New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	4040817 =	NA (NA)	6 (0.420)	4/228	1.4	NA	intergenic (+181/+89)	rrfA/mobB	5S ribosomal RNA of rrnA operon/molybdopterin‑guanine dinucleotide biosynthesis protein B
	?	NC_000913_3_pae_tpiA	4040841 =	NA (NA)					intergenic (+205/+65)	rrfA/mobB	5S ribosomal RNA of rrnA operon/molybdopterin‑guanine dinucleotide biosynthesis protein B

GTGAACGCTCTCCTGAGTAGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCTTATCCGTTCTGCTTTTGCATCCACTCCACCACAAAATCAGCCAGCCCCTCAACATCATTAATATCCAGTAATGCGACATCAA  >  NC_000913_3_pae_tpiA/4040697‑4040988                                                                                                                                                 |                                                                                                                                                    gTGAACGCTCTCCTGAGTAGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCa                                                                                                                                                <  4:19577/150‑1 (MQ=11)     aCGCTCTCCTGAGTAGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTgg                                                                                                                                            <  4:76132/150‑1 (MQ=33)      cGCTCTCCTGAGTAGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAATCTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGgc                                                                                                                                           <  1:87141/150‑1 (MQ=21)                  tAGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAAt                                                                                                                               >  3:79612/1‑150 (MQ=255)                    ggACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGc                                                                                                                             >  2:42685/1‑150 (MQ=255)                                        gATTTGAACGTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCCTAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGt                                                                                                         <  2:120150/150‑1 (MQ=255)                                        gATTTGAACGTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGgcgc                                                                                                                                         <  2:187395/118‑1 (MQ=38)                                        gATTTGAACGTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGgcgc                                                                                                                                         >  1:187395/1‑118 (MQ=38)                                             gAACGTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTAt                                                                                                    >  2:90922/1‑150 (MQ=255)                                               aacggataagcaagagtaggctggataagacgcgccagcgtcgcatccggcatttttttctgcgccaatgcaaaAAGGCCATCCTGACGGATGGCCTTTTTGCAt                                                                                                                                               <  1:70809‑M1/31‑1 (MQ=255)                                               aacggataagcaagagtaggctggataagacgcgccagcgtcgcatccggcatttttttctgcgccaatgcaaaAAGGCCATCCTGACGGATGGCCTTTTTGCAt                                                                                                                                               >  2:70809‑M1/75‑105 (MQ=255)                                                 gTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAg                                                                                                <  2:7390/150‑1 (MQ=255)                                                 gTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAg                                                                                                <  3:71997/150‑1 (MQ=255)                                                     cGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGaaaaaa                                                                                                                                 >  3:62079/1‑113 (MQ=255)                                                     cGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGaaaaaa                                                                                                                                 <  4:62079/113‑1 (MQ=255)                                                        gcaagagtaggctggataagacgcgccagcgtcgcatccggcatttttttctgcgccaatgcaaaAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGAc                                                                                                                   <  4:44382‑M1/59‑1 (MQ=255)                                                        gcaagagtaggctggataagacgcgccagcgtcgcatccggcatttttttctgcgccaatgcaaaAAGGCCATCCTGACGGAGGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGAc                                                                                                                   >  3:44382‑M1/66‑124 (MQ=255)                                                             cGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGcc                                                                                              <  1:174350/140‑1 (MQ=255)                                                             cGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGcc                                                                                              >  2:174350/1‑140 (MQ=255)                                                                   ggAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCTTATCCg                                                                              >  1:93371/1‑150 (MQ=255)                                                                            cGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTg                                                                                                               <  4:83602/108‑1 (MQ=255)                                                                            cGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTg                                                                                                               >  3:83602/1‑108 (MQ=255)                                                                            cGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTg                                                                                                               >  3:83607/1‑108 (MQ=255)                                                                            cGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTg                                                                                                               <  4:83607/108‑1 (MQ=255)                                                                            cGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCTTATCCGTTCTGCttt                                                                     <  2:182313/150‑1 (MQ=255)                                                                               gCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCTTATCCGTTCTGCTTTTGc                                                                  <  3:17068/150‑1 (MQ=255)                                                                                cAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCTTATCCGTTCTGCTTTTGCa                                                                 >  3:108285/1‑150 (MQ=255)                                                                                      gtcgcatccggcatttttttctgcgccaatgcaaaaaggccctccgtcaggatggccttTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGc                                                                                     >  3:44382‑M2/60‑124 (MQ=255)                                                                                      gtcgcatccggcatttttttctgcgccaatgcaaaaaggccatccgtcaggatggccttTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGc                                                                                     <  4:44382‑M2/65‑1 (MQ=255)                                                                                        ccgccATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCTTATCCGTTCTGCTTTTGCAtccactcc                                                         >  1:165950/1‑150 (MQ=255)                                                                                              tAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCt                                                                                    <  2:175737/117‑1 (MQ=255)                                                                                              tAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCt                                                                                    >  1:175737/1‑117 (MQ=255)                                                                                                    gCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCTTATCCGTTCTGCTTTTGCATCCACTCCACCACAAAATca                                             <  2:42507/150‑1 (MQ=255)                                                                                                       aGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCTTATCCGTTCTGCTTTTGCAtccactcc                                                         <  2:20063/135‑1 (MQ=255)                                                                                                       aGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCTTATCCGTTCTGCTTTTGCAtccactcc                                                         >  1:20063/1‑135 (MQ=255)                                                                                                           aTCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCTTATCCGTTCTGCTTTTGCATCCACTCCACCACAAAATCagccagcc                                      >  3:56597/1‑150 (MQ=255)                                                                                                              aaaTTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTc                                                                                                        <  2:180289/81‑1 (MQ=255)                                                                                                              aaaTTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTc                                                                                                        >  1:180289/1‑81 (MQ=255)                                                                                                               aaTTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCTTATCCGTTCTGCTTTTGCATCCACTCCACCACAAAATCAGCCAGCCCCTc                                  <  4:108285/150‑1 (MQ=255)                                                                                                                  atgcaaaaaggccatccgtcaggatggccttTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCTTATCCGtt                                                                            <  1:70809‑M2/74‑1 (MQ=255)                                                                                                                  atgcaaaaaggccatccgtcaggatggccttTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCTTATCCGtt                                                                            >  2:70809‑M2/32‑105 (MQ=255)                                                                                                                   aaGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCTTATCCGTTCTGCTTTTGCAtccactc                                                          >  2:80579/1‑122 (MQ=255)                                                                                                                   aaGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCTTATCCGTTCTGCTTTTGCAtccactc                                                          <  1:80579/122‑1 (MQ=255)                                                                                                                        gAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCTTATCCGTTCTGCTTTTGCATCCACTCCACCACAAAATCAGCCAGCCCCTCAACATCAtt                         <  1:42685/150‑1 (MQ=255)                                                                                                                         AAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCTTATCCGTTCTGCTTTTGCATCCACTCCACCACAAAATCAGCCAGCCCCTCAACATCATTa                        >  4:79612‑M1/1‑150 (MQ=255)                                                                                                                          AGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCTTATCCGTTCTGCTTTTGCATCCACTCCACCACAAAATCGGCCAGCCCCTCAACATCATTaa                       >  2:93371‑M1/1‑150 (MQ=255)                                                                                                                           GGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCACAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCACCACTTGCTTATCCGTTCTGCTTTTGCACCCCCTCCACCACAAAATCAGCCAGCCCCTCAACATCATTAat                      >  1:28107‑M1/1‑150 (MQ=255)                                                                                                                                 ccgtcaggatggccttTTTGCATTGGCGCAGAAAAAAATGCCTGATGCGACGCtgc                                                                                                              >  2:108352‑M2/17‑55 (MQ=255)                                                                                                                                 ccgtcaggatggccttTTTGCATTGGCGCAGAAAAAAATGCCTGATGCGACGCtgc                                                                                                              <  1:108352‑M2/40‑2 (MQ=255)                                                                                                                                 CCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCTTATCCGTTCTGCTTTTGCATCCACTCCACCACAAAATCAGCCAGCCCCTCAACATCATTAATATCCAg                >  1:90922‑M1/1‑150 (MQ=255)                                                                                                                                    gACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCTTAt                                                                                 >  4:107409/1‑82 (MQ=255)                                                                                                                                    gACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCTTAt                                                                                 <  3:107409/82‑1 (MQ=255)                                                                                                                                              cttTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCTTATCCGTTCTGCTTTTGCATCCACTCCACCACAAAATCAGCCAGCCCCTCAACATCATTAATATCCAGTAATGCGACATCa   >  1:124580‑M2/4‑150 (MQ=255)                                                                                                                                              cttTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCTTATCCGTTCTGCTTTTGCATCCACTCCACCACAAAATCAGCCAGCCCCTCAACATCATTAATATCCAGTAATGCGACATCa   >  1:188657‑M2/4‑150 (MQ=255)                                                                                                                                               ttTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCTTATCCGTTCTGCTTTTGCATCCACTCCACCACAAAATCAGCCAGCCCCTCAACATCATTAATATCCAGTACTGCGACATCaa  <  2:59250‑M2/148‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                    GTGAACGCTCTCCTGAGTAGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCTTATCCGTTCTGCTTTTGCATCCACTCCACCACAAAATCAGCCAGCCCCTCAACATCATTAATATCCAGTAATGCGACATCAA  >  NC_000913_3_pae_tpiA/4040697‑4040988

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ 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.