Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913	296,229	Δ6 bp	coding (863‑868/1401 nt)	intF ←	CP4‑6 prophage; putative phage integrase

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	296229	296234	6	51 [0]	[0] 51	intF	CP4‑6 prophage; putative phage integrase

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 296228	0 (0.000)	51 (1.080)	39/276	0.2	100%	coding (869/1401 nt)	intF	CP4‑6 prophage; putative phage integrase
	?	NC_000913	296235 =	0 (0.000)					coding (862/1401 nt)	intF	CP4‑6 prophage; putative phage integrase

CCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGACGCAATTTCTTCACGCCGAGCACCAGTGAGCAAAAGTACTTGGAGATAGGCCGATGCAATAGGATTATTGAGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCTGACACGGGAACCATTTTTCTTACGTTGTAATCTTGTGCCAGATCGCCAGGAATGATCCCTTGATATTTTTT  >  NC_000913/296099‑296373                                                                                                                                         |                                                                                                                                           cgttcaccttcgatcttgtctttaattcgcatgcttgaccatttgaaatctacgtctgaccagcgaagcgacgcaatttcttcacgccgagcaccagtgagcaaaagtacttggagataggccgatgcaataggatGGCt                                                                                                                                         >  2:370225‑M2/137‑140 (MQ=255)    tcaccttcgatcttgtctttaattcgcatgcttgaccatttgaaatctacgtctgaccagcgaagcgacgcaatttcttcacgccgagcaccagtgagcaaaagtacttggagataggccgatgcaataggatGGCTACg                                                                                                                                      >  2:381446‑M2/134‑140 (MQ=255)     caccttcgatcttgtctttaattcgcatgcttgaccatttgaaatctacgtctgaccagcgaagcgacgcaatttcttcacgccgagcaccagtgagcaaaagtacttggagataggccgatgcaataggatGGCTACGc                                                                                                                                     >  2:635197‑M2/133‑140 (MQ=255)       ccttcgatcttgtctttaattcgcatgcttgaccatttgaaatctacgtctgaccagcgaagcgacgcaatttcttcacgccgagcaccagtgagcaaaagtacttggagataggccgatgcaataggatGGCTACGCAc                                                                                                                                   <  1:406517‑M2/10‑1 (MQ=255)            gatcttgtctttaattcgcatgcttgaccatttgaaatctacgtctgaccagcgaagcgacgcaatttcttcacgccgagcaccagtgagcaaaagtacttggagataggccgatgcaataggatGGCTACGCACGGCAc                                                                                                                              <  1:370225‑M2/15‑1 (MQ=255)             atcttgtctttaattcgcatgcttgaccatttgaaatctacgtctgaccagtgaagcgacgcaatttcttcacgccgagcaccagtgagcaaaagtacttggagataggccgatgcaataggatGACTACGCAc                                                                                                                                   <  1:199018‑M2/10‑1 (MQ=255)             atcttgtctttaattcgcatgcttgaccatttgaaatctacgtctgaccagtgaagcgacgcaatttcttcacgccgagcaccagtgagcaaaagtacttggagataggccgatgcaataggatGACTACGCAc                                                                                                                                   >  2:199018‑M2/125‑134 (MQ=255)             atcttgtctttaattcgcatgcttgaccatttgaaatctacgtctgaccagcgaagcgacgcaatttcttcacgccgagcaccagtgagcaaaagtacttggagataggccgatgcaataggatGGCTACGCACGGCACt                                                                                                                             >  1:90964‑M2/125‑140 (MQ=255)                 tgtctttaattcgcatgcttgaccatttgaaatctacgtctgaccagcgaagcgacgcaatttcttcacgccgagcaccagtgagcaaaagtacttggagataggccgatgcaataggatGGCTACGCACGGCACTAAAc                                                                                                                         <  2:710867‑M2/20‑1 (MQ=255)                 tgtctttaattcgcatgcttgaccatttgaaatctacgtctgaccagcgaagcgacgcaatttcttcacgccgagcaccagtgagcaaaagtacttggagataggccgatgcaataggatGGCTACGCACGGCACTAAAc                                                                                                                         <  1:534039‑M2/20‑1 (MQ=255)                  gtctttaattcgcatgcttgaccatttgaaatctacgtctgaccagcgaagcgacgcaatttcttcacgccgagcaccagtgagcaaaagtacttggagataggccgatgcaataggatGGCTACGCACGGCACTAAAcc                                                                                                                        >  1:626676‑M2/120‑140 (MQ=255)                    ctttaattcgcatgcttgaccatttgaaatctacgtctgaccagcgaagcgacgcaatttcttcacgccgagcaccagtgagcaaaagtacttggagataggccgatgcaataggatGGCTACGCACGGCACTAAACCAg                                                                                                                      <  2:174426‑M2/23‑1 (MQ=255)                    ctttaattcgcatgcttgaccatttgaaatctacgtctgaccagcgaagcgacgcaatttcttcacgccgagcaccagtgagcaaaagtacttggagataggccgatgcaataggatGGCTACGCACGGCACTAAACCAg                                                                                                                      <  1:587973‑M2/23‑1 (MQ=255)                        aattcgcatgcttgaccatttgaaatctacgtctgaccagcgaagcgacgcaatttcttcacgccgagcaccagtgagcaaaagtacttggagataggccgatgcaataggatGGCTACGCACGGCACTAAACCAGCttt                                                                                                                  >  2:218576‑M2/114‑140 (MQ=255)                             gcatgcttgaccatttgaaatctacgtctgaccagcgaagcgacgcaatttcttcacgccgagcaccagtgagcaaaagtacttggagataggccgatgcaataggatGGCTACGCACGGCACTAAACCAGCTTTTTAgt                                                                                                             <  1:381446‑M2/32‑1 (MQ=255)                             gcatgcttgaccatttgaaatctacgtctgaccagcgaagcgacgcaatttcttcacgccgagcaccagtgagcaaaagtacttggagataggccgatgcaataggatGGCTACGCACGGCACTAAACCAGCTTTTTAgt                                                                                                             >  1:424313‑M2/109‑140 (MQ=255)                             gcatgcttgaccatttgaaatctacgtctgaccagcgaagcgacgcaatttcttcacgccgagcaccagtcagcaaaagtacttggagataggccgatgcaataggatGGCTACGCACGGCACTAAACCAGCTTTTTAgt                                                                                                             >  2:264132‑M2/109‑140 (MQ=255)                              catgcttgaccatttgaaatctacgtctgaccagcgaagcgacgcaatttcttcacgccgagcaccagtgagcaaaagtacttggagataggccgatgcaataggatGGCTACGCACGGCACTAAACCAGCTTTTTAgtt                                                                                                            >  2:787003‑M2/108‑140 (MQ=255)                              catgcttgaccatttgaaatctacgtctgaccagcgaagcgacgcaatttcttcacgccgagcaccagtgagcaaaagtacttggagataggccgatgcaataggatGGCTACGCACGGCACTAAACCAGCTTTTTAgtt                                                                                                            >  1:536776‑M2/108‑140 (MQ=255)                               atgcttgaccatttgaaatctacgtctgaccagcgaagcgacgcaatttcttcacgccgagcaccagtgagcaaaagtacttggagataggccgatgcaataggatGGCTACGCACGGCACTAAACCAGCTTTTTAgttg                                                                                                           >  1:440652‑M2/107‑140 (MQ=255)                                         atttgaaatctacgtctgaccagcgaagcgacgcaatttcttcacgccgagcaccagtgagcaaaagtacttggagataggccgatgcaataggatGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGc                                                                                                 <  1:629299‑M2/44‑1 (MQ=255)                                          tttgaaatctacgtctgaccagcgaagcgacgcaatttcttcacgccgagcaccagtgagcaaaagtacttggagataggccgatgcaataggatGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCa                                                                                                >  1:491072‑M2/96‑140 (MQ=255)                                                                 gaagcgacgcaatttcttcacgccgagcaccagtgagcaaaagtacttggagataggccgatgcaataggatGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCt                                                                         >  2:662828‑M2/73‑140 (MQ=255)                                                                         gcaatttcttcacgccgagcaccagtgagcaaaagtacttggagataggccgatgcaataggatGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCTGACACggg                                                                 <  1:218576‑M2/76‑1 (MQ=255)                                                                               tcttcacgccgagcaccagtgagcaaaagtacttggagataggccgatgcaataggatGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCTGACACGGGAACCAt                                                           <  2:440652‑M2/82‑1 (MQ=255)                                                                                 ttcacgccgagcaccagtgagcaaaagtacttggagataggccgatgcaataggatGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCTGACACGGGAACCAttt                                                         <  2:424313‑M2/84‑1 (MQ=255)                                                                                  tcacgccgagcaccagtgagcaaaagtacttggagataggccgatgcaataggatGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCTGACACGGGAACCAtttt                                                        >  2:707512‑M2/56‑140 (MQ=255)                                                                                  tcacgccgagcaccagtgagcaaaagtacttggagataggccgatgcaataggatGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCTGACACGGGAACCAtttt                                                        >  2:176408‑M2/56‑140 (MQ=255)                                                                                      gccgagcaccagtgagcaaaagtacttggagataggccgatgcaataggatGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCTGACACGGGAACCATTTTTCtt                                                    <  1:514943‑M2/89‑1 (MQ=255)                                                                                      gccgagcaccagtgagcaaaagtacttggagataggccgatgcaataggatGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCTGACACGGGAACCATTTTTCtt                                                    >  2:762356‑M2/52‑140 (MQ=255)                                                                                       ccgagcaccagtgagcaaaagtacttggagataggccgatgcaataggatGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCTGACACGGGAACCATTTTTCTTa                                                   >  2:75928‑M2/51‑140 (MQ=255)                                                                                       ccgagcaccagtgagcaaaagtacttggagataggccgatgcaataggatGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCTGACACGGGAACCATTTTTCTTa                                                   <  1:176408‑M2/90‑1 (MQ=255)                                                                                       ccgagcaccagtgagcaaaagtacttggagataggccgatgcaataggatGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCTGACACGGGAACCATTTTTCTTa                                                   <  2:76046‑M2/90‑1 (MQ=255)                                                                                       ccgagcaccagtgagcaaaagtacttggagataggccgatgcaataggatGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCTGACACGGGAACCATTTTTCTTa                                                   <  1:762356‑M2/90‑1 (MQ=255)                                                                                               cagtgagcaaaagtacttggagataggccgatgcaataggatGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCTGACACGGGAACCATTTTTCTTACGTTGTaa                                           <  1:726972‑M2/98‑1 (MQ=255)                                                                                                 gtgagcaaaagtacttggagataggccgatgcaataggatGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCTGACACGGGAACCATTTTTCTTACGTTGTAATc                                         <  2:491072‑M2/100‑1 (MQ=255)                                                                                                    agcaaaagtacttggagataggccgatgcaataggatGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCTGACACGGGAACCATTTTTCTTACGTTGTAATCTtg                                      >  1:701738‑M2/38‑140 (MQ=255)                                                                                                         aagtacttggagataggccgatgcaataggatGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCTGACACGGGAACCATTTTTCTTACGTTGTAATCTTGTGCCa                                 <  2:549448‑M2/108‑1 (MQ=255)                                                                                                          agtacttggagataggccgatgcaataggatGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCTGACACGGGAACCATTTTTCTTACGTTGTAATCTTGTGCCAg                                <  1:662828‑M2/109‑1 (MQ=255)                                                                                                          agtacttggagataggccgatgcaataggatGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCTGACACGGGAACCATTTTTCTTACGTTGTAATCTTGTGCCAg                                <  2:706741‑M2/109‑1 (MQ=255)                                                                                                          agtacttggagataggccgatgcaataggatGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCTGACACGGGAACCATTTTTCTTACGTTGTAATCTTGTGCCAg                                <  1:787003‑M2/109‑1 (MQ=255)                                                                                                           gtacttggagataggccgatgcaataggatGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCTGACACGGGAACCATTTTTCTTACGTTGTAATCTTGTGCCAGa                               >  2:249347‑M2/31‑140 (MQ=255)                                                                                                                tggagataggccgatgcaataggatGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCTGACACGGGAACCATTTTTCTTACGTTGTAATCTTGTGCCAGATCGcc                          >  2:516484‑M2/26‑140 (MQ=255)                                                                                                                tggagataggccgatgcaataggatGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCTGACACGGGAACCATTTTTCTTACGTTGTAATCTTGTGCCAGATCGcc                          <  1:540295‑M2/115‑1 (MQ=255)                                                                                                                  gagataggccgatgcaataggatGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCTGACACGGGAACCATTTTTCTTACGTTGTAATCTTGTGCCAGATCGCCAg                        <  1:75928‑M2/117‑1 (MQ=255)                                                                                                                       aggccgatgcaataggatGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCTGACACGGGAACCATTTTTCTTACGTTGTAATCTTGTGCCAGATCGCCAGGAATg                   >  1:417214‑M2/19‑140 (MQ=255)                                                                                                                        ggccgatgcaataggatGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCTGACACGGGAACCATTTTTCTTACGTTGTAGTCTTGTGCCAGATCGCCAGGAATGa                  <  2:689698‑M2/123‑1 (MQ=255)                                                                                                                         gccgatgcaataggatGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCTGACACGGGAACCATTTTTCTTACGTTGTAATCTTGTGCCAGATCGCCAGGAATGAt                 >  2:752125‑M2/17‑140 (MQ=255)                                                                                                                           cgatgcaataggatGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCTGACACGGGAACCATTTTTCTTACGTTGTAATCTTGTGCCAGATCGCCAGGAATGATcc               >  2:786599‑M2/15‑140 (MQ=255)                                                                                                                                        tGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCTGACACGGGAACCATTTTTCTTACGTTGTAATCTTGTGCCAGATCGCCAGGAATGATCCCTTGATAtttttt  >  1:516151‑M2/2‑140 (MQ=255)                                                                                                                                        tGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCTGACACGGGAACCATTTTTCTTACGTTGTAATCTTGTGCCAGATCGCCAGGAATGATCCCTTGATAtttttt  >  1:439624‑M2/2‑140 (MQ=255)                                                                                                                                         |                                                                                                                                           CCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGACGCAATTTCTTCACGCCGAGCACCAGTGAGCAAAAGTACTTGGAGATAGGCCGATGCAATAGGATTATTGAGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCTGACACGGGAACCATTTTTCTTACGTTGTAATCTTGTGCCAGATCGCCAGGAATGATCCCTTGATATTTTTT  >  NC_000913/296099‑296373

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑