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	0 (0.000)	47 (0.700) +GGC	36/280	1.3	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

AGGTAGCGGCCGGTGACCAGGCTTTGCCATTGATAGAACGG‑GGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_002947/4980449‑4980585 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CGCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTAGTTGCTCTGCGCCTTGATCAGGTTTACCAGCTCG  >  NC_002947/4980586‑4980731                                                                                                                                           |||                                                                                                                                                   AGGTAGCGGCCGGTGACCAGGCTTTGCCATTGATAGAACGG‑GGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCCGCTTTGCG                                                                                                                                           >  2:94051/1‑149    TAGCGGCCGGTGACCAGGCTTTGCCATTGATAGAACGG‑GGCGGGGGCAGCGGGGGCAGGCAGAACCAGCGCCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCCGCTTTGCGGCC                                                                                                                                        >  2:168265/1‑149      ggGGCCGGTTACCAGGCTTTGCCATTTATTGATCGG‑GGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCCGCAAAGCGGCCC                                                                                                                                       <  3:86918/146‑1        GGCCGGTGACCAGGCTTTGCCATTGATAGAACGGAGGCGGGGCCAGCGGGGGCAGGCAGACCCAGCCCCAGCAGGGGGAACAAGGCCAGTAAGGCCAGCCGATTCATTCCCGTGAACCTTCACATTATTGGGGCCGGTTTGCGGCCCC                                                                                                                                      >  1:52402/1‑148        GGCCGGTGACCAGGCTTTGCCATTGATAGAACGG‑GGCGGGGGCAGCCGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGATCCTTCACATTCTTGGGGCCGCTTGGCGGCCCCAA                                                                                                                                    >  3:65067/1‑149         GCCGGTGACCAGGCTTTGCCATTGATAGAACGG‑GGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCCGCAAAGCGGCCCCAA                                                                                                                                    <  6:154612/148‑1             gttACCTGGATTTGCAATTGATAGAACGG‑GGCGGGGGCAGCGTGGGCAGGCAGAACAAGCACAAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCCGCTATGCGGCCCCACTTACA                                                                                                                               <  7:355869/146‑1                ACCAGGCTTTGCCATTGATAGAACGG‑GGCGGGGGCAGCGGGGGCAGGCAGAACCAGCCCCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCCGCTTTGCGGCCCCAATTACAAAC                                                                                                                            <  1:168265/149‑1                  CAGGCTTTGCCATTGATAGAACGG‑GGCGGGGGCAGCGGGGGCAGGCAGACCCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGACGCTTTGCGGGCCCAATTACAAACAC                                                                                                                          >  3:303453/1‑149                  CAGGCTTTGCCATTGATAGAACGG‑GGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCCGCTTTGCGGCCCCAATTACAAACAC                                                                                                                          >  3:338620/1‑149                    GGCTTTGCCATTGATAGAACGG‑GGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCCGCTTTGCGGCCCCAATTACAAACACCA                                                                                                                        <  1:94051/149‑1                    GGCTTTGCCATTGATAGAACGG‑GGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCCGCTTTGCGGCCCCAATTACAAACACC                                                                                                                         >  3:38900/1‑148                            CATTGATAGAACGG‑GGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCCGCTTTGCGGCCCCAATTACAAACACCAAAGCCAAT                                                                                                                <  4:38900/149‑1                                 ATAGAACGG‑GGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCCGCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAA                                                                                                            >  7:140780/1‑148                                  agctcCGG‑GGCGGGGCCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCCGCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATC                                                                                                          <  3:336753/144‑1                                   AGAACGG‑GGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCCGCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAAT                                                                                                           >  6:334898/1‑147                                       CGG‑GGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGCCAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCCGCAAAGCGGCCCCAAgaat                                                                                                                                >  7:176987/1‑118                                       CGG‑GGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCCGCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATC                                                                                                          >  4:336753/1‑144                                       CGG‑GGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCCGCAAAGCGGCCCCAAgaat                                                                                                                                <  8:176987/122‑5                                              GGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCCGCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATC                                                                                               <  7:323757/149‑1                                                GGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCCGCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCT                                                                                              >  4:157480/1‑148                                                GGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCCGCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATC                                                                                               >  6:153587/1‑147                                                  GCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCCGCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAA                                                                                           <  4:338620/149‑1                                                   CAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCCGCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAA                                                                                           <  6:160516/148‑1                                                            CAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCCGCTTTGCGGCCCCAATTTCAAACACCAAAGCCAATACCATCATCAGGGCATCTGAATGATGGTCTG                                                                                 >  4:93134/1‑149                                                             AGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCCGCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAG                                                                                                     >  4:284071/1‑128                                                             AGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCCGCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAG                                                                                                     <  3:284071/128‑1                                                              gcCAGAACCAGCACCAGAAAGGTGAACAAGGCCAGTAAAGACAGCCGCTTCATTCGCTTGAACCTTCACATTCTTGGGGCCGCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATTATGGTCTGCA                                                                               <  4:303453/147‑1                                                              cgctGAACCAGCACCAGCAAGGGGAACATGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCCTCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCTTCAGGTCATCTGAATGATGGTCTGga                                                                               <  4:65067/145‑3                                                                    ACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCCGCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATG                                                                          <  8:241577/148‑1                                                                                AAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCCGCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGG                                                             <  1:198515/149‑1                                                                                AAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCCGCATTGCGGCCCCAATTACAAACACCAAAGCCAAAACAATCATAAGGTCATCTGAATTAAGGTCTGGATGAAGGTGCTTTAAGT                                                               >  5:261490/1‑147                                                                                   GGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCCGCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAA                                                          >  8:234290/1‑149                                                                                         AAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCTCATTCTTGGGGCCGCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTC                                                     <  5:334898/148‑1                                                                                          AGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCCGCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTT                                                   <  8:140780/149‑1                                                                                          AGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCCGCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTT                                                   <  2:52402/149‑1                                                                                              aAGTAACTACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTCGGGCCGCATTTCGGCCCCAAATACAAACACAAAACCCAATACAAACATCAGCTCATCTGAATGATGGTCTTAAAGATTGTGCTTTCAGTGGAAATGGTCTTGGga                                               >  2:7370/2‑147                                                                                              CAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCCGCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGC                                                >  5:244621/1‑148                                                                                              CAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCCGCTTTGCGGCCCCAATTAAAAACACCAAAGCCAATACAATCATCAGGTCATCTTAATGATGGTCTGCATGATGGTGCTTTAAGTGGAAATGGTCTTTGCA                                               >  3:66643/1‑149                                                                                                          CCGCTTCATTCGCGTGAACCTTCACATTCTTGGGGCCGCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTAG                                   >  8:38164/1‑149                                                                                                            GCTTCATTCGCGTGAACCTTCACATTCTTGGGGCCGCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTAGTT                                 <  3:157480/149‑1                                                                                                             CTTCATTCGCGTGAACCTTCACATTCTTGGGGCCGCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTAGTT                                 <  5:153587/148‑1                                                                                                                       GTGAACCTTCACATTCTTGGGGCCGCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTAGTTGCTCTGCGCCT                      >  1:286325/1‑149                                                                                                                          AACCTTCACATTCTTGGGGCCGCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTAGTTGCTCTGCGCCTTGA                   <  7:38164/149‑1                                                                                                                             CTTCACATTCTTGGGGCCGCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTGTTGGCATTGGCCTGGTAGTTGCGGTGCGCCTTGAT                  >  8:291499/1‑147                                                                                                                                CACATTCTTGGGGCCGCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTAGTTGCTCTGCGCCTTGATCAGG              <  7:234290/148‑1                                                                                                                                          GGGCCGCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTAGTTGCTCTGCGCCTTGATCAGGTTTACCAGCTC   >  1:242974/1‑149                                                                                                                                           GGCCGCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTAGTTGCTCTGCGCCTTGATCAGGTTTACCAGCTCG  >  7:238565/1‑149                                                                                                                                           |||                                                                                                                                                   AGGTAGCGGCCGGTGACCAGGCTTTGCCATTGATAGAACGG‑GGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_002947/4980449‑4980585 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CGCTTTGCGGCCCCAATTACAAACACCAAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTAGTTGCTCTGCGCCTTGATCAGGTTTACCAGCTCG  >  NC_002947/4980586‑4980731

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.