New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	392448 =	52 (0.230)	56 (0.250)	13/192	23.0	0.68	intergenic (‑96/+47)	RCAP_rcc00363/trmD	hypothetical protein/tRNA (guanine‑N1)‑methyltransferase
	?	NC_014034	= 1253888	NA (NA)					intergenic (+46/+45)	RCAP_rcc01181/hisH	hypothetical protein/imidazole glycerol phosphate synthase subunit HisH
Rejected: Position hash score below cutoff.

GAAGCTTTGACGCGGGACCGGCGGCCGGATTTGTGGGAGAAGTTCGGCAAGTGATTTCGCCTCGGCTGCGCCGAGGCGACCCGCCGGGGGCTCCGCCCCCG....................................................................................................  <  NC_014034/392548‑392448 .................................................................................................CCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAGCACCAT  <  NC_014034/1253888‑1253789                                                                                                                                                                                                                                                                       tcggctttCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGA                                          <  2:1064642/93‑1 (MQ=32)                                                              cggctttCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAA                                         <  1:1918177/94‑1 (MQ=32)                                                               ggctttCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAG                                        <  2:1202929/95‑1 (MQ=32)                                                               ggctttCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAG                                        <  2:2482313/95‑1 (MQ=32)                                                                 ctttCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGC                                      <  2:3524689/97‑1 (MQ=32)                                                                   ttCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGC                                    <  1:1728870/99‑1 (MQ=32)                                                                   TGCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGC                                    <  2:672034/101‑1 (MQ=11)                                                                    tCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCA                                   <  1:3116211/100‑1 (MQ=32)                                                                    tCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCA                                   <  1:318428/100‑1 (MQ=32)                                                                    tCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCA                                   <  2:3860756/100‑1 (MQ=32)                                                                    tCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCA                                   <  2:3475905/100‑1 (MQ=32)                                                                    tCGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCA                                   <  1:3802596/100‑1 (MQ=32)                                                                     CGCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAG                                  <  2:1661055/101‑1 (MQ=32)                                                                      GCCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGC                                 <  2:3480649/101‑1 (MQ=32)                                                                       CCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTTGAAGGCGCAGCC                                <  1:3667614/101‑1 (MQ=17)                                                                       CCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCC                                <  1:1761035/101‑1 (MQ=32)                                                                       CCGAGGCGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCC                                <  2:464518/101‑1 (MQ=32)                                                                          AGGCGACCCGGGGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGT                             <  1:2258761/101‑1 (MQ=17)                                                                            ggggCCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCT                           <  1:6911/97‑1 (MQ=17)                                                                            GCGACCCGGCGGGGGCTCCGCCCCCGCCCCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCT                           <  2:729317/101‑1 (MQ=17)                                                                             cgcCCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTG                          <  1:851113/98‑1 (MQ=17)                                                                             CGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTG                          <  2:156109/101‑1 (MQ=32)                                                                             CGACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTG                          <  2:4606596/101‑1 (MQ=32)                                                                              GACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGG                         <  2:425803/101‑1 (MQ=32)                                                                               gCCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGA                        <  2:2475433/100‑1 (MQ=17)                                                                               cCCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGA                        <  1:3511123/100‑1 (MQ=17)                                                                               ACCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGA                        <  1:2304504/101‑1 (MQ=32)                                                                                CCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAA                       <  1:3475024/101‑1 (MQ=32)                                                                                CCCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAA                       <  1:336941/101‑1 (MQ=32)                                                                                 CCGGCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAG                      <  2:635117/101‑1 (MQ=32)                                                                                  cggCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGC                     <  2:3903681/98‑1 (MQ=32)                                                                                   ggCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCC                    <  1:1166198/99‑1 (MQ=31)                                                                                   ggCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCC                    <  1:1319769/99‑1 (MQ=31)                                                                                   ggCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGGTTATTTCGCCTCGAAGGCGCAGCCGGGCTGGAAGCC                    >  2:4250487/3‑101 (MQ=9)                                                                                    gCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCG                   <  2:717039/100‑1 (MQ=11)                                                                                    gCGGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCG                   <  1:3911154/100‑1 (MQ=11)                                                                                      GGGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGCCTGGAAGCCGAG                 >  2:3545062/1‑101 (MQ=1)                                                                                       GGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGC                <  1:2231121/101‑1 (MQ=1)                                                                                       GGGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGC                >  1:2587790/1‑101 (MQ=1)                                                                                        GGGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCT               <  1:1981053/101‑1 (MQ=1)                                                                                         GGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTc              <  1:2367116/101‑2 (MQ=1)                                                                                         GGCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTT              >  1:137938/1‑101 (MQ=1)                                                                                          GCTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTG             <  2:1572530/101‑1 (MQ=1)                                                                                           CTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGC            <  2:3067263/101‑1 (MQ=1)                                                                                           CTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGC            <  1:2495775/101‑1 (MQ=1)                                                                                           CTCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGC            >  1:1557360/1‑101 (MQ=1)                                                                                            TCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCC           <  2:3840892/101‑1 (MQ=1)                                                                                            TCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCC           >  2:3112627/1‑101 (MQ=1)                                                                                            TCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCC           >  2:2827144/1‑101 (MQ=1)                                                                                            TCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCC           <  1:4188148/101‑1 (MQ=1)                                                                                            TCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCC           >  1:3545165/1‑101 (MQ=1)                                                                                            TCCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGCTTATTTCGCCTCGAAGGCGCAGCCGGGCTGGAAGCCGGGCTTGCC           >  2:1825986/1‑101 (MQ=0)                                                                                             CCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCC          <  2:2443667/101‑1 (MQ=1)                                                                                             CCGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCCGTCTGGAAGCCGAGCTTGCCC          <  1:2703583/101‑1 (MQ=1)                                                                                              CGCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCA         <  1:2025731/101‑1 (MQ=1)                                                                                               GCCCCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAG        <  1:661798/101‑1 (MQ=1)                                                                                                                                                                                                           GAAGCTTTGACGCGGGACCGGCGGCCGGATTTGTGGGAGAAGTTCGGCAAGTGATTTCGCCTCGGCTGCGCCGAGGCGACCCGCCGGGGGCTCCGCCCCCG....................................................................................................  <  NC_014034/392548‑392448 .................................................................................................CCCGCACCCCCGAGGTATTTAGGGCAAGATGAGAGCGGGGCGGGATCGGTTTATTTCGCCTCGAAGGCGCAGCCGGTCTGGAAGCCGAGCTTGCCCAGCACCAT  <  NC_014034/1253888‑1253789 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 29 ≤  ATCG  < 34 ≤  ATCG  < 40 ≤  ATCG