New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	= 313714	1 (0.020)	49 (0.840)	42/296	0.4	98.0%	coding (317/594 nt)	rclC	reactive chlorine species (RCS) stress resistance inner membrane protein
	?	CP009273	376716 =	NA (NA)					intergenic (‑1/‑91)	yaiX/insC1	pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase/IS2 repressor TnpA

CCGGATAAATAAGGGAAACCATGATGAGCGTCACCCAATGCGGGTACCCATGCCTCCGGGGTGGTGATTAAAAATGAGAGTGTTACCAGCGGCGTGGTAAATGCCATCAGTCCTCCCAATAAACCTAACCAGCGATTGACAGGATTAG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  CP009273/313567‑313714 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAG  >  CP009273/376716‑376860                                                                                                                                                                                                                                                                                                       CCGGATAAATAAGGGAAACCATGATGAGCGTCACCCAATGCGGGTACCCATGCCTCCGGGGTGGTGATTAAAAATGAGAGTGTTACCAGCGGCGTGGTAAATGCCATCAGTCCTCCCAATAAACCTAACCAGCGATTGACAGGATTAGT                                                                                                                                                  >  2:57867/1‑149   GGATACATAAGGGAAACCATGATGAGCCTCACCCAATGCGGGTACCCATGCCTCCGGGGTGGTGATTAAAAATGAGAGTGTTACCAGCGGCGTGGTAAATGCCATCAGTCCTCCCAATAAACCTAACCAGCGATTGACAGGATTAGTAG                                                                                                                                                <  2:813762/149‑1   GGATAAATAAGGGAAACCATGATGAGCGTCACCCAATGCGGGTACCCATGCCTCCGGGGTGGTGATTAAAAGTGAGAGTGTTACCAGCGTCGTGGTAAATGCCATCAGTCCTCCCAATAAACCTAACCAGCGATTGACAGGATTAGTAG                                                                                                                                                <  2:706914/149‑1   GGATAAATAAGGGAAACCATGATGAGCGTCACCCAATGCGGGTACCCATGCCTCCGGGGTGGTGATTAAAAATGAGAGTGTTACCAGCGGCGTGGTAAATGCCATCAGTCCTCCCAATAAACCTAACCAGCGATTGACAGGATTAGTAG                                                                                                                                                <  2:706972/149‑1          TAAGGGAAACCATGATGAGCGTCACCCAATGCGGGTACCCATGCCTCCGGGGTGGTGATTAAAAATGAGAGTGTTACCAGCGGCGTGGTAAATGCCATCAGTCCTCCCAATAAACCTAACCAGCGATTGACAGGATTAGTAGACTGGCC                                                                                                                                         >  1:660917/1‑149             GGGAAACCATGATGAGCGTCCCCCAATGCGGGTACCCATGCCTCCGGGGCGGTCATTAAAAATGAGAGTGTTACCAGCGGCGTGGTAAATGCCATCAGTCCTCCCAATAAACCAAACCAGCGATTGACAGGATTAGTAGACTGGCCCCC                                                                                                                                      >  2:510723/1‑149              GGAAACCATGATGAGCGTCACCCAATGCGGGTACCCATGCCTCCGGGGTGGTGATTAAAAATGAGAGTGTTACCAGCGGCGTGGTAAATGCCATCAGTCCTCCCAATAACCCTAACCAGCGATTGACAGGATTAGTAGACTGGCCCCCT                                                                                                                                     >  1:296307/1‑149              GGAAACCATGATGAGCGTCACCCAATGCGGGTACCCATGCCTCCGGGGTGGTGATTAAAAATGAGAGTGTTACCAGCGGCGTGGTAAATGCCATCAGTCCTCCCAATAAACCTAACCAGCGATTGACAGGATTAGTAGACTGGCCCCCT                                                                                                                                     <  2:127654/149‑1                            GCGTCACCCAATGCGGGTACCCATGCCTCCGGGGTGGTGATTAAAAATGAGAGTGTTACCAGCGGCGTGGTAAATGCCATCAGTCCTCCCAATAAACCTAACCAGCGATTGACAGGATTAGTAGACTGGCCCCCTGAATCTCCAGACAA                                                                                                                       <  2:931209/149‑1                            GCGTCACCCAATGCGGGTACCCATGCCTCCGGGGTGGTGATTAAAAATGAGAGTGTTACCAGCGGCGTGGTAAATGCCATCAGTCCTCCCAATAAACCTAACCAGCGATTGACAGGATTAGTAGACTGGCCCCCTGAATCTCCAGACAA                                                                                                                       >  1:25357/1‑149                            GCGTCACCCAATGCGGGTACCCATGCCTCCGGGGTGGTGATTAAAAATGAGAGAGTTACCAGCGGCGTGGTAAATGCCATCAGTCCTCCCAATAAACCTAACCAGCGATTGACAGGAATAGTAGACTGGCCCCCTGAATCTCCAGACAA                                                                                                                       >  1:395499/1‑149                             CGTCACCCAATGCGGGTACCCATGCCTCCGGGGTGGTGATTAAAAATGAGAGTGTTACCAGCGGCGTGGTAAATGCCATCAGTCCTCCCAATAAACCTAACCAGCGATTGACCGGATTAGTAGACTGGCCCCCTGAATCTCCAGAacac                                                                                                                      >  1:69144/1‑145                              GTCACCCGACGCGGGCACCAATGCCTTCGGGGTGGTGATTAAAAATGACAGTGTTACCAGCGGCGTGGTAAATGCCATCAGTCCTCCCAATAAACCTAACCACCGATTGACAGGATTAGTAGACTGGCCCCCTGAATCTCCAGACAACC                                                                                                                     <  2:239266/149‑1                                   CCAATGCGGGTACCCATGCCTCCGGGGGGGTGATTAAAAATGAGAGTGTTACCAGCGGCGTGGTAAATGCCATCAGTCCTCCCAATAAACCTAACCAGCGATTGACAGGATTAGTAGACTGGCCCCCCGAATCTCCAGACACCCAATAT                                                                                                                >  2:366592/1‑149                                         CGGGTACCCATGCCTCCGGGGTGGTGATTAAAAATGAGAGTGTTACCAGCGGCGTGGTAAATGCCATCAGTCCTCCCAATAAACCTAACCAGCGACAACCAGGTTTAGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTA                                                                                                          >  1:218522/1‑149                                          GGGTACCCATGCCTCCGGGGTGGTGATTAAAAATGAGAGTGTTACCAGCGGCGTGGTAAATGCCATCAGTCCTCCCAATAAACCTAACCAGCGATTGACAGGCTTAGTAGACTGGCCCCCTGAATCTCCAGACAACCAATCTGCCTTAA                                                                                                         >  2:694239/1‑149                                                CCATGCCTCCGGGGTGGTGATTAAAAATGAGAGTGTTACCAGCGGCGTGGTAAATGCCATCAGTCCTCCCAATAAACCTAACCAGCGATTGACAGGATTAGTAGACTGGCCCCCCGAATCTCCAGACAACCAATATCACTTAAATAAGT                                                                                                   >  2:150836/1‑149                                                  ATGCCTCCGGGGTGGTGATTAAAAATGAGAGTGTTACCAGCGGCGTGGTAAATGCCATCAGTCCTCCCAATAAACCTAACCACCGATTGACAGGATTAGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGA                                                                                                 >  1:510934/1‑149                                                   TGCATCCGGGGTGGTGATTAAAAATGAGAGTGTTACCAGCGGCGTGGTAAATGCCATCAGTCCTCCACATAAAACTAACCAGCGATTGACAGGATTAGTAGACTCGACCCCTGACTCTCCAGACAACACATATCACTGAAATGAGTGAT                                                                                                >  2:787055/1‑149                                                                    TTAAAAATGAGAGTGTTACCAGCGGAGCGGAGCGTTCCGACAGTCCTCCCAATAAACCTAACCAGCGATTGACAGGGTTAGTAGGCTGGCCCCCTCAAGCTCCAGACAACCAATATCACGTAAATAAGTGATAGTCTTAATACTAGTTT                                                                               >  1:466020/1‑149                                                                            GAGAGTGTTACCAGCGGCGTGGTAAATGCCATCAGTCCTCCCAATAAACCTAACCAGCGATTGACAGGATTAGTAGACTGGCCCCCTGAATCCCCAGACAACCAATATCACGTAAATAAGTGATCGTCTTAATACTCGTTCTTAGctca                                                                       >  2:849579/1‑145                                                                               AGTGTTACCAGCGGCGTGGTAAATGCCATCAGTCCTCCCAATAAACCTAACCAGCGATTGACAGGATTAGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTGGTTTTTCGACTAGTC                                                                    >  1:32306/1‑149                                                                                 TGTTACCAGCGGCGTGGTAAATGCCATCAGTCCTCCCAATAAACCTAACCAGCGATTGACAGGATTAGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCAT                                                                  >  2:107359/1‑149                                                                                  GTTACCAGCGGCGTGGTAAATGCCATCAGTCCCCCCAATAAACCTAACCAGCGATTGACAGGATTAGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATT                                                                 <  1:791638/149‑1                                                                                   tgACCAGCGGCGTGGTAAATGCCATCAGTCCTCCCAATAAACCTAACCAGCGATTGACAGGATTAGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTG                                                                <  1:287928/147‑1                                                                                      CCAGCGGCGTGGTAAATGCCATCAGTCCTCCCAATAAACCTAACCAGCGATTGACAGGATTAGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAG                                                             >  1:416640/1‑149                                                                                       CAGCGGCGTGGTAAATGCCATCAGTCCTCCCAATAAACCTAACCAGCGATTGACAGGATTAGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGA                                                            >  1:215315/1‑149                                                                                          ctgcatgccacATGCCATCAGTCCTCCCACTACACCTAACCAGCGATTGACAGGAATAGCAGACTGGTCCTCTGAATCTTCAGACAACCTATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACA                                                         <  2:819629/138‑1                                                                                          CGGCGTGGTAAATGCCATCAGTCCTCCCAATAACCCTAACCAGCGATTGACAGGATTAGTAGACTGGCCCCCTGAATCTCCAGACAACCGATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACA                                                         <  1:633304/149‑1                                                                                            gggttGTAAATGCCATCAGTCCTCCCAATAAACCTAACCAGCGATTGACAGGATTAGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGA                                                       <  2:472916/144‑1                                                                                               TGGTAAATGCCATCAGTCCTCCCAATAAACCTACCCAGCGATGTACAGGATTAGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGA                                                    <  1:256374/149‑1                                                                                                   AAATGCCATCAGTCCTCCCAATAAACCTAACCAGCGATTGACAGGATTAGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCCCTTAAATAAGTGATAGTCTTAATACTAGTTTTTAAACTAGTCATTGAAGCAGACATGATTGA                                                >  2:782009/1‑149                                                                                                      TGCCATCAGGCCTCCCAATAAACCTAACCAGCGATTGACAGGATTAGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTTTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGT                                             <  2:107279/149‑1                                                                                                       GCCATCGGTCCTCCCAATAAACCTAACCAGCGATTGACAGGATTAGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTC                                            >  2:904500/1‑149                                                                                                       GCCATCAGTCCTCCCAATAAACCTAACCAGCGATTGACAGGATTAGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTC                                            >  1:487397/1‑149                                                                                                          ATCAGTCCTCCCAATAAACCTAACCAGCGATTGACAGGATTAGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTA                                         <  1:8192/149‑1                                                                                                             cGTCCTCCCAATCAACCTAACCAGCGATTGACAGGATTAGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGG                                      <  2:96482/148‑1                                                                                                                     CAATAAACCTAACCAGCGATTGACAGGATTAGTAGACTGACCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAA                              >  1:467803/1‑149                                                                                                                        gAAACCTAACCAGCGATTGACAGGATTAGTAGACTGGCCCCCTGAATCTCCAGACACCCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGACGGAGAAACG                           <  2:485466/148‑1                                                                                                                              tacCCAGCGATTGACAGGATTAGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACG                     <  1:107023/146‑1                                                                                                                                    GCGATTGACAGGATTAGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGGACAGGTGCTTGATGTCTTGGGGCCGGAGGAACGCAGACGGCGTAg               >  1:860606/1‑148                                                                                                                                      GATTGACAGGATTAGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCACTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCA             <  2:510934/149‑1                                                                                                                                      GATTGACAGGATTAGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGGCTTAATACTAGGTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCGTAGGGCCGGAGAAACGCAAACGGCGTACCA             >  2:268527/1‑149                                                                                                                                        TTGACAGGATTAGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGCCTAGTCATTGGAGAACACATGATTGAGGTCTTAGGGCCGGAGAAAGGCAGACGGCGTACgcca           >  1:33890/1‑145                                                                                                                                        TTGACAGGATTAGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACA           <  1:107359/149‑1                                                                                                                                           ACAGGATTAGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAG        >  1:135628/1‑149                                                                                                                                           ACAGGATTAGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGACTGATGTCTTAGGGCCGGAGGAACGCAGACGGCGTACCACACAG        >  2:491783/1‑149                                                                                                                                           ACAGGATTAGTAGACTGGCCCCCGGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAG        >  1:523599/1‑149                                                                                                                                                 TTAGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAG  >  1:892129/1‑149                                                                                                                                                                                                                                                                                                       CCGGATAAATAAGGGAAACCATGATGAGCGTCACCCAATGCGGGTACCCATGCCTCCGGGGTGGTGATTAAAAATGAGAGTGTTACCAGCGGCGTGGTAAATGCCATCAGTCCTCCCAATAAACCTAACCAGCGATTGACAGGATTAG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  CP009273/313567‑313714 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAG  >  CP009273/376716‑376860

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.