New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	2330179 =	37 (0.160)	42 (0.180)	21/194	17.1	0.25	intergenic (+154/+158)	RCAP_rcc02161/mrcA	hypothetical protein/penicillin‑binding protein 1A
	?	NC_014034	2555842 =	218 (0.890)					intergenic (‑705/+41)	mraZ/RCAP_rcc02384	protein MraZ/Mrp/NBP35 family protein
Rejected: Position hash score below cutoff.

GGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGG....................................................................................................  <  NC_014034/2330281‑2330179 ....................................................................................................GGGGCGGAGCCCCCGCCCGGGTCGCCGCGCCAGGCGCGGCGAAATCAGGCCACGCCGCGCCCGATCAGCTCTGCCGCGATCGCCGCATAGGCCCCGGCCGCGG  >  NC_014034/2555842‑2555941                                                                                                                                                                                                                TCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGG                                                                                                     >  1:751538/1‑101 (MQ=1)    TCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGG                                                                                                     >  2:4705572/1‑101 (MQ=1)     CTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGC                                                                                                    <  2:4928537/101‑1 (MQ=1)     CTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGC                                                                                                    >  2:4792911/1‑101 (MQ=1)      TTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCG                                                                                                   >  1:3366130/1‑101 (MQ=1)       TTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGG                                                                                                  <  2:4738882/101‑1 (MQ=1)        TGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGA                                                                                                 >  2:2278230/1‑101 (MQ=1)         GGCCCCAGGGGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAG                                                                                                <  1:2714118/101‑1 (MQ=1)            CCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCC                                                                                             >  2:467884/1‑101 (MQ=1)             CCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCC                                                                                            <  2:200388/101‑1 (MQ=1)             CCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCC                                                                                            <  1:562456/101‑1 (MQ=1)             CCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCC                                                                                            <  1:446818/101‑1 (MQ=1)             CCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCC                                                                                            <  1:2599669/101‑1 (MQ=1)              CAGGTGAAGGCCGCCCGGGCCGCCGGTGATCCGGGGGCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCC                                                                                           <  2:3308763/101‑1 (MQ=0)              CAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCC                                                                                           <  2:4483172/101‑1 (MQ=1)              CAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCC                                                                                           <  1:741048/101‑1 (MQ=1)               AGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCG                                                                                          >  1:2548062/1‑101 (MQ=1)                GGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATCCGCCGGGGGTGCGGGGGCGGAGCCCCCGC                                                                                         <  1:2849175/101‑1 (MQ=1)                GGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCGC                                                                                         <  1:2199084/101‑1 (MQ=1)                  TGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCGCCC                                                                                       >  1:3028264/1‑101 (MQ=31)                   GAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCGCCCG                                                                                      <  1:4527835/101‑1 (MQ=32)                   GAAAGCCGCCCGGGCCGCCGGTGAT.CGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGGGCGGGGGCGGAGCCCCCGCCCGG                                                                                     >  1:1640001/1‑101 (MQ=12)                   GAAACCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCGCCCG                                                                                      <  1:4305479/101‑1 (MQ=17)                     AAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCGCCCGGG                                                                                    >  2:3547384/1‑101 (MQ=32)                     AAGCCGCCCGGGCCGCCGCTGATCTGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCGCCCGGG                                                                                    <  2:821741/101‑1 (MQ=12)                        CCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCGCCCGGGTCG                                                                                 >  1:1690297/1‑101 (MQ=32)                          GCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCGCCCGGGTCGCC                                                                               >  1:345115/1‑101 (MQ=32)                           CCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCGCCCGGGTCGCCG                                                                              >  2:1136171/1‑101 (MQ=32)                                GCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCGCCCGGGTCGCCGCGCCt                                                                         >  1:825149/1‑100 (MQ=14)                                  CGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCGCCCGGGTCGCCGCGCCtgc                                                                       <  2:1187710/101‑4 (MQ=1)                                  CGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCGCCCGGGTCGCCGCGCCtgc                                                                       <  2:1494986/101‑4 (MQ=1)                                   GCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCGCCCGGGTCGCCGCGCCtgcg                                                                      >  1:3783662/1‑97 (MQ=11)                                   GCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCGCCCGGGTCGCCGCGCCtgcg                                                                      >  1:1677987/1‑97 (MQ=11)                                    CCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCGCCCGGGTCGCCGCGCCtgcgc                                                                     >  1:4388744/1‑96 (MQ=14)                                     CGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCGCCCGGGTCGCCGCGCCtgcgcg                                                                    >  1:3569662/1‑95 (MQ=17)                                     CGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCGCCCGGGTCGCCGCGCCtgcgcg                                                                    >  1:2044245/1‑95 (MQ=17)                                      GGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCGCCCGGGTCGCCGCGCCtgcgcgg                                                                   >  1:1504161/1‑94 (MQ=18)                                       GTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCGCCCGGGTCGCCGCGCC.TGCGCGGC                                                                 >  2:3783694/1‑101 (MQ=21)                                       GTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCGCCCGGGTCGCCGCGCC.TGCGCGGC                                                                 >  1:801459/1‑101 (MQ=21)                                          ATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCGCCCGGGTCGCCGCGCC.TGCGCGGCGAA                                                              >  2:4501526/1‑101 (MQ=21)                                           TCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCGCCCGGGTCGCCGCGCC.TGCGCGGCGAAA                                                             >  1:3365170/1‑101 (MQ=21)                                            CCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGGGCGGAGCCCCCGCCCGGGTCGCCGCGCC.TGCGCGGCGAAAT                                                            >  1:25900/1‑101 (MQ=21)                                                                                                                                                                                                             GGATCTTTGGCCCCAGGTGAAAGCCGCCCGGGCCGCCGGTGATCCGGGGCCCCGCATGCGCGCCCCGGCTTTTTCTTGGCGCAAATACGCCGGGGGTGCGGGG....................................................................................................  <  NC_014034/2330281‑2330179 ....................................................................................................GGGGCGGAGCCCCCGCCCGGGTCGCCGCGCCAGGCGCGGCGAAATCAGGCCACGCCGCGCCCGATCAGCTCTGCCGCGATCGCCGCATAGGCCCCGGCCGCGG  >  NC_014034/2555842‑2555941 Base quality scores:  ATCG  < 3 ≤  ATCG  < 15 ≤  ATCG  < 24 ≤  ATCG  < 33 ≤  ATCG  < 39 ≤  ATCG