New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 1207805	4 (0.120)	19 (0.740)	18/128	0.4	84.1%	coding (305/630 nt)	ycfK	e14 prophage; protein StfP
	?	NC_000913	= 1209602	4 (0.160)					pseudogene (54/537 nt)	stfE	e14 prophage; putative side tail fiber protein fragment

CGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/1207711‑1207805 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttggtttgggagaaggCTCTGCATTACCTGTTGGTGTCCCGGTTCCGTGGCCTTCAGCCACTCCGCCAACAGGCTGGCTGAAATGC  <  NC_000913/1209602‑1209533                                                                                                                                                                       CGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCT                                                                                       <  2:238861/80‑1  GCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTG                                                                                     >  2:238870/1‑81   CGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGG                                                                                    <  1:238862/81‑1    GCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGT                                                                                   >  1:239031/1‑81       CTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTG                                                                                >  2:238871/1‑81            GTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAG                                                                            >  2:238876/1‑80                        GAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGCTCTGCAT                                                                >  2:239075/1‑80                        GAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGCTCTGCAT                                                                >  2:239074/1‑80                         AATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGCTCTGCATTA                                                              >  1:239073/1‑81                           TCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGCTCTGCATTACC                                                            <  2:238863/81‑1                            CCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGCTCTGCATTACCT                                                           >  1:239072/1‑81                                  GGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGCTCTGCATTACCTGTTGGT                                                     >  2:239071/1‑81                                  GGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGCTCTGCATTACCTGTTGG                                                      <  2:238865/80‑1                                     GATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGCTCTGCATTACCTGTTGGTGTC                                                  >  1:239070/1‑81                                        ATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGCTCTGCATTACCTGTTGGTGTCCCG                                               >  2:239069/1‑81                                         TCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGCTCTGCATTACCTGTTGGTGTCCCGG                                              >  2:239068/1‑81                                          CAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGCTCTGCATTACCTGTTGGTGTCCCGGT                                             >  2:239067/1‑81                                            AATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGCTCTGCATTACCTGTTGGTGTCCCGGTTC                                           <  2:238866/81‑1                                             ATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGCTCTGCATTACCTGTTGGTGTCCCGGTTCC                                          <  2:238867/81‑1                                                GGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGCTCTGCATTACCTGTTGGTGTCCCGGTTCCGTG                                       <  1:238868/81‑1                                                                       TCGAAAACCTTGGTTTGGGAGAAGGCTCTGCATTACCTGTTGGTGTCCCGGTTCCGTGGCCTTCAGCCACTCCGCCAAC                  <  2:239066/79‑1                                                                         GAAAACCTTGGTTTGGGAGAAGGCTCTGCATTACCTGTTGGTGTCCCGGTTCCGTGGCCTTCAGCCACTCCGCCAACAGGC              >  2:239065/1‑81                                                                           AAACCTTGGTTTGGGAGAAGGCTCTGCATTACCTGTTGGTGTCCCGGTTCCGTGGCCTTCAGCCACTCCGCCAACAGGCTG            <  2:239064/81‑1                                                                              CCTTGGTTTGGGAGAAGGCTCTGCATTACCTGTTGGTGTCCCGGTTCCGTGGCCTTCAGCCACTCCGCCAACAGGCTGGCT         <  1:239062/81‑1                                                                               CTTGGTTTGGGAGAAGGCTCTGCATTACCTGTTGGTGTCCCGGTTCCGTGGCCTTCAGCCACTCCGCCAACAGGCTGGCT         >  1:239061/1‑80                                                                                   GTTTGGGAGAAGGCTCTGCATTACCTGTTGGTGTCCCGGTTCCGTGGCCTTCAGCCACTCCGCCAACAGGCTGGCTGAAAT    <  1:239060/81‑1                                                                                      TGGGAGAAGGCTCTGCATTACCTGTTGGTGTCCCGGTTCCGTGGCCTTCAGCCACTCCGCCAACAGGCTGGCTGAAATGC  <  1:239059/80‑1                                                                                                                                                                       CGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/1207711‑1207805 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttggtttgggagaaggCTCTGCATTACCTGTTGGTGTCCCGGTTCCGTGGCCTTCAGCCACTCCGCCAACAGGCTGGCTGAAATGC  <  NC_000913/1209602‑1209533

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ 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.