Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC	NC_002947	4,980,585	+GGC	intergenic (‑24/+44)	PP_4387 ← / ← flgE	hypothetical protein/flagellar hook protein FlgE

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 4980585	2 (0.040)	37 (0.810) +GGC	33/276	0.5	95.0%	intergenic (‑24/+44)	PP_4387/flgE	hypothetical protein/flagellar hook protein FlgE
	?	NC_002947	4980586 =	2 (0.040)					intergenic (‑25/+43)	PP_4387/flgE	hypothetical protein/flagellar hook protein FlgE

AGGTAGCGGCCGGTGACCAGGCTTTGCCATTGATAGAACGGGGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTT‑‑GG‑‑‑CGCTTT‑‑‑GCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTAGTTGCTCTGCGCCTTGATCAGGTT  >  NC_002947/4980449‑4980721                                                                                                                                           |                                                                                                                                               aGGTAGCGGCCGGTGACCAGGCTTTGCCATTGATAGAACGGGGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTT‑‑GGggccgctttgcg                                                                                                                                    <  8:59549‑M1/149‑13 (MQ=255)          ccGGTTACCAGGATTTGCCATTGATATAACGGGGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTT‑‑GGggccgctttgcggccccaatt                                                                                                                           <  8:173861‑M1/149‑22 (MQ=255)            ggTGACCAGGCTTTGCCATTGATAGAACGGGGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTT‑‑GGggccggtttggggcccccatta                                                                                                                          >  2:327729‑M1/1‑126 (MQ=255)                  cAGGCTTTGCCATTGATAGAACGGGGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTT‑‑GGgg                                                                                                                                              >  5:284436‑M1/1‑120 (MQ=255)                           ccATTGATAGAACGGGGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTT‑‑GGggccgctttgcggccccaattacaaacaccaaagcca                                                                                                           >  2:6436‑M1/1‑111 (MQ=255)                           ccATTGATAGAACGGGGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTT‑‑GGggccgctttgcggccccaattac                                                                                                                         <  6:200682‑M1/134‑24 (MQ=255)                           ccATTGATAGAACGGGGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTT‑‑GGggccgctttgcggccccaattac                                                                                                                         >  5:200682‑M1/1‑111 (MQ=255)                                gATAGAACGGGGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTT‑‑GGggccgctttgcggccccaattacaaacaccaaagccaatacaa                                                                                                     >  7:76141‑M1/1‑106 (MQ=255)                                 aTAGAACGGGGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTT‑‑GGggccgctttgcggccccaattacaaacaccaaagccaatacaa                                                                                                     >  2:261841‑M1/1‑105 (MQ=255)                                  tAGAACGGGGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTT‑‑GGggccgctttgcggccccaattacaaacaccaaagccaatacaatc                                                                                                   <  1:240639‑M1/149‑46 (MQ=255)                                  tAGAACGGGGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTT‑‑GGggccgctttgcggccccaattacaaacaccaaagccaatacaat                                                                                                    >  4:134486‑M1/1‑104 (MQ=255)                                  tAGAACGGGGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGCGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTT‑‑GGggccgctttgcggccccaattacaaacaccaaagccaatacaatc                                                                                                   <  1:236033‑M1/149‑46 (MQ=255)                                             gggggcagcgggggcagGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTT‑‑GGggccgctttgcggccccaattacaaacaccaaagccaatacaatcatcaggtcatc                                                                                        <  3:134486‑M1/149‑57 (MQ=255)                                                    gcgggggcagGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTT‑‑GGggccgctttgcggccccaattacaaacaccaaagccaatacaatcatcaggtcatctgaatga                                                                                 <  1:22591‑M1/149‑64 (MQ=255)                                                      gggggcagGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTT‑‑GGggccgctttgcggccccaattacaaacaccaaagccaatacaatcatcaggtcatctgaatgatg                                                                               <  1:252572‑M1/149‑66 (MQ=255)                                                                 gAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTT‑‑GGggccgctttgcggccccaattacaaacaccaaagccaatacaatcatcaggtcatctgaatgatggtctgcatgat                                                                    <  8:76141‑M1/149‑77 (MQ=255)                                                                   ccaagcacaagaaATGGGAACAAGCCCAGAAAAGACAGCCGCTTCTTTCTCGTGAACATTCACAATCTTTGGGC‑‑CGCTTTCTAGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCatga                                                                  <  1:261841/146‑1 (MQ=255)                                                                           cagcaAAGGGAACAAGGCCAGTAACGACAGCAGCTTCATTCGCGTGAACCTTCACTTTCTT‑‑GGggccgctttgcggccccaattacaaacaccaaagccaatacaatcatcaggtcatctgaatgatggtctgcatgatggtgctttca                                                          <  1:299984‑M1/149‑87 (MQ=255)                                                                              caAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTT‑‑GGggccgctttgcggccccaattacaaacaccaaagccaatacaatcatcaggtcatctgaatgatggtctgcatgatggtgctttcagtg                                                       <  1:327729‑M1/149‑90 (MQ=255)                                                                                  gggAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTT‑‑GGggccgctttgcggccccaattacaaacaccaaagccaatacaatcatcaggtcatctgaatgatggtc                                                                            >  1:287702‑M1/1‑56 (MQ=255)                                                                                  gggAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTT‑‑GGggccgctttgcggccccaattacaaacaccaaagccaatacaatcatcaggtcatctgaatgatggtc                                                                            <  2:287702‑M1/124‑69 (MQ=255)                                                                                       cAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTT‑‑GGggccgctttgcggccccaattacaaacaccaaagccaatacaatcatcaggtcatctgaatgatggtctgcatgatggtgctttcagtggaaatggtc                                              >  6:116231‑M1/1‑51 (MQ=255)                                                                                        aaGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTT‑‑GGggccgctttgcggccccaattacaaacaccaaagccaatacaatcatcaggtcatctgaatgatggtctgcat                                                                       >  6:321356‑M1/1‑50 (MQ=255)                                                                                          ggCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTT‑‑GGggccgctttgcggccccaattacaaaccccaaagcccataccatcagcaggtcatgtgaatgttggtgtggctgattggggtttgagtggaaatggtcttg                                           >  8:266387‑M1/1‑48 (MQ=255)                                                                                          ggCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTT‑‑GGggccgctttgcggccccaattacaaacaccaaagccaatacaatcatcaggtcatctgaatgatggtctgcatgatggtgctttcagtggaaatggtcttg                                           >  1:191776‑M1/1‑48 (MQ=255)                                                                                             cAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTT‑‑GGggccgctttgcggccccaattacaaacaccaaagccaatacaatcatcaggtcatctgaatgatggtctgcatgatggtgctttcagtggaaa                                                   <  8:39026‑M1/138‑94 (MQ=255)                                                                                             cAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTT‑‑GGggccgctttgcggccccaattacaaacaccaaagccaatacaatcatcaggtcatctgaatgatggtctgcatgatggtgctttcagtggaaa                                                   >  7:39026‑M1/1‑45 (MQ=255)                                                                                                    gACAGCCGCTTCATTCGCGTGAACCTTCACATTCTT‑‑GGggccgctttgcggccccaattacaaacaccaaagccaatacaatcatcaggtcatctgaatgatggtctgcatgatggtgctttcagtggaaatggtcttggcattggcct                                 <  1:6436‑M1/149‑112 (MQ=255)                                                                                                        gCCGCTTCATTCGCGTGAACCTTCACATTCTT‑‑GGggccgctttgcggccccaattacaaacaccaaagccaatacaatcatcaggtcatctgaatgatggtctgcatgatggtgctttcagtggaaatggtcttggcattggcctggta                             <  2:191776‑M1/149‑116 (MQ=255)                                                                                                          gacctcattCGCGTGAACCTTCACATTCTT‑‑GGggccgctttgcggccccaattacaaacaccaaagccaatacaatcatcaggtcatctgaatgatggtctgcatgatggtgctttcagtggaaatggtcttggcattggcctggtagt                           <  5:129456‑M1/145‑118 (MQ=255)                                                                                                            cTTCATTCGCGTGAACCTTCACATTCTT‑‑GGCGCCGCTTT‑‑‑GCGGGCCCAATTAACAACACCAAAGCCAATACAATCAACAGGTCATAGGAATGCTAGGCTGCTAGATTGGCCGTTCAGTGGGAATGGTGTTTGCATTGGACTGGTAGTTg                      >  4:183603/1‑149 (MQ=255)                                                                                                             ttCATTCGCGTGAACCTTCACATTCTT‑‑GGggccgctttgcggccccaattacaaacaccaaagccaatacaatcatcaggtcatctgaatgatggtctgcatgatggtgctttcagtggaaatggtcttg                                           >  6:60981‑M1/1‑29 (MQ=255)                                                                                                             ttCATTCGCGTGAACCTTCACATTCTT‑‑GGggccgctttgcggccccaattacaaacaccaaagccaatacaatcatcaggtcatctgaatgatggtctgcatgatggtgctttcagtggaaatggtcttg                                           <  5:60981‑M1/130‑102 (MQ=255)                                                                                                                aTTCGCGTGAACCTTCACATTCTT‑‑GGggccgctttgcggccccaattacaaacaccaaagccaatacaatcatcaggtcatctgaatgatggtctgcatgatggtgctttcagtggaaatggtcttggcattggcctggtagt                           >  6:129456‑M1/1‑26 (MQ=255)                                                                                                                         aaCCTTCACATTCTT‑‑GGggccgctttgcggccccaattacaaacaccaaagccaatacaatcatcaggtcatctgaatgatggtctgcatgatggtgctttcagtgg                                                      >  6:329695‑M1/1‑17 (MQ=255)                                                                                                                         aaCCTTCACATTCTT‑‑GGggccgctttgcggccccaattacaaacaccaaagccaatacaatcatcaggtcatctgaatgatggtctgcatgatggtgctttcagtgg                                                      <  5:329695‑M1/107‑91 (MQ=255)                                                                                                                            cTTCACATTCTT‑‑GGggccgctttgcggccccaattacaaacaccaaagccaatacaatcatcaggtcatctgaatgatggtctgcatgatggtgctttcagtggaaatggtcttggcattggcctggtagttgctctgcgccttgat           >  5:180342‑M1/1‑14 (MQ=255)                                                                                                                               cacaTTCTT‑‑GGggccgctttgcggccccaattacaaacaccaaagccaatacaatcatcaggtcatctgaatgatggtctgcatgatggtgctttcagtggaaattgtcttggcattggcctggtagttgctctgcgccttgatcaggt      >  8:123780‑M1/1‑11 (MQ=255)                                                                                                                               cacaTTCTT‑‑GGggccgctttgcggccccaattacaaacaccaaagccaatacaatcatcaggtcatctgaatgatggtctgcatgatggtgatttaagtggtaatggtcttggcattggcctggtagttgctatgcgccttgatcaggt      >  8:128113‑M1/1‑11 (MQ=255)                                                                                                                                    tCTT‑‑GGggccgctttgcggccccaattacaaacaccaaagccaatacaatcatcaggtcatctgaatgatggtctgcatgatggtgctttcagtggaaatggtcttggcattggcctggtagttgctctgcgccttgatcaggtttac  >  6:191373‑M1/1‑6 (MQ=255)                                                                                                                                           |                                                                                                                                               AGGTAGCGGCCGGTGACCAGGCTTTGCCATTGATAGAACGGGGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTT‑‑GG‑‑‑CGCTTT‑‑‑GCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTAGTTGCTCTGCGCCTTGATCAGGTT  >  NC_002947/4980449‑4980721

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ 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.