  2:35082/94‑1 (MQ=32)                                                                                  acccgggCGGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCT                         <  1:5934745/94‑1 (MQ=32)                                                                                  acccgggCGGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCT                         <  1:2491985/94‑1 (MQ=32)                                                                                   cccgggCGGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTT                        <  1:2573829/95‑1 (MQ=32)                                                                                    ccgggCGGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAGAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTT                       <  2:2384349/96‑1 (MQ=17)                                                                                    ccgggCGGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTT                       <  2:6308445/96‑1 (MQ=32)                                                                                    ccgggCGGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTT                       >  1:7465567/6‑101 (MQ=32)                                                                                    ccgggCGGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTT                       <  1:7463416/96‑1 (MQ=32)                                                                                    ccgggCGGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGAATCACCGGCGGCCCGGGCGGCTTT                       <  2:4374494/96‑1 (MQ=17)                                                                                     cgggCGGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTC                      <  1:1876139/97‑1 (MQ=32)                                                                                     cgggCGGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTC                      <  2:664981/97‑1 (MQ=32)                                                                                     cgggCGGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTC                      >  1:2520852/5‑101 (MQ=32)                                                                                      gggCGGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCA                     <  2:4905411/98‑1 (MQ=31)                                                                                      gggCGGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCA                     >  1:4876337/4‑101 (MQ=31)                                                                                      gggCGGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCA                     <  2:8428962/98‑1 (MQ=31)                                                                                      gggCGGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCGTTCA                     >  1:7358714/4‑101 (MQ=14)                                                                                        gCGGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACC                   <  1:4893771/100‑1 (MQ=1)                                                                                         CGGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCT                  <  2:6414103/101‑1 (MQ=1)                                                                                         CGGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCT                  >  2:61668/1‑101 (MQ=1)                                                                                          gtGGGCTCCGCCCCCGCACCCGCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGGTCACCGGCGGCCCGGGCGCCTTTCACCTG                 <  2:5927235/99‑1 (MQ=0)                                                                                          GGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGGTTTCACCTG                 >  2:5152762/1‑101 (MQ=1)                                                                                          GGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTG                 >  2:2240470/1‑101 (MQ=1)                                                                                          GGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTG                 >  1:3251473/1‑101 (MQ=1)                                                                                          GGGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTG                 <  1:4970507/101‑1 (MQ=1)                                                                                           GGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGG                >  2:3125504/1‑101 (MQ=1)                                                                                           GGGGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGG                <  1:3408849/101‑1 (MQ=1)                                                                                             GGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGG              >  2:2442547/1‑101 (MQ=1)                                                                                             GGCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGG              >  1:2044991/1‑101 (MQ=1)                                                                                              GCTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGC             >  1:1864588/1‑101 (MQ=1)                                                                                               CTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCGCCTGGGGCC            <  2:8197461/101‑1 (MQ=1)                                                                                               CTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCC            >  2:926224/1‑101 (MQ=1)                                                                                               CTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCC            <  2:3338735/101‑1 (MQ=1)                                                                                               CTCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCC            >  1:7542780/1‑101 (MQ=1)                                                                                                TCCGCCCCCGCCCCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCA           <  2:3844652/101‑1 (MQ=1)                                                                                                TCCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCA           <  2:6556200/101‑1 (MQ=1)                                                                                                 CCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAA          >  2:3622222/1‑101 (MQ=1)                                                                                                 CCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAA          <  2:3512847/101‑1 (MQ=1)                                                                                                 CCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAA          <  1:8890607/101‑1 (MQ=1)                                                                                                 CCGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAA          >  2:6384677/1‑101 (MQ=1)                                                                                                  CGCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAA         >  2:3653227/1‑101 (MQ=1)                                                                                                   GCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAG        <  1:7714350/101‑1 (MQ=1)                                                                                                   GCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAG        >  1:2738513/1‑101 (MQ=1)                                                                                                   GCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAG        <  1:2616822/101‑1 (MQ=1)                                                                                                   GCCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAG        >  1:1802358/1‑101 (MQ=1)                                                                                                    CCCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGA       >  1:6494911/1‑101 (MQ=1)                                                                                                                                                                                                               AGGCAGGCGGACCGGCGCCGCGACGGAGAGGTCCGAACGCGGGGGGCGCCTCGGGGCGATTTCGCCGCGCGGCCGCGCGGCGATCCGCCGGGGGCTCCGCCCCCG....................................................................................................  >  NC_014034/1103270‑1103374 ....................................................................................................CCCCGCACCCCCGGCGTATTTGCGCCAAGAAAAAGCCGGGGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCG  >  NC_014034/2330184‑2330283 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 27 ≤  ATCG  < 33 ≤  ATCG  < 39 ≤  ATCG