Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
JC	NC_002947	4,980,585	+GGC	100%	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	0 (0.000)	40 (0.720) +GGC	38/252	NT	100%	intergenic (‑24/+44)	PP_4387/flgE	hypothetical protein/flagellar hook protein FlgE
	?	NC_002947	4980586 =	0 (0.000)					intergenic (‑25/+43)	PP_4387/flgE	hypothetical protein/flagellar hook protein FlgE

GGCCGAACACAGGTAGCGGCCGGTGACCAGGCTTTGCCATTGATAGAACGGGGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_002947/4980439‑4980585 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑C‑GCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTAGTTGCTCTGCGCCTTGATCAGGTTTACCAG  >  NC_002947/4980586‑4980727                                                                                                                                                    |||                                                                                                                                                GGCCGAACACAGGTAGCGGCCGGTGACCAGGCTTTGCCATTGATAGAACGGGGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGG                                                                                                                                                  >  7:132852/1‑149 GGCCGAACACAGGTAGCGGCCGGTGACCAGGCTTTGCCATTGATAGAACGGGGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGG                                                                                                                                                  >  2:297214/1‑149  GCCGAACACAGGTAGCGGCCGGTGACCAGGCTTTGCCATTGATAGAACGGGGCGGGGGCAGCGGGGGCAGACAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGC                                                                                                                                                 >  8:216601/1‑149   CCGAACACAGGTAGCGGCCGGTGACCAGGCTTTGCCATTGATAGAACGGGGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCC                                                                                                                                                >  3:130355/1‑149        CACAGGTTCCCGCCGGTGACCAGGCTTTGCCATTGATCGACCGGGGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCC‑GCTTT                                                                                                                                          <  4:130355/149‑1                  GGCCGGTGCCCCGGCTTTGCCATTGATAGACCGGGGCGGGGGCCGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCC‑GCaaa                                                                                                                                          <  4:327166/139‑4                  GGCCGGTGACCAGGCTTTGCCATTGATAGAACGGGGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCC‑GCaaa                                                                                                                                          >  3:327166/1‑136                  GGCCGGTGACCAGGCTTTGCCATTGATAGAACGGGGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCC‑GCTTTGCGGCCCCAA                                                                                                                                >  7:240917/1‑149                   GCCGGTGACCAGGCTTTGCCATTGATAGAACGGGGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCC‑GCTTTGCGGCCCCAAT                                                                                                                               >  3:53906/1‑149                    CCGGTGACCAGGCTTTGCCATTGATAGAACGGGGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCC‑GCTTTGCGGCCCCAATT                                                                                                                              <  8:132852/149‑1                            CAGGCTTTGCCATTGATAGAACGGGGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCC‑GCTTTGCGGCCCCAATTACAAACAC                                                                                                                      >  7:241191/1‑149                                           aaccacCGGGGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCC‑GCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAA                                                                                                        <  3:344685/142‑1                                            taaAACGGGGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCC‑GCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATC                                                                                                      <  6:238726/146‑1                                               AACGGGGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCC‑GCTTTGCGGCCCCAATTA                                                                                                                             >  5:277429/1‑123                                               AACGGGGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCC‑GCTTTGCGGCCCCAATTA                                                                                                                             <  6:277429/123‑1                                                atGGGGCGGGGGCAGCTGGGGCAGGCAGAACCAGCACCAGCAAGGGTAACAAGTCCAGTAACGACAGCCGCTTCATTCGCGTTAACCTTCACATTATTGGGGCC‑GCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATC                                                                                                      <  3:288040/143‑1                                                           GCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCC‑GCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAA                                                                                       <  5:71645/149‑1                                                                        GCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCC‑GCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCAT                                                                          >  1:69903/1‑149                                                                         CAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCC‑GCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATG                                                                         <  8:119346/149‑1                                                                            AACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCC‑GCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATG                                                                      >  2:13980/1‑149                                                                              CCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCC‑GCTTTGCGGCCCCAATTACAAACACCAAACCCAATACAATCATCAGGTCATCTCAAAGATGGACTGCATGATGGT                                                                    >  2:22680/1‑149                                                                                AGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCC‑GCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGC                                                                  >  2:305835/1‑149                                                                                  CACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCC‑GCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTT                                                                >  3:88596/1‑149                                                                                   ACCAGCAAGGGGAACAAGGCCAGTAACTACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCC‑GCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTT                                                               <  8:240917/149‑1                                                                                     CAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCC‑GCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCA                                                             <  7:216601/149‑1                                                                                       GCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCC‑GCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCT                                                                                          >  1:34267/1‑118                                                                                       GCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCC‑GCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCT                                                                                          <  2:34267/118‑1                                                                                         AAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCC‑GCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGG                                                         <  4:88596/149‑1                                                                                                 CAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCC‑GCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTC                                                 <  6:242099/149‑1                                                                                                  AAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCC‑GCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCT                                                <  1:13980/149‑1                                                                                                          TAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCC‑GCTTTGCGGCCCCAATTAGAAACACCAAAGCCATTACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTG                                        <  1:22680/149‑1                                                                                                             CGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCC‑GCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCC                                     >  1:212325/1‑149                                                                                                              GACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCC‑GCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCc                                    <  2:69903/149‑2                                                                                                                 AGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCC‑GCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGT                                 >  4:130740/1‑149                                                                                                                  GCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCC‑GCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTA                                <  1:305835/149‑1                                                                                                                      CTTCATTCGCGTGAACCTTCACATTCTTGGGGCC‑GCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTAGTTG                            >  8:43506/1‑149                                                                                                                              GCGTGAACCTTCACATTCTTGGGGCC‑GCTTTGCGGCGCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGAATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTAGTTGCTCTGCGC                    >  6:44931/1‑149                                                                                                                               CGTGAACCTTCACATTCTTGGGGCCGGCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTAGTTGCTCTGCGC                    >  1:185680/1‑149                                                                                                                                GTGAACCTTCACATTCTTGGGGCC‑GCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTAGTTGCTCTGCGCCT                  <  2:212325/149‑1                                                                                                                                   AACCTTCACATTCTTGGGGCC‑GCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTAGTTGCTCTGCGCCTTGA               <  3:130740/149‑1                                                                                                                                          ACATTCTTGGGGCC‑GCTTTGCGGCCCCAATTACAAACACCAAAGCCACTACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTAGTTGCTCTGCGCCTTGATCAGGT         <  8:241191/148‑1                                                                                                                                          ACATTCTTGGGGCC‑GCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTAGTTGCTCTGCGCCTTGATCAGGTT        >  2:10125/1‑149                                                                                                                                            ATTCTTGGGGCC‑GCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTAGTTGCTCTGCGCCTTGATCAGGTTTA      <  2:185680/149‑1                                                                                                                                            ATTCTTGGGGCC‑GCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTAG                               >  7:301104/1‑124                                                                                                                                            ATTCTTGGGGCC‑GCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTAG                               <  8:301104/124‑1                                                                                                                                              TCTTGGGGCC‑GCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTAGTTGCTCTGCGCCTTGATCAGGTTTAC     >  2:259581/1‑148                                                                                                                                                TTGGGGCC‑GCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTAGTTGATCTGCGCCTTGATCAGGTTTACCAG  >  3:47235/1‑149                                                                                                                                                    |||                                                                                                                                                GGCCGAACACAGGTAGCGGCCGGTGACCAGGCTTTGCCATTGATAGAACGGGGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_002947/4980439‑4980585 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑C‑GCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTAGTTGCTCTGCGCCTTGATCAGGTTTACCAG  >  NC_002947/4980586‑4980727

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.