New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	= 1103383	162 (0.500)	59 (0.180)	24/180	22.8	0.32	intergenic (‑383/+35)	ugpB/regA2	sn‑glycerol‑3‑phosphate‑binding periplasmic protein ugpB/photosynthetic apparatus regulatory protein RegA
	?	NC_014034	= 2330280	89 (0.250)					intergenic (+255/+57)	RCAP_rcc02161/mrcA	hypothetical protein/penicillin‑binding protein 1A
Rejected: Position hash score below cutoff.

GCGGACCGGCGCCGCGACGGAGAGGTCCGAACGCGGGGGGCGCCTCGGGGCGATTTCGCCGCGCGGCCGCGCGGCGATCCGCCGGGGGCTCCGCCCCCGGACCCCCGG....................................................................................................  >  NC_014034/1103276‑1103383 ..................................................................................................GGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGG  <  NC_014034/2330280‑2330181                                                                                                                                                                                                                                                                                  gatgcctCGGCGACCCGCCGGGGGCTCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATG                                             >  1:1453312/8‑101 (MQ=18)                                                                  atgcctCGGCGACCCGCCGGGGGCTCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGC                                            <  1:1864656/95‑1 (MQ=17)                                                                   ggcccCGGCGCCCCGCCGGGGGCTCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCG                                           <  2:6277288/96‑1 (MQ=9)                                                                    gcctCGGCGACCCGCCGGGGGCTCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGC                                          >  2:3696255/5‑101 (MQ=11)                                                                      ctCGGCGACCCGCCGGGGGCTCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGC                                        >  2:324748/3‑101 (MQ=11)                                                                       cgcgcgccCCGCCGGGGGCTCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCC                                       <  2:1156672/93‑1 (MQ=9)                                                                        cggccccCCGCCGGGGGCTCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCC                                      <  2:6576552/94‑1 (MQ=2)                                                                         ggccccCCGCCGGGGGCTCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCC                                     <  1:1797384/95‑1 (MQ=11)                                                                          gcgccCCGCCGGGGGCTCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCG                                    <  1:5046149/96‑1 (MQ=14)                                                                          gcgccCCGCCGGGGGCTCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCG                                    <  2:6421033/96‑1 (MQ=14)                                                                          gccccCCGCCGGGGGCTCCGCCCCCGGACCCCCGGGCTCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGCTGATCCGGGGCCCCGCATGCGCGCCCCG                                    <  1:5061690/96‑1 (MQ=2)                                                                          GCGACCCGCCGGGGGCTCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCG                                    <  2:4128519/101‑1 (MQ=32)                                                                           ccccCCGCCGGGGGCTCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGG                                   <  2:5458140/97‑1 (MQ=11)                                                                              cCCGCCGGGGGCTCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTT                                <  2:1575031/100‑1 (MQ=11)                                                                              cCCGCCGGGGGCTCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTT                                <  2:2237382/100‑1 (MQ=11)                                                                              cCCGCCGGGGGCTCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTT                                <  1:4137164/100‑1 (MQ=11)                                                                               CCGCCGGGGGCTCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTT                               >  1:131828/1‑101 (MQ=1)                                                                               CCGCCGGGGGCTCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTT                               <  2:355284/101‑1 (MQ=1)                                                                               CCGCCGGGGGCTCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTT                               <  1:3060943/101‑1 (MQ=1)                                                                                CGCCGGGGGCTCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTT                              <  1:5648823/101‑1 (MQ=1)                                                                                CGCCGGGGGCTCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTT                              <  2:5061064/101‑1 (MQ=1)                                                                                 GCCGGGGGCTCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTT                             <  1:1427995/101‑1 (MQ=1)                                                                                  CCGGGGGCTCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTC                            <  2:4550684/101‑1 (MQ=1)                                                                                  CCGGGGGCTCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTC                            <  1:2120823/101‑1 (MQ=1)                                                                                  CCGGGGGCTCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTC                            <  2:3666101/101‑1 (MQ=1)                                                                                   CGGGGGCTCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCT                           >  1:6726111/1‑101 (MQ=1)                                                                                   CGGGGGCTCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCT                           >  1:3049544/1‑101 (MQ=1)                                                                                    GGGGGCTCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTT                          <  1:2913119/101‑1 (MQ=1)                                                                                    GGGGGCTCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTT                          >  2:3081204/1‑101 (MQ=1)                                                                                    GGGGGCTCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTT                          >  2:488404/1‑101 (MQ=1)                                                                                     GGGGCTCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTG                         <  1:5214454/101‑1 (MQ=1)                                                                                     GGGGCTCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTG                         >  2:545113/1‑101 (MQ=1)                                                                                      GGGCTCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGG                        <  2:1080742/101‑1 (MQ=1)                                                                                      GGGCTCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGG                        <  1:3020236/101‑1 (MQ=1)                                                                                        cttccgatctCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCG                      <  1:6147828/91‑1 (MQ=0)                                                                                        GCTCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCG                      >  2:4880701/1‑101 (MQ=1)                                                                                        GCTCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCG                      >  2:2824134/1‑101 (MQ=1)                                                                                         CTCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGC                     >  2:1584100/1‑101 (MQ=1)                                                                                         CTCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGC                     <  1:1800642/101‑1 (MQ=1)                                                                                          TCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTGTTGGCGCA                    >  2:5646693/1‑101 (MQ=1)                                                                                          TCCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCA                    <  1:6898405/101‑1 (MQ=1)                                                                                           CCGCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAA                   >  2:6597681/1‑101 (MQ=1)                                                                                             GCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAAT                 >  2:4033966/1‑101 (MQ=1)                                                                                             GCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAAT                 <  2:113886/101‑1 (MQ=1)                                                                                             GCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAAT                 <  1:6673074/101‑1 (MQ=1)                                                                                             GCCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGCCTTTTTCTTGGCGCAAAT                 >  2:3577094/1‑101 (MQ=1)                                                                                              CCCCCGGCCCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGTCGCAAATA                <  2:2102633/101‑1 (MQ=0)                                                                                              CCCCCGGCCCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATA                <  2:680591/101‑1 (MQ=1)                                                                                              CCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATA                <  1:3538518/101‑1 (MQ=1)                                                                                              CCCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATA                <  1:1169066/101‑1 (MQ=1)                                                                                               CCCCGGACCCCGGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATAC               <  2:6681898/101‑1 (MQ=1)                                                                                               CCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATAC               <  2:5821613/101‑1 (MQ=1)                                                                                               CCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATAC               <  1:3738365/101‑1 (MQ=1)                                                                                               CCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATAC               <  1:3635343/101‑1 (MQ=1)                                                                                               CCCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATAC               <  2:6994677/101‑1 (MQ=1)                                                                                                CCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACG              <  1:4174193/101‑1 (MQ=1)                                                                                                CCCGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACG              >  1:1657309/1‑101 (MQ=1)                                                                                                  CGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGagatcggaag            >  2:6147509/1‑91 (MQ=0)                                                                                                  CGGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCC            <  1:4201343/101‑1 (MQ=1)                                                                                                                                                                                                                  GCGGACCGGCGCCGCGACGGAGAGGTCCGAACGCGGGGGGCGCCTCGGGGCGATTTCGCCGCGCGGCCGCGCGGCGATCCGCCGGGGGCTCCGCCCCCGGACCCCCGG....................................................................................................  >  NC_014034/1103276‑1103383 ..................................................................................................GGACCCCCGGGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGG  <  NC_014034/2330280‑2330181 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 29 ≤  ATCG  < 34 ≤  ATCG  < 40 ≤  ATCG