New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1103354 =	80 (0.380)	7 (0.030)	3/178	35.2	0.10	intergenic (‑354/+64)	ugpB/regA2	sn‑glycerol‑3‑phosphate‑binding periplasmic protein ugpB/photosynthetic apparatus regulatory protein RegA
	?	NC_014034	2330307 =	46 (0.190)					intergenic (+282/+30)	RCAP_rcc02161/mrcA	hypothetical protein/penicillin‑binding protein 1A
Rejected: Position hash score below cutoff.

GGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCCGGG..G....G.....CCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCTGTTCCCCGGTCG  >  NC_014034/2330218‑2330407                                                                                                     |                                                                                                     ggCGCGCAGGCGGGGCCCCGGATCCCCGGCGGCCCGGGCGGCTTTCCCCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGCGGGTCGCCGa                                                                                               <  1:3371816/101‑1 (MQ=18)      gcATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGCGGGGCGCCCCGGCAt                                                                                          >  1:2255344/1‑101 (MQ=21)        aTGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGCGGGGCGCCGAGGccacc                                                                                        >  2:2723659/1‑97 (MQ=21)           gggggCCCCGGCCCCCGGGCGGCCCGGGCGGC.TCCCCCGGGGGGCAAAAGCCCCGGGGGGCGGGGG..G....GCGGCCCCCCCGGCGGGTCGCCGAGGCATCGCCt                                                                                     <  2:1905488/100‑1 (MQ=255)            ggggCCCCGGATCCCCGGCGGCCCGGGCGGCTTTCCCCGGGGGCCAAAGATCCGGGGGGTCCGGGG..GCGGAG.....CCCCCGGCGGGTCGCCGAGGCATCGCCTc                                                                                    <  1:2632290/101‑1 (MQ=18)            ggggCCCCGGATCACCGGCGGCCGGGGCGGCTTTCCCCGGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGCGGGTCGCCGAGGCATCGCCTc                                                                                    <  1:1361394/101‑1 (MQ=18)            ggggCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGCGGGGCGGCGCGGCACCGcccc                                                                                    >  1:824036/1‑99 (MQ=18)             gggCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGCGGGGCGGCGGGGCAGCGccccc                                                                                   >  2:3098302/1‑98 (MQ=18)             gggCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGCGGGGCGCCGGGGCGACGCCCCg                                                                                   >  1:2811404/1‑101 (MQ=18)               gCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGCGGGGCGGCGCGGGCCCGCCTCggg                                                                                 >  2:1370207/1‑100 (MQ=16)                ccccGGACCCCGGGCGGCCGGGGCGGCTTTCGCCGGGGGCCAAAGACCCGGGGGGTCGGGGG..GCGGAG.....CCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCg                                                                                <  1:202039/101‑1 (MQ=12)                      aTCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGCGGGGCGGCGCGGCCTCGCCCCGGCGGAAAcc                                                                          >  2:3536347/1‑101 (MQ=12)                              cggcCCGGGGGGCTTGCACGTGGGGCCAAGGTGCCGGGGGGTCGGGGG..GCGGAG.....CCCCGGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTaa                                                                  <  1:4313617/101‑1 (MQ=255)                                gcCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGCGGGGGGCCGAGGCATCGCCCCGGGGAAAAccccttttaaaa                                                                >  2:4086862/1‑92 (MQ=12)                                   cGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGAcc                                                             <  1:4092047/101‑1 (MQ=25)                                   cGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGCGGGGGGCCCGGGGATCGCCCCGGCGACAAACCTTATTaaaaaac                                                             >  2:68326/1‑97 (MQ=9)                                   cGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGCGGGGCGCCGGGGGAGCGCCCCGGGGGAAACCCTTAGTaaaaaac                                                             >  1:3467715/1‑97 (MQ=9)                                    gggCGGCTTTCCCCTGGGGCCAAAGACCCCGGGGGTCCGGGGGCG....GAC...CCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGAccg                                                            <  1:3098546/101‑1 (MQ=21)                                    gggCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGCGGGGGGGCGAGGCGTCGCCTCCGCGGCATCCCCTTGGAAAAAccg                                                            >  1:1609374/1‑101 (MQ=9)                                     ggcggcTTTCCCCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGAccgc                                                           <  2:2971730/101‑1 (MQ=21)                                       cggcTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGCGGGGCGGCGAGGCGGCGCCCCCGCGGAAACCCCTCGTACAAAccgccc                                                         >  1:1623131/1‑101 (MQ=9)                                        gtcTTTCGCCGGGGGCCAAAGACCCGGGGGGTCGGGGG..GCGGAG.....CCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGAccgcccg                                                        <  2:2799186/99‑1 (MQ=16)                                        gtcTTTCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGAccgcccg                                                        <  2:4542101/99‑1 (MQ=21)                                         gcTTTCCCCTGGGGCCAAAGATCCCGGGGGTCCGGGGGCG....GCC...CCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGAccgcccgc                                                       <  1:3843164/101‑1 (MQ=25)                                           tttCACCTGGGGCCAAAGATCCCGGGGGTCGGGGG..GCGGAG.....CCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCgg                                                     <  1:3074994/101‑1 (MQ=21)                                           tttCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGCGGGGCGCCGAGGGAACGCCCCGGCGAAAACCCCTTGTAAAAAACCNCCNCgg                                                     >  1:737228/1‑101 (MQ=9)                                            ttCACCTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGCGGGGCGCCCGGGGAACGCCTCGGCGAAAACCCCTTGTAAAAACCACCCCCGGa                                                    >  2:1469658/1‑101 (MQ=2)                                                 cTGGGGCCAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAggg                                               <  2:3498500/101‑1 (MQ=21)                                                       ccAAAGATCCGGGGGGTCCGGGG..GCGGAG.....CCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGa                                         <  2:2870567/101‑1 (MQ=21)                                                       ccAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGa                                         <  2:651872/101‑1 (MQ=21)                                                        cAAAGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGCGGGGCGCCGGGGGGTCGCCCCGGCGCAATACCCTAGTAAAAAACGCCCCCGGACCGGGAGCCGaa                                        >  1:199387/1‑101 (MQ=2)                                                         aaaGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGCGGGGCGCCGAGGGATCGCCTCGGCGAAAACCCTTAGTAAAAACCCCCCGCGGGCAggggaccgcag                                       >  2:1128968/1‑93 (MQ=12)                                                           aGATCCCGGGGGTCCGGGG..GCGGTG.....CCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGt                                     <  1:4255922/101‑1 (MQ=25)                                                           aGATCCCGGGGGTCCGGGG..GCGGAG.....CCCCCGGCGGGGCGCCGCGGGATCGCCTCGGCGCAAACCCTTAGTAAAAACCCCCCCCGGACAcggggccccaggg                                     >  2:1815489/1‑91 (MQ=2)                                                                  ggccgggggcgg..g....c.....CCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCg                          <  2:1616190/91‑1 (MQ=38)                                                                             ggggcggag.....CCCCCGGCGGGTCGCCCAGGCATCGCCCCCGCGAAATCCCTTTGTAAAAAACGCCCGCGGACAGGGGTCCGAAGGGCGCCTTCTTCGGGATc                     >  2:457036/9‑101 (MQ=25)                                                                               ggcggag.....CCCCCGGCGGGGCGCCGAGGCATCGCCCCGGCGAAAACCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGCAGGGCGCCTTCTTCGGGATCAc                   >  2:1453403/7‑101 (MQ=38)                                                                                  ggggcggaccccccGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATc                     <  2:2137317/92‑1 (MQ=255)                                                                                       gcccccccgGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCg                <  1:3536605/97‑1 (MQ=255)                                                                                         ccgcgcgcgcggGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCt              <  2:1623026/93‑1 (MQ=255)                                                                                           cccccGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTTGTAAAAACCGCCCGCGGACAGGGATCCGCAGGGCGCCTTCTTCCGGATCACCCGCTGt            >  2:4493558/1‑101 (MQ=255)                                                                                            ccccGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCGTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCTGtt           <  2:783284/101‑1 (MQ=255)                                                                                                ggcggGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCTGTTcccc       <  1:1370302/101‑1 (MQ=255)                                                                                                ggcggGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCTGTTcccc       <  1:4475292/101‑1 (MQ=255)                                                                                                 gcggGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCTGTTCCCCg      <  1:3933976/101‑1 (MQ=255)                                                                                                 gcggGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCTGTTCCCCg      <  2:17309/101‑1 (MQ=255)                                                                                                  ggggTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCTCCCGCTGTTCCCCgg     <  1:2572209/100‑1 (MQ=255)                                                                                                  cggGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCTGTTCCCCgg     <  2:993628/101‑1 (MQ=255)                                                                                                  cggGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCTGTTCCCCgg     >  1:2102275/1‑101 (MQ=255)                                                                                                   gggTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCTGTTCCCCGGt    >  2:1993093/1‑101 (MQ=255)                                                                                                   gggTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCTGTTCCCCGGt    >  2:1090519/1‑101 (MQ=255)                                                                                                   gggTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCTGTTCCCCGGt    <  1:4396055/101‑1 (MQ=255)                                                                                                     gTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCTGTTCCCCGGTCg  >  1:4109831/1‑101 (MQ=255)                                                                                                     |                                                                                                     GGCGCGCATGCGGGGCCCCGGATCACCGGCGGCCCGGGCGGCTTTCACCTGGGGCCAAAGATCCCGGGGGTCCCGGG..G....G.....CCCCCGGCGGGTCGCCGAGGCATCGCCTCGGCGAAATCCCTTAGTAAAGACCGCCCGCGGACAGGGATCCGAAGGTCGCCTTCTTCGGGATCACCCGCTGTTCCCCGGTCG  >  NC_014034/2330218‑2330407 Base quality scores:  ATCG  < 3 ≤  ATCG  < 15 ≤  ATCG  < 25 ≤  ATCG  < 33 ≤  ATCG  < 40 ≤  ATCG