New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1049778 =	152 (0.780)	18 (0.090)	3/478	NT	14.9%	intergenic (‑34/‑55)	gfcA/insA	O‑antigen capsule production threonine‑rich inner membrane protein/IS1 repressor TnpA
	?	NC_000913	= 4507640	53 (0.270)					coding (979/1152 nt)	insI1	IS30 transposase

AACGCCCATAATGCGGGCTGTTGCCCGGCATCCAACGCCATTCATGGCCATATCAATGATTTTCTGGTGCGTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTACGGCAGTGAGAGCAGAGATAGCG‑CTGATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/1050057‑1049778 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GAGAACACAAATGGGCTAATTCGGCAGTACTTTCCTAAAAAGACATGTCTTGCCCAATATACTCAACATGAACTAGATCTGGTTGCTGCTCAGCTAAACAACAGACCGAGAAAGACACTGAAGTTCAAAACACCGAAAGAGATAATTGAAAGGGGTGTTGCATTGACAGATTGAATCTACAGTAGC  <  NC_000913/4507640‑4507455                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     AACGCCCATAATGCGGTGTGTTGCCCGGCATCCAACGCCATTCATGGCCATATCAATGATTTTCTGGTGCGTACCGGGTGGAGAAGCGGTGTAAGTGAACGGCAGTTGCCAAGTTTTACGGCAGGGAGAGCAGAGATAGCG‑CTGATGTCCTGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAATAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAATTCAGTAAGTTGGCAGCATCACCGA                                                                                                                                                                                          <  1:838935/282‑1              CGGGCGGTTGCCCGGCATCCAACGCCATTCATGGCCATATCCATGATTTTCTGGTGCGTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTACGGCAGTGAGCGCAGAGATAGCG‑CTGATGTTCGGCAGTGCTTTTGCCGTTACGAACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGAAGAACCTCAAAAACACCACCATGCACCAAATCAGTAAGTTGCCAGAATCACCGAGACCACAAATGt                                                                                                                                                                              >  1:864050/1‑280                                                                   gtggtTACCGGGTTGAGGAGCAGTGTAAGGGAAGGGGCGTTGCAAGGTTTTACCGAAGTACGAGCAGAGATAGCG‑TTGCTGTCGGGCAGTGCTGTTGCCGTTACGGACGACCCCGTCAGTAGCTGAACAGGAGGGACAGCGGATAGAAACAGAAGCCACTGGAGAACGTCAAAAACTCCATCTTACACTAAATCAGTAAGTTAGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAGTACTTTCCTAAAAAGACATGTCTTGCCCAATATACTCAACA                                                                                                                        <  1:1939836/277‑1                                                                                                                       aGGCGGTGAAGGCAGAGATAGCGAGTGGTG‑CCGGCAATGCTTTAGCCGTTAACAACCACCCCGGCAGTAGCTGAACAGGAGGGACGTCTGATAGAAAAAGAAACCACTGGAGAACCTCAAAAACAGCATCATACACTAAATCAGTAAGTTGGCGGCATCACCGCGAAAACAAATGGGCTAATTCGGCAGTACTTTCCTAAAAAGACATGTCTTGCCCAATATACTCAACATGAACGAGATTTGGTTGCTGCCCAGCTAAACAACAGACCGAGAAAGACACTG                                                                    <  1:1963846/281‑1                                                                                                                                                                                          GTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAGAACACCAATGGGCTAATTCGGCAGTACTCACCTAAAAAGACATGTCTTGCCCAATATACTCAACATTACCTCGATATGGTTGCTGCTCAGCTCACCAACAGACCGAGAACGCCACTGAAGTTCAAAACACCGACAGATACAGATAAAAGGGGTGTTGCATTTACGGATGAAATCTcaagcagc  >  1:1997009/1‑274                                                                                                                                                                                                                                                        TCATACACTAAATCAGTAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAGTACTTTCCTAAAAAGACATGTCTTGCCCAATATACTCAACATGAAC                                                                                                                   >  1:1416785/1‑107                                                                                                                                                                                                                                                        TCATACACTAAATCAGTAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAGTACTTTCCTAAAAAGACATGTCTTGCCCAATATACTCAACATGAAC                                                                                                                   <  2:1416785/107‑1                                                                                                                                                                                                                                                                 AAATCAGTAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAGTACTTTCCTAAAAAGACATGTCTTGCCCAATATACTCAACATGAACTAGATCTGGTTGCTGCTCAGCTAAACAACAGACCGAGAAAGACACTGAAGTTCAAAACACCGAAAGAGATAATTGAAAGGGGTGTTGCATTGA                      <  2:515279/191‑1                                                                                                                                                                                                                                                                 AAATCAGTAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAGTACTTTCCTAAAAAGACATGTCTTGCCCAATATACTCAACATGAACTAGATCTGGTTGCTGCTCAGCTAAACAACAGACCGAGAAAGACACTGAAGTTCAAAACACCGAAAGAGATAATTGAAAGGGGTGTTGCATTGA                      >  1:515279/1‑191                                                                                                                                                                                                                                                                  AATCAGTAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAGTACTTTCCTAAAAAGACATGTCTTGCCCAATATACTCAACATGAACTAGATCTGGTTGCTGCTCAGCTAAACAACAGACCGAGAAAGACACTGAAGTTCAAAACACCGAAAGAGATAATTGAAAGGGGT                                >  1:40016/1‑180                                                                                                                                                                                                                                                                  AATCAGTAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAGTACTTTCCTAAAAAGACATGTCTTGCCCAATATACTCAACATGAACTAGATCTGGTTGCTGCTCAGCTAAACAACAGACCGAGAAAGACACTGAAGTTCAAAACACCGAAAGAGATAATTGAAAGGGGT                                <  2:40016/180‑1                                                                                                                                                                                                                                                                  AATCAGTAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAGTACTTTCCTAAAAAGACATGTCTTGCCCAATATACTCAACATGAACTAGATCTGGTTGCTGCTCAGCTAAACAACAGACCGAGAA                                                                            >  2:639432/1‑136                                                                                                                                                                                                                                                                  AATCAGTAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAGTACTTTCCTAAAAAGACATGTCTTGCCCAATATACTCAACATGAACTAGATCTGGTTGCTGCTCAGCTAAACAACAGACCGAGAA                                                                            <  1:639432/136‑1                                                                                                                                                                                                                                                                  AATCAGTAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAGTACTTTCCTAAAAAGACATGTCTTGCCCAATATACTCAACATGAACTAGATCTGGTTGCTGCTCAGCTAAACAACAGACC                                                                                 <  2:1859655/131‑1                                                                                                                                                                                                                                                                  AATCAGTAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAGTACTTTCCTAAAAAGACATGTCTTGCCCAATATACTCAACATGAACTAGATCTGGTTGCTGCTCAGCTAAACAACAGACC                                                                                 >  1:1859655/1‑131                                                                                                                                                                                                                                                                        TAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAGTACTTTCCTAAAAAGACATGTCTTGCCCAATATACTCAACATGAACTAGATCTGGTTGCTGCTCAGCTAAACAACAGACCGAGAAAGACACTGAAGTTCAAAACACCGAAAGAGATAATTGAAAGGGGTGTTGCATTGACAG                   <  2:1143358/187‑1                                                                                                                                                                                                                                                                        TAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAGTACTTTCCTAAAAAGACATGTCTTGCCCAATATACTCAACATGAACTAGATCTGGTTGCTGCTCAGCTAAACAACAGACCGAGAAAGACACTGAAGTTCAAAACACCGAAAGAGATAATTGAAAGGGGTGTTGCATTGACAG                   >  1:1143358/1‑187                                                                                                                                                                                                                                                                        TAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAGTACTTTCCTAAAAAGACATGTCTTGCCCAATATACTCAACATGAACTAGATCTGGTTG                                                                                                       <  1:614755/103‑1                                                                                                                                                                                                                                                                        TAAGTTGGCAGCATCACCGAGAACACAAATGGGCTAATTCGGCAGTACTTTCCTAAAAAGACATGTCTTGCCCAATATACTCAACATGAACTAGATCTGGTTG                                                                                                       >  2:614755/1‑103                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     AACGCCCATAATGCGGGCTGTTGCCCGGCATCCAACGCCATTCATGGCCATATCAATGATTTTCTGGTGCGTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTACGGCAGTGAGAGCAGAGATAGCG‑CTGATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/1050057‑1049778 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GAGAACACAAATGGGCTAATTCGGCAGTACTTTCCTAAAAAGACATGTCTTGCCCAATATACTCAACATGAACTAGATCTGGTTGCTGCTCAGCTAAACAACAGACCGAGAAAGACACTGAAGTTCAAAACACCGAAAGAGATAATTGAAAGGGGTGTTGCATTGACAGATTGAATCTACAGTAGC  <  NC_000913/4507640‑4507455

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ 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.