New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1103354 =	318 (0.780)	50 (0.120)	18/178	27.9	0.16	intergenic (‑354/+64)	ugpB/regA2	sn‑glycerol‑3‑phosphate‑binding periplasmic protein ugpB/photosynthetic apparatus regulatory protein RegA
	?	NC_014034	2330307 =	189 (0.410)					intergenic (+282/+30)	RCAP_rcc02161/mrcA	hypothetical protein/penicillin‑binding protein 1A
Rejected: Position hash score below cutoff.

AGGCGGCGGGCGAAGACCTGGGCGGCATGATCGATTTCGAGGACTGATCCCCGGCCCCCGTTTTTTCTTGGCCCAAATACGCCGGGGGTCCGGGGGCGGAGCCCCCGGCGG....................................................................................................  <  NC_014034/1103464‑1103354 ....................................................................................................GCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCTGTTCCCCGGTC  >  NC_014034/2330307‑2330406                                                                                                                                                                                                                                                                                          GGCCCAAAGATCCCGGGGGTCCGGGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATC                                           <  2:1800591/101‑1 (MQ=0)                                                                        gccaaagatcCCGGGGGTCCGGGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCG                                         <  1:3913409/91‑1 (MQ=14)                                                                         ccaaagatcCCGGGGGTCCGGGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGA                                        <  1:5332044/92‑1 (MQ=11)                                                                          caaagatcCCGGGGGTCGGGGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAA                                       <  2:7300537/93‑1 (MQ=0)                                                                          caaagagccgGGGGGTCCGGGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAA                                       <  2:2722835/91‑1 (MQ=0)                                                                           aaagatcCCGGGGGTCGGGGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAG                                      <  2:4452820/94‑1 (MQ=0)                                                                           aaagatcCCGGGGGTCCGGGGGCGGAGCCCCCTGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAG                                      <  1:4562716/94‑1 (MQ=0)                                                                           aaagatcCCGGGGGTCCGGGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAG                                      <  2:1662097/94‑1 (MQ=1)                                                                           aaagatcCCGGGGGTCCGGGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAG                                      <  2:8231772/94‑1 (MQ=1)                                                                           aaagatcCCGGGGGTCCGGGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAG                                      <  2:2350690/94‑1 (MQ=1)                                                                           aaagatcCCGGGGGTCCGGGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAG                                      <  2:4819042/94‑1 (MQ=1)                                                                                 cCCGGGGGTCCGGGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCC                                <  1:7144184/100‑1 (MQ=11)                                                                                  CCGGGGGTCCGGGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCT                               <  1:4263030/101‑1 (MQ=1)                                                                                  CCGGGGGTCCGGGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCT                               <  1:3622330/101‑1 (MQ=1)                                                                                   CGGGGGTCCGGGGGCGGCGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTT                              <  2:3884057/101‑1 (MQ=1)                                                                                   CGGGGGTCCGGGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTT                              <  2:3389751/101‑1 (MQ=1)                                                                                   CGGGGGTCCGGGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTT                              <  1:7182019/101‑1 (MQ=1)                                                                                   CGGGGGTCCGGGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTT                              <  1:2306776/101‑1 (MQ=1)                                                                                    GGGGGTCCGGGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTC                             <  2:3327024/101‑1 (MQ=1)                                                                                    GGGGGTCCGGGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTC                             <  2:7536419/101‑1 (MQ=1)                                                                                     ggaGTCCGGGGGCGGAGCCCCCGGGGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCT                            <  2:9128374/98‑1 (MQ=0)                                                                                     GGGGTCCGGGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCT                            <  2:4576452/101‑1 (MQ=1)                                                                                     GGGGTCCGGGGGCGAGGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCT                            <  2:5351079/101‑1 (MQ=14)                                                                                     GGGGGCCGGGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCT                            <  1:7322/101‑1 (MQ=1)                                                                                      GGGTCCGGGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTT                           <  2:6494659/101‑1 (MQ=1)                                                                                      GGGTCCGGGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTT                           <  2:6091866/101‑1 (MQ=1)                                                                                      GGGTCCGGGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTT                           <  1:3963894/101‑1 (MQ=1)                                                                                       GGTCCGGGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTC                          <  1:2986037/101‑1 (MQ=1)                                                                                       GGTCCGGGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTC                          <  1:7414075/101‑1 (MQ=1)                                                                                       GGTCCGGGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTC                          <  2:5644090/101‑1 (MQ=1)                                                                                        GTCCGGGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCG                         <  1:5555653/101‑1 (MQ=1)                                                                                         TCCGGGGGCGGAGCCCTCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGG                        <  2:7949400/101‑1 (MQ=1)                                                                                         TCCGGGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGG                        <  2:8469746/101‑1 (MQ=1)                                                                                           CGGGGGCGGCGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGA                      <  1:304192/101‑1 (MQ=1)                                                                                           CGGGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGA                      <  2:1030154/101‑1 (MQ=1)                                                                                             GGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATC                    <  2:3778070/101‑1 (MQ=1)                                                                                             GGGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATC                    <  2:7358390/101‑1 (MQ=1)                                                                                              GGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCA                   <  1:3998006/101‑1 (MQ=1)                                                                                              GGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCA                   <  2:6609037/101‑1 (MQ=1)                                                                                              GGGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCA                   <  1:174713/101‑1 (MQ=1)                                                                                               GGCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCAC                  <  1:1405047/101‑1 (MQ=1)                                                                                                GCGGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACC                 <  1:5679867/101‑1 (MQ=1)                                                                                                  GGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGGCAGGGATCCGAAGGTCGCCTTCTTCGGGATAACCCG               >  2:449526/1‑101 (MQ=0)                                                                                                  GGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCG               <  2:2243939/101‑1 (MQ=1)                                                                                                  GGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCG               <  1:2442620/101‑1 (MQ=1)                                                                                                  GGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGGCGCCTTCTTCGGGATCACCCc               >  2:8748282/1‑100 (MQ=1)                                                                                                  GGAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAAACCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGGCGCCTTCTTCGGGATCACCCG               >  2:7882979/1‑101 (MQ=0)                                                                                                   GAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGGTCACCCGC              >  2:8301907/1‑101 (MQ=1)                                                                                                   GAGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGC              <  2:1918051/101‑1 (MQ=1)                                                                                                    AGCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCT             <  2:2044929/101‑1 (MQ=1)                                                                                                                                                                                                                     AGGCGGCGGGCGAAGACCTGGGCGGCATGATCGATTTCGAGGACTGATCCCCGGCCCCCGTTTTTTCTTGGCCCAAATACGCCGGGGGTCCGGGGGCGGAGCCCCCGGCGG....................................................................................................  <  NC_014034/1103464‑1103354 ....................................................................................................GCCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCTGTTCCCCGGTC  >  NC_014034/2330307‑2330406 Base quality scores:  ATCG  < 3 ≤  ATCG  < 19 ≤  ATCG  < 27 ≤  ATCG  < 34 ≤  ATCG  < 41 ≤  ATCG