New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 1434336	26 (0.420)	13 (0.210)	13/388	2.8	30.9%	coding (71/114 nt)	ynaM	Rac prophage; protein YnaM
	?	NC_000913	= 1632955	32 (0.520)					coding (66/114 nt)	ynfT	Qin prophage; protein YnfT

CTTACTTCAGGAAGCTGCGCAGGGAACCACTTTAGGGTGTCTTTTGATTTCATGAAGATATTCCTTAAAATATTATTGA‑TTTTCA‑TTGCGATATTGTATGTC‑TGATTCAGGATATG‑TTGACTTATACATCGG‑TTTTGTCTGGGTTATTGGATATGCCAA‑TC‑C‑‑CT‑A‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/1434172‑1434336 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TATTAGGGCATGACT‑‑‑AAAAATGCTGAATATGATAAGGAGAGATGTGATTATCAGTATGCTGTTCATATAGCCTCGAATTAGT‑AATGTG‑TTATATATGATATAG‑TTGAC‑AATTTTTATC‑TTGGGTG‑TTCTT‑‑AAAG‑TTCGTAGATAAACATTGTCGTTTCAGGTATACAGGAATGCTAACAGGTGGCAGCAAAAATCAGGCGG‑TTTATGGCGCAAGCTGAAGCGGCAACTGCAAACTATCTTATGTAGAGACTCTACACGGATTGGGTTTAAAAGTATACATAGAT  <  NC_000913/1632955‑1632672                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          CTTACTTCAGGAAGCTGCGCAGGGAACCACTTTAGGGTGTCTTTTGATTTCATGAAGATATTCCTT‑AAATATTATTGA‑TTTTCA‑TTGCGATATTGTATGTC‑TGATTCAGGATATG‑TTGACTTATACATCGG‑TTTTGTCTGGG‑TATTGGATATGCCAA‑CT‑C‑‑CT‑ATATTAGGGCATGACT‑‑‑AAAAATGCTGAATATGATAAGGAGAGATGTGATTATCAGTATGCTGTTCATATAGCCTCGAATTAGT‑AATGTG‑‑TATATATGATATAG‑TTGAC‑A‑‑TTTTATCTTTGGGTG‑TTCTT‑‑AAAG‑TTCGTAGATAAACA                                                                                                                                           <  1:326680/309‑1                          ACCACTTTAGGGTGTC‑TTTGATTT‑ATGAAGATATTCCTTAAAAATATATTGA‑TTTTCA‑TTGCGATATTGTATGTC‑TGATTCAGGATATG‑TTGACTTATACATCGG‑‑TTTG‑CTGGG‑TATTGGATATGCCAA‑CT‑C‑‑CT‑ATATTAGGGCATGACTAAAAAAAATGCTGAATATGATAAGGAGAGATGTGATTATCAGTATGCTGTTCATATAGCCTCGAATTAGTAAATGTG‑‑TATATATGATATAG‑TTGAC‑AATTTTTATC‑TT                                                                                                                                                                           <  1:326688/258‑1                                     tgtctTTTTGATTTCATGAAGATATTCCTTAAAATATTATTGA‑TTTTCA‑TTGCGATATTGTATGTC‑TGATTCAGGATATG‑TTGACTTATACATCGG‑TTTTGTCTGGGTTATTGGATATGCCAA‑CT‑A‑‑CT‑ATATTAGGGCATGACT‑‑‑AAAAATGCTGAATATGATAAGGAGAGATGTGATTATCAGTATGCTGTTCATATAGCCTCGAATTAGT‑AATGTG‑TTATATATGATATAG‑TTGAC‑AA‑TTTTATC‑TTGGGTG‑TTCTT‑‑AAAG‑TTCGTAGATA                                                                                                                                               <  1:326682/267‑1                                                             TTCCTTAAAATATTATTGA‑TTTTCA‑TTGCGATATTGTATGTC‑TGATTCAGGATATG‑TTGACTTATACATCGG‑TTTTGTCTGGGTTATTGGATATGCCAA‑CCTA‑‑CT‑ATATTAGGGCATGACT‑‑‑AAAAATGCT                                                                                                                                                                                                                                                                                <  1:326701/130‑1                                                                 taAAAATATTATTGATTTTTCATTTGCGATATTG‑ATGTC‑TGATTCAGGATATG‑TTGACTTATACATCGG‑‑TTTGTCTGGGTTATTGGATATGCCAA‑CT‑A‑‑CT‑ATATTAGGGCATGACT‑‑‑AAAAATGCTGAATATGATAAGGAGAGATGTGATTATCAG                                                                                                                                                                                                                                                  <  1:326697/153‑1                                                                           ATTGA‑TTTTCA‑TTGCGATATTGTATGTCTTGATTCAGGATATGTTTGACTTATACATCGG‑TTTTGTCTGG‑‑TATTGGATATGCCAA‑CT‑A‑‑CT‑ATATTAGGGCATGACT‑‑‑AAAAATGCTGAATATGATAAGGAGAGATGTGATTATCAGTATGCTGTTCATATAGCCTCGAATTAGT                                                                                                                                                                                                                      <  1:326696/173‑1                                                                                     CA‑TTGCGATATTGTATGTC‑TGATTCAGGATATG‑TTGACTTATACATCGG‑TTTTGTCTGGGTTATTGGATATGCCAACTA‑C‑‑CT‑ATATTAGGGCATGACT‑‑‑AAAAATGCTGAATATGATAAGGAGAGATGTGATTATCAGTATGCTGTTCATATAGCCTCGAATTAGTAAATGTG‑TTATATATGATATAGTTTGACAAATTTTTATC‑TTGGGTG‑TTCTTA‑AAAG‑TTCGTAGATAAAC‑TTG‑CGTTTCAGGTATACAGGAATGCTAACAGGTGGCAGCAAAAATCAGGCGGTTTTATGGCGCAAGCTGAAGCGGCAACTGCAAACTATCTTATGTA                                         <  1:326669/331‑1                                                                                         TGCGATATTGTATGTC‑TGATTCAGGATATG‑TTGACTTATACATCGG‑TTTTGTCTGGGTTATTGGATATGCCAA‑CT‑C‑‑CT‑ATATTAGGGCATGACT‑‑‑AAAAATGCTGAATATGATAAGGAGAGATGTGATTATCAGTATGCTGTTCATATAGCCTCGAATTAGT‑AATGTG‑TTATATATGATATAG‑TTGAC‑AATTTTTATC‑TTGGGTG‑TTCTTA‑AAAGTTTCGTAGATAAACATTGTCGTTTCAGGTATACAGGAATGCTAACAGGTGGCAGCAAAAATCAGGCGG‑TTTATGGCGCAAGCTGA                                                                    <  1:326673/299‑1                                                                                          GCGATATTGTATGTC‑TGATTCAGGATATG‑TTGACTTATACATCGG‑TTTTG‑CTGGGTTATTGGATATGCCAACTA‑C‑‑CTAATATTAGGGCATGACT‑‑‑AAAAATGCTGAATATGATAAGGAGAGATGTGATTATCAGTATGCTGTTCATATAGCCTCGAATTAGT‑AATGTG‑TTATATATGATATAG‑TTGACAAATTTTTATCTTTGGGTGTTTCTTTAAAAGTTTCGTAGATAAACATTGTCGTTTCAGG‑ATACAGGAATGCTAACAGGTGGCAGCAAAAATCAGGCGG‑TTTTAGGCGCAAGCTGAAGCGGCAACTGCAAACTATCTTATGTAGAGACTCTA                                <  1:326665/338‑1                                                                                                                    TATG‑TTGACTTATACATCGG‑‑TTTGTCTGGGTTATTGGATATGCCAA‑CT‑A‑‑CT‑ATATTAGGGCATGACT‑‑‑AAAAATGCTGAATATGATAAGGAGAGATGTGATTATCAGTATGCTGTTCATATAGCCTCGAATTAGT‑AATGTG‑TTATATATGATATAG‑TTGAC‑AA‑TTTTATC‑TTGGGTG‑TTCTT‑‑‑AAG‑TTCGTAGATAAACATTGTCGTTTCAGGTATACAGGAATGCTAACAGGTGGCA                                                                                                     <  1:326677/236‑1                                                                                                                                ATACATCGG‑TTTTGTCTGGG‑TATTGGATATGCCAACTC‑C‑‑TA‑ATATTAGGGCATGACT‑‑‑AAAAATGCTGAATATGATAAGGAGAGATGTGATTATCAGTATGCTGTTCATATAGCCTCGAATTAGT‑AATGTG‑TTATATATGA                                                                                                                                                                                                    <  1:326693/140‑1                                                                                                                                  ACATCGGTTTTTGTCTGGGTTATTGGATATGCCAA‑CT‑C‑‑CT‑ATATTAGGGCATGACT‑‑‑AAAAATGCTGAATATGATAAGGAGAGATGTGATTATCAGTATGCTGTTCATATAGCCTCGAATTAGTAAATGTG‑T                                                                                                                                                                                                             <  1:326694/131‑1                                                                                                                                   CATCGG‑TTTTGTCTGGGTTATTGGATATGCCAA‑TC‑CTACT‑ATATTAGGGCATGACT‑‑‑AAAAATGCTGAATATGATAAGGAGAGATGTGATTATCAGTATGCTGTTCATATAGCCTCGAATTAGT‑AATGTGTTTATATATGATATAG‑TTGAC‑AA‑TTTTATCTTTGGGTG‑TTCTT‑‑AAAG‑TTCGTAGATAAACATTG‑CGTTTCAGG‑ATACAGGAATGCTAACAGGTGGCAGCAAAAATCAGGCGG‑TTTA‑GGCGCAAGCTGAAGCGGCAACTGCAAACTATCTTATGTAGAGACTCTACACGGATTGGGTTTAAAAGTATACATAGAT  <  1:326663/323‑1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          CTTACTTCAGGAAGCTGCGCAGGGAACCACTTTAGGGTGTCTTTTGATTTCATGAAGATATTCCTTAAAATATTATTGA‑TTTTCA‑TTGCGATATTGTATGTC‑TGATTCAGGATATG‑TTGACTTATACATCGG‑TTTTGTCTGGGTTATTGGATATGCCAA‑TC‑C‑‑CT‑A‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/1434172‑1434336 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TATTAGGGCATGACT‑‑‑AAAAATGCTGAATATGATAAGGAGAGATGTGATTATCAGTATGCTGTTCATATAGCCTCGAATTAGT‑AATGTG‑TTATATATGATATAG‑TTGAC‑AATTTTTATC‑TTGGGTG‑TTCTT‑‑AAAG‑TTCGTAGATAAACATTGTCGTTTCAGGTATACAGGAATGCTAACAGGTGGCAGCAAAAATCAGGCGG‑TTTATGGCGCAAGCTGAAGCGGCAACTGCAAACTATCTTATGTAGAGACTCTACACGGATTGGGTTTAAAAGTATACATAGAT  <  NC_000913/1632955‑1632672

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 35 ≤ 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.