New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1411899 =	61 (1.680)	9 (0.310)	9/198	2.0	19.1%	coding (50/936 nt)	ttcA	tRNA s(2)C32 thioltransferase, iron sulfur cluster protein
	?	NC_000913	= 1434958	28 (0.970)					pseudogene (51/51 nt)	ttcC	pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related
Rejected: Frequency below/above cutoff threshold.

GGATTGATGACATGAACGACGAACAGATAGCCATGTTGAATGCGCGGTTATCGTAGTTGCAAAGTTTGCCCCCAATTTGCCCCATTTAGTACCAGAGAACTGAAATAATGCAAGAAAATCAACAAATTACAAAGAAAGAACAATACAACCTGAACAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/1412055‑1411899 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aagaaagaacaatacaacctgaacaaGTAAGGGCAAAAATCACAACTCTCTGACTCATAAGTATTTTACTTATTTTTCAATGTGTTAAATATCATCAGCGACAACAATAAGCTACGATAATCCACTCTTTTTTTGCCCCTTTTTTGCCCCTTTTGCAGCGTTTTGCCC  <  NC_000913/1434958‑1434817                                                                                                                                                                                                                                                                                                             GGATTGATGACATGAACGACGAACAGATAGCCATGTTGAATGCGCGGTTATCGTAGTTGCAAAGTTTGCCCCCAATTTGCCCCATTTAGTACCAGAGAACTGAAATAATGCAAGAAAATCAACAAATTACAAAGAAAGAACAATACAAC                                                                                                                                                        >  4:32779/1‑149  GATTGATGACATGAACGACGAACAGATAGCCATGTTGAATGCGCGGTTATCGTAGTTGCAAAGTTTGCCCCCAATTTGCCCCATTTAGTACCAGAGAACTGAAATAATGCAAGAAAATCAACAAATTACAAAGAAAGAACAATACAACC                                                                                                                                                       >  3:4554/1‑149   ATTGATGACATGAACGACGAACAGATAGCCATGTTGAATGCGCGGTTATCGTAGTTGCAAAGTTTGCCCCCAATTTGCCCCATTTAGTACCAGAGAACTGAAATAATGCAAGAAAATCAACAAATTACAAAGAAAGAACAATACAACCT                                                                                                                                                      >  1:138583/1‑149       ATGACATGAACGACGAACAGATAGCCATGTTGAATGCGCGGTTATCGTAGTTGCAAAGTTTGCCCCCAATTTGCCCCATTTAGTACCAGAGAACTGAAATAATGCAAGAAAATCAACAAATTACAAAGAAAGAACAATACAACCTGAA                                                                                                                                                   <  4:4554/148‑1        TGACATGAACGACGAACAGATAGCCATGTTGAATGCGCGGTTATCGTAGTTGCAAAGTTTGCCCCCAATTTGCCCCATTTAGTACCAGAGAACTGAAATAATGCAAGAAAATCAACAAATTACAAAGAAAGAACAATACAACCTGAAC                                                                                                                                                  >  6:164942/1‑148              GAACGACGAACAGATAGCCATGTTGAATGCGCGGTTATCGTAGTTGCAAAGTTTGCCCCCAATTTGCCCCATTTAGTACCAGAGAACTGAAATAATGCAAGAAAATCAACAAATTACAAAGAAATAAAAATACAACCTGAACAAGTAAG                                                                                                                                           >  3:30834/1‑149                ACGACGAACAGATAGCCATGTTGAATGCGCGGTTATCGTAGTTGCAAAGTTTGCCCCCAATTTGCCCCATTTAGTACCAGAGAACTGAAATAATGCAAGAAAATCAACAAATTACAAAGAAAGAACAATACAACCTGAACAAGTAAGG                                                                                                                                          <  4:30834/148‑1                         AGATAGCCATGTTGAATGCGCGGTTATCGTAGTTGCAAAGTTTGCCCCCAATTTGCCCCATTTAGTACCAGAGAACTGAAATAATGCAAGAAAATCAACAAATTACAAAGAAAGAACAATACAACCTGAACAAGTAAGGGCAAAAATCA                                                                                                                                <  4:23425/149‑1                                      GAATGCGCGGTTATCGTAGTTGCAAAGTTTGCCCCCAATTTGCCCCATTTAGTACCAGAGAACTGAAATAATGCAAGAAAATCAACAAATTACAAAGAAAGAAC                                                                                                                                                                >  1:143931/1‑104                                      GAATGCGCGGTTATCGTAGTTGCAAAGTTTGCCCCCAATTTGCCCCATTTAGTACCAGAGAACTGAAATAATGCAAGAAAATCAACAAATTACAAAGAAAGAAC                                                                                                                                                                <  2:143931/104‑1                                                                                CCCCATTTAGTACCAGAGAACTGAAATAATGCAAGAAAATCAACAAATTACAAAGAAAGAACAATACAACCTGAACAAGTAAGGGCAAAAATCACAACTCTCTGACTCATAAGTATTTTACTTATTTTTCAATGTGTTAAATATCAT                                                                           >  1:77532/1‑147                                                                                              AGAGAACTGAAATAATGCAAGAAAATCAACAAATTACAAAGAAAGAACAATACAACCTGAACAAGTAAGGGCAAAAATCACAACTCTCTGACTCATAAGTATTTTACTTATTTTTCAATGTGTTAAATATCATCAGCGACAACAATAAG                                                           <  2:77532/149‑1                                                                                              AGAGAACTGAAATAATGCAAGAAAATCAACAAATTACAAAGAAAGAACAATACAACCTGAACAAGTAAGGGCAAAAATCACAACTCTCTGACTCAT                                                                                                                >  4:121131/1‑96                                                                                              AGAGAACTGAAATAATGCAAGAAAATCAACAAATTACAAAGAAAGAACAATACAACCTGAACAAGTAAGGGCAAAAATCACAACTCTCTGACTCAT                                                                                                                <  3:121131/96‑1                                                                                               GAGAACTGAAATAATGCAAGAAAATCAACAAATTACAAAGAAAGAACAATACAACCTGAACAAGTAAGGGCAAAAATCACAACTCTCTGACTCATAAGTATTTTACTTATTTTTCAATGTGTTAAATA                                                                               <  8:62100/128‑1                                                                                               GAGAACTGAAATAATGCAAGAAAATCAACAAATTACAAAGAAAGAACAATACAACCTGAACAAGTAAGGGCAAAAATCACAACTCTCTGACTCATAAGTATTTTACTTATTTTTCAATGTGTTAAATA                                                                               >  7:62100/1‑128                                                                                                                                       AAAGAACAATACAACCTGAACAAGTAAGGGCAAAAATCACAACTCTCTGACTCATAAGTATTTTACTTATTTTTCAATGTG                                                                                      <  5:183253/81‑1                                                                                                                                       AAAGAACAATACAACCTGAACAAGTAAGGGCAAAAATCACAACTCTCTGACTCATAAGTATTTTACTTATTTTTCAATGTG                                                                                      >  6:183253/1‑81                                                                                                                                         AGAACAATACAACCTGAACAAGTAAGGGCAAAAATCACAACTCTCTGACTCATAAGTATTTTACTTATTTTTCAATGTGTTAAATATCATCAGCGACAACAATAAGCTACGATAATCCACTCTTTTTTTGCCCCTTTTTTGCCCCTTTT                <  8:110451/149‑1                                                                                                                                         AGAACAATACAACCTGAACAAGTAAGGGCAAAAATCACAACTCTCTGACTCATAAGTATTTTACTTATTTTTCAATGTGTTAAATATCATCAGCGACAACAATAAGCTACGATAATCCACTCTTTTTTTGCCCCTTTTTTGCCCCTTTT                <  6:55062/149‑1                                                                                                                                           AACAATACAACCTGAACAAGTAAGGGCAAAAATCACAACTCTCTGACTCATAAGTATTTTACTTATTTTTCAATGTGTTAAATATCATCAGCGACAACAATAAGCT                                                         <  8:21156/106‑1                                                                                                                                           AACAATACAACCTGAACAAGTAAGGGCAAAAATCACAACTCTCTGACTCATAAGTATTTTACTTATTTTTCAATGTGTTAAATATCATCAGCGACAACAATAAGCT                                                         >  7:21156/1‑106                                                                                                                                                TACAACCTGAACAAGTAAGGGCAAAAATCACAACTCTCTGACTCATAAGTATTTTACTTATTTTTCAATGTGTTAAATATC                                                                             <  5:94484/81‑1                                                                                                                                                TACAACCTGAACAAGTAAGGGCAAAAATCACAACTCTCTGACTCATAAGTATTTTACTTATTTTTCAATGTGTTAAATATC                                                                             >  6:94484/1‑81                                                                                                                                                     CCTGAACAAGTAAGGGCAAAAATCACAACTCTCTGACTCATAAGTATTTTACTTATTTTTCAATGTGTTAAATATCATCAGCGACAACAATAAGCTACGATAATCCACTCTTTTTTTGCCCCTTTTTTGCCCCTTT                 >  6:177373/1‑136                                                                                                                                                     CCTGAACAAGTAAGGGCAAAAATCACAACTCTCTGACTCATAAGTATTTTACTTATTTTTCAATGTGTTAAATATCATCAGCGACAACAATAAGCTACGATAATCCACTCTTTTTTTGCCCCTTTTTTGCCCCTTT                 <  5:177373/136‑1                                                                                                                                                     CCTGAACAAGTAAGGGCAAAAATCACAACTCTCTGACTCATAAGTATTTTACTTATTTTTCAATGTGTTAAATATCATCAGCGACAACAA                                                               <  7:50946/90‑1                                                                                                                                                     CCTGAACAAGTAAGGGCAAAAATCACAACTCTCTGACTCATAAGTATTTTACTTATTTTTCAATGTGTTAAATATCATCAGCGACAACAA                                                               >  8:50946/1‑90                                                                                                                                                     CCTGAACAAGTAAGGGCAAAAATCACAACTCTCTGACTCATAAGTATTTTACTTATTTTTCAATGTGTTAAATATCATAAGCGACAACAATA                                                             >  4:112033/1‑92                                                                                                                                                     CCTGAACAAGTAAGGGCAAAAATCACAACTCTCTGACTCATAAGTATTTTACTTATTTTTCAATGTGTTAAATATCATAAGCGACAACAATA                                                             <  3:112033/92‑1                                                                                                                                                       TGAACAAGTAAGGGCAAAAATCACAACTCTCTGACTCATAAGTATTTTACTTATTTTTCAAT                                                                                         >  1:49092/1‑62                                                                                                                                                       TGAACAAGTAAGGGCAAAAATCACAACTCTCTGACTCATAAGTATTTTACTTATTTTTCAAT                                                                                         <  2:49092/62‑1                                                                                                                                                        GAACAAGTAAGGGCAAAAATCACAACTCTCTGACTCATAAGTATTTTACTTATTTTTCAATGTGTTAAATATCATCAGCGACAACAATAAGCTACGATAATCCACTCTTTTTTTGCCCCTTTTTTGCCCCTTTTGCAGCGTTTTGCCC  >  7:109767/1‑148                                                                                                                                                                                                                                                                                                             GGATTGATGACATGAACGACGAACAGATAGCCATGTTGAATGCGCGGTTATCGTAGTTGCAAAGTTTGCCCCCAATTTGCCCCATTTAGTACCAGAGAACTGAAATAATGCAAGAAAATCAACAAATTACAAAGAAAGAACAATACAACCTGAACAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/1412055‑1411899 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aagaaagaacaatacaacctgaacaaGTAAGGGCAAAAATCACAACTCTCTGACTCATAAGTATTTTACTTATTTTTCAATGTGTTAAATATCATCAGCGACAACAATAAGCTACGATAATCCACTCTTTTTTTGCCCCTTTTTTGCCCCTTTTGCAGCGTTTTGCCC  <  NC_000913/1434958‑1434817

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ 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.