New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_vch_pgi	1411899 =	20 (1.040)	4 (0.250)	4/238	1.8	24.0%	coding (50/936 nt)	ttcA	tRNA s(2)C32 thioltransferase, iron sulfur cluster protein
	?	NC_000913_3_vch_pgi	= 1434958	9 (0.570)					pseudogene (51/51 nt)	ttcC	pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related

AAAAATGGGGCAAAACGCTGCAAAAGGGGCAAAAAAGGGGCAAAAAAAGAGTGGATTATCGTAGCTTATTGTTGTCGCTGATGATATTTAACACATTGAAAAATAAGTAAAATACTTATGAGTCAGAGAGTTGTGATTTTTGCCCTTACTTGTTCAGGTTGTATTGTTCTTTCTTACTAATTTCTTGATTTTGCGACATTTAAAAGCGACTCAATTCGTTATATGGCATCAGAAGAGTATGCGTCATGCCGGAACGCCCAGCATAAGAAATCTGATATAAAAAACTGTGGCGT  >  NC_000913_3_vch_pgi/1434810‑1435102                                                                                                                                                     |                                                                                                                                                 aagaaTGGGGCAAAACGCTGAAAAAGGGGAAAAAAAGGGGCAAAAAAAGAGTGGATTATCGTAGTTTATTGTTGTCGCTGATGATATTTAACAAAATGAAAAATAAGTAAAATACTTATGAGTCAGAGAGTTGTGATTTTTGCCCTTAc                                                                                                                                                  <  2:43119/146‑1 (MQ=255)         ggCAAAACGCTGCAAAAGGGGCAAAAAAGGGGCAAAAAAAGAGTGGATTGTGGTAGCTTGTTGTTGTCTCGGCTGGTATTTAACACATTGAGGAGTAAGTAGAGTACGCATGAATCAGAGAGTTTGGATTGTTAGCCGTCCTTGTTcgg                                                                                                                                          >  2:86171/1‑147 (MQ=255)                              caaaaaaggggcaaaaaaAGAGTGGATTATCGTAGCTTATTGTTGTCGCTGATGATATTTAACACATTGAAAAATAAGTAAAATACTTATGAGTCAGAGAGTTGTGATTTTTGCCCTTACTTGTTCAGGTTGTATTGTTCTTTCTTACt                                                                                                                     <  1:141093/149‑1 (MQ=255)                                   aaggggcaaaaaaAGAGTGAATTATCGTAGCTTAATGTTGTCGCTGATGATATTTAACACATTGAAAAATAAGTAAAAGACGTATGAGTCAGAGAGTTGTGATTTTTGCCCTGACTTGTTCAGGTTGTATTGTTCTTTCTTACTAAttt                                                                                                                <  1:183577/149‑1 (MQ=255)                                                agagTGGATTTTCTGAGCTTATTGTTGTCGCTGATGATATTTAACACATTGAAAAATAAGTAAAATACTTATGAGTCAGAGAGTTGTGATTTTTGCCCTTACttgttcaggttgtattgttctttctttgtaatttgttgattttcttg                                                                                                   >  1:151121‑M2/1‑102 (MQ=255)                                                              tAGCTTATTGTTGTCGCTGATGATATTTAACACATTGAAAAATAAGTAAAATACTTATGAGTCAGAGAGTTGTGATTTTTGCCCTTACttgttcaggttgtattgttctttctttgtaatttgttgattttcttgcattatttcagttc                                                                                     <  1:238449‑M2/149‑62 (MQ=255)                                                                 cTTATTGTTGTCGCTGATGATATTTAACACATTGAAAAATAAGTAAAATACTTATGAGTCAGAGAGTTGTGATTTTTGCCCTTACTTGTTCAGGTTGTATTGTTCTTTCTTACTAATTTCTTGATTTTGCGACATTTAAAAGCGACTCa                                                                                  >  2:214740/1‑149 (MQ=255)                                                                                       tttAACACATTGAAAAATAAGTAAAATACTTATGAGTCAGAGAGTTGTGATTTTTGCCCTTACttgttcaggttgtattgttctttctttgtaatttgttgattttcttgcattatttcagttctctggtactaaatggggcaaattgg                                                            <  2:20569‑M2/149‑87 (MQ=255)                                                                                        ttAACACATTGAAAAATAAGTAAAATACTTATGAGTCAGAGGGTGGTGATTTTTGCCCTTACTTGTTCAGGTTGTATCGTTCTTTCTTACTAATTTCTTGATTTTGCGACATTTAAAAGCGACTCAATTCGTTATATGGCATCagaaga                                                           <  2:247501/149‑1 (MQ=255)                                                                                                           gTAAAATACTTATGAGTCAGAGAGTTGTGATTTTTGCCCTTACTTGTTCAGGTTGTATTGTTCTTTCTTACTAATTTCTTGATTTTGCGACATTTAAAAGCGTCTCAATTCGTTAGATGGCATCAGAAGAGTATGCGTCATGCCGGAAc                                        >  1:178675/1‑149 (MQ=255)                                                                                                              aaaTACTTATAAGTCAGAGAGTTGTGATTTTTGCCCTTACTTGTTCAGGTTGTATTGTTCTTTCTTACTAATTTCTTGATTTTGCGACATTTAAAAGCGACTCAATTCGTTATATGGCATCAGAAGAGTATGCGTCATGCCGGAACGcc                                     <  2:235742/149‑1 (MQ=255)                                                                                                                 tACTTATGAGTCAGAGAGTTGTGATTTTTGCCCTTACttgttcaggttgtattgttctttctttgtaatttgttgattttcttgcattatttcagttctctggtactaaatggggcaaattgggggcaaactttgcaactacgataacc                                  >  2:238449‑M2/1‑37 (MQ=255)                                                                                                                                           tttGCCCTTACTTGTTCAGGTTGTATTGTTCTTTCTTACTAATTTCTTGATTTTGCGACATTTAAAAGCGACTCAATTCGTTATATGGCATCAGAAGAGTATGCGTCATGCCGGACCGCCCAGCATAAGCAATCTGATAAAAAAAACtg        >  1:84993/1‑149 (MQ=255)                                                                                                                                                ccTTACTTGTTCAGGTTGTATTGTTCTTTCTTACTAATTTCTTGATTTTGCGACATTTAAAAGCGACTCAATTCGTTATATGGCATCAGAAGAGTATGCGTCATGCCGGAACGCCCAGCATAAGAAATCTGATATAAAAAACTGTGGCg   >  1:193136/1‑149 (MQ=255)                                                                                                                                                 cTTACTTGTTCAGGTTGTATTGTTCTTTCTTACTAATTTCTTGATTTTGCGACATTTAAAAGCGACTCAATTCGTTATATGGCATCAGTAGATTATGCGTCATGCCGGACCGCCGCGCATAAGAAGTCTGATATAAAAAACTGTGCCgt  >  2:124131/1‑149 (MQ=255)                                                                                                                                                     |                                                                                                                                                 AAAAATGGGGCAAAACGCTGCAAAAGGGGCAAAAAAGGGGCAAAAAAAGAGTGGATTATCGTAGCTTATTGTTGTCGCTGATGATATTTAACACATTGAAAAATAAGTAAAATACTTATGAGTCAGAGAGTTGTGATTTTTGCCCTTACTTGTTCAGGTTGTATTGTTCTTTCTTACTAATTTCTTGATTTTGCGACATTTAAAAGCGACTCAATTCGTTATATGGCATCAGAAGAGTATGCGTCATGCCGGAACGCCCAGCATAAGAAATCTGATATAAAAAACTGTGGCGT  >  NC_000913_3_vch_pgi/1434810‑1435102

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ 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.