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)	40 (0.770) +GGC	35/278	0.7	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

GGGCCGAACACAGGTAGCGGCCGGTGACCAGGCTTTGCCATTGATAGAACGGGGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGCGCTTTGCGGCCCCAATTACAAACACC‑AAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTAGTTGCTCTGCGCCTTGATCAGGTTTACCAGCTCGCCG  >  NC_002947/4980438‑4980734                                                                                                                                                     |                                                                                                                                                      ccgaacacaggtagcggccggtgaccaggctttgccattgatagaacggggcgggggcagcgggggcaggcagaaccagcaccagcaaggggaacaaggccagtaacgacagccgcttcattcgcgtgaaccttcacattcttggggcc                                                                                                                                                       >  7:104549‑M2/149‑149 (MQ=255)       acaggtagcggccggtgaccaggctttgccattgatagaacggggcgggggcagcgggggcaggcagaaccagcaccagcaaggggaacaaggccagtaacgacagccgcttcattcgcgtgaaccttcacattcttggggcCGCTTTg                                                                                                                                                 >  7:130910‑M2/143‑149 (MQ=255)       aaaggtagcggccggtccccaggcattgccatttatagaactgggcgggggcagcgggggcaggcagaaccaccaccagcaaggggaacaaggccagtaacgacagccgcttcattcgcgtgaaccttcacattcttggggcCGCTTTg                                                                                                                                                 <  8:130910‑M2/7‑1 (MQ=255)         aggtagcggcgggttaccaggctttgccatttatagaacggggcgtgggaatcgtgggcaggcagaaccaggacgagcaaggggaacaaggccagtaacgacagccgcttcattcgcgtgaaccttcacattcttggggcCGCTTTGCg                                                                                                                                               <  8:97153‑M2/9‑1 (MQ=255)                ggccggtgaccaggctttgccattgatagaacggggcgggggcagcgggggcaggcagaaccagcaccagcaaggggaacaaggccagtaacgacagccgcttcattcgcgtgaaccttcacattcttggggcCGCTTTGCGGCCCCaa                                                                                                                                        >  2:262271‑M2/134‑149 (MQ=255)                ggccggtgaccaggctttgccattgatagaacggggcgggggcagcgggggcaggcagaaccagcaccagcaaggggaacaaggccagtaacgacagccgcttcattcgcgtgaaccttcacattcttggggcCGCAAAGCGGCCCCaa                                                                                                                                        <  8:217734‑M2/16‑1 (MQ=255)                        accaggctttgccattgatagaacggggcgggggcagcgggggcaggcagaaccagcaccagcaaggggaacaaggccagtaacgacagccgcttcattcgcgtgaaccttcacattcttggggcCGCTTTGCGGCCCCAATTACaaa                                                                                                                                 <  5:140082‑M2/23‑1 (MQ=255)                         ccaggctgtgccattgatagaccggggcgggggcagcgggggcaggcagaaccagcaccagcaaggggaacaaggccagtaacgacagccgcttcattcgcgtgaaccttcacattcttggggcCGCTTTGCGGCCCCAATTACAAaca                                                                                                                               <  2:284997‑M2/25‑1 (MQ=255)                                 tgccattgatagaacgggccgggggcagcgggggcaggcagaaccagcaccagcaaggggaacaaggccagtaacgacagccgcttcattcgcgtgaaccttcacattcttggggcCGCTTTGCGGCCCCAATTACAAACACC‑AAAGc                                                                                                                       <  8:254268‑M2/32‑1 (MQ=255)                                     attgatagaacggggcgggggcagcgggggcaggcagaaccagcaccagcaaggggaacaaggccagtaacgacagccgcttcattcgcgtgaaccttcacattcttggggcCGCTTTGCGGCCCCAATTACAAACACC‑AAAGCCAAt                                                                                                                   >  2:1524‑M2/113‑148 (MQ=255)                                                        ggcagcgggggcaggcagaaccagcaccagcaaggggaacaaggccagtaacgacagccgcttcattcgcgtgaaccttcacattcttggggcCGCTTTGCGGCCCCAATTACAAACACC‑AAAGCCAATACAATCATCAGGTCATCTg                                                                                                >  4:257294‑M2/94‑148 (MQ=255)                                                               ggggcaggcagaaccagcaccagcaagaggtacaaggccagtaacgacagccgcttcattcgcgtgaaccttcacattcttggggcCGCTTTGCGGCCCCAATTACAAACACC‑AAAGCCAATACAATCATCAGGTCATCTGAATGATgg                                                                                        >  4:218373‑M2/87‑149 (MQ=255)                                                                       cagaaccagcaccagcaaggggaacaaggccagtaacgacagccgcttcattcgcgtgaaccttcacattcttggggcCGCTTTGCGGCCCCAATTACAAACACC‑AAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGcaa                                                                                 >  2:249276‑M2/79‑147 (MQ=255)                                                                           accagcaccagcaaggggaacaaggccagtaacgacagccgcttcattcgcgtgaaccttcacattcttggggcCGCTTTGCGGCCCCAATTACAAACACC‑AAAGCCAATACAATCATCAGGTCATCTGAatgatg                                                                                         >  8:71270‑M2/75‑136 (MQ=255)                                                                           accagcaccagcaaggggaacaaggccagtaacgacagccgcttcattcgcgtgaaccttcacattcttggggcCGCTTTGCGGCCCCAATTACAAACACC‑AAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATgg                                                                            >  3:95364‑M2/75‑149 (MQ=255)                                                                            ccagcaccagcaaggggaacaaggccagtaacgacagccgcttcattcgcgtgaaccttcacattcttggggcCGCTTTGCGGCCCCAATTACAAACACC‑AAAGCCAATACAATCATCAGGTCATCTGAatgatg                                                                                         >  1:149504‑M2/74‑135 (MQ=255)                                                                            ccagcaccagcaaggggaacaaggccagtaacgacagccgcttcattcgcgtgaaccttcacattcttggggcCGCTTTGCGGCCCCAATTACAAACACC‑AAAGCCAATACAATCATCAGGTCATCTGAatgatg                                                                                         <  2:149504‑M2/62‑1 (MQ=255)                                                                            ccagcaccagcaaggggaacaaggccagtaacgacagccgcttcattcgcgtgaaccttcacattcttggggcCGCTTTGCGGCCCCAATTACAAACACC‑AAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTgcatgatgtt                                                                           >  8:266494‑M2/74‑147 (MQ=255)                                                                                 accagcaaggggaacaaggccagtaacgacagccgcttcattcgcgtgaaccttcacattcttggggcCGCGTTGCGGCCCCAATTACAAACACC‑AAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCttt                                                                      >  1:156896‑M2/69‑149 (MQ=255)                                                                                     gcaaggggaacaaggccagtaacgacagccgcttcattcgcgtgaaccttcacattcttggggcCGCTTTGCGGCCCCAATTACAAACACC‑AAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGt                                                                  >  2:250545‑M2/65‑149 (MQ=255)                                                                                      caaggggaacaaggccagtaacgacagccgcttcattcgcgtgaaccttcacattcttggggcCGCTTTGCGGCCCCAATTACAAACACC‑AAAGCCAATACAATCATCAGGTCATCTGAATGAAGGTCTGCATGATGGTGCTTTCAGTg                                                                 <  2:289530‑M2/86‑1 (MQ=255)                                                                                        agtgtaacaaggccagtaacgacagccgcttcattctcgtgaaccttcacattcttgggtgCGATTTGCGGCCCCAATTACAAACACCTTCAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTg                                                                 <  1:249276‑M2/87‑1 (MQ=255)                                                                                         ggggaacaaggccagtaacgacagccgcttcattcgcgtgaaccttcacattcttggggcCGCTTTGCGGCCCCAATTACAAACACC‑AAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGaa                                                              <  4:95364‑M2/89‑1 (MQ=255)                                                                                              acaaggccagtaacgacagccgcttcattcgcgtgaaccttcacattcttggggcCGCTTTGCGGCCCCAATTACAAACACC‑AAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGt                                                         <  1:262271‑M2/94‑1 (MQ=255)                                                                                               aaaggccagtaacgacagccgcttcattcgcgtgaaccttcacattcttggggcCGCTTTGCGGCCCCAATTACAAACACC‑AAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATTGTc                                                        <  8:9540‑M2/95‑1 (MQ=255)                                                                                                aaggccagtaacgacagccgcttcattcgcgtgaaccttcacattcttggggcCGCTTTGCGGCCCCAATTACAAACACC‑AAAGCCAATCCAATCATCAGGTCAGCTGTATGATGGTGTGCATGATGGTGGTTTGAGGGGAAATGGTCt                                                       >  8:110801‑M2/54‑149 (MQ=255)                                                                                                 aggccagtaacgacagccgcttcattcgcgtgaaccttcacattcttggggcCGCTTTGCGGCCCCAATTACAAACACC‑AAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCtt                                                      <  1:1524‑M2/97‑1 (MQ=255)                                                                                                  ggccagtaacgacagccgcttcattcgcgtgaaccttcacattcttggggcCGCTTTGCGGCCCCAATTACAAACACC‑AAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTg                                                     <  3:218373‑M2/98‑1 (MQ=255)                                                                                                     cagtaacgacagccgcttcattcgcgtgaaccttcacattcttggggcCGCTTTGCGGCCCCAATTACAAACACC‑AAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCa                                                  >  5:291607‑M2/49‑149 (MQ=255)                                                                                                        taacgacagccgcttcattcgcgtgaaccttcacattcttggggcCGCTTTGCGGCCCCAATTACAAACACC‑AAAGCCAATACAAACATCAGGTCATATTAATGATGGTCTGCATGATGGTGCTTTAAGTGGAAATGGTGTTGGCattt                                               >  6:27348‑M2/46‑148 (MQ=255)                                                                                                            gacagccgcttcattcgcgtgaaccttcacattcttggggcCGCTTTGCGGCCCCAATTACAAACACC‑AAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCt                                           <  3:257294‑M2/108‑1 (MQ=255)                                                                                                                                 aaccttcacattcttggggcCGCTTTGCGGCCCCAATTACAAACACC‑AAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTAGTTGCTCTGCGCCTTg                       <  5:27348‑M2/128‑1 (MQ=255)                                                                                                                                    cttcacattcttggggcCGCTTTGCGGCCCCAATTACAAACACC‑AAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTAGTTGCTCTGCGCCTTGAt                     >  1:130676‑M2/18‑147 (MQ=255)                                                                                                                                    cttcacattcttggggcCGCTTTGCGGCCCCAATTACAAACACC‑AAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTAAGTGGAAATGGTCTTGGCATTGGCCTGGTAGTTGCTCTGCGCCTTGAt                     >  5:50388‑M2/18‑147 (MQ=255)                                                                                                                                       cacattcttggggcCGCTTTGCGGCCCCAATTACAAACACC‑AAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTAGTTGCTCTGCGCCTTGATCAgg                 <  1:250545‑M2/134‑1 (MQ=255)                                                                                                                                          attcttggggcCGCTTTGCGGCCCCAATTACAAACACC‑AAAGCCTATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTAGTTGCTCTGCGCCTTGATCAGGTTTa             >  5:220730‑M2/12‑149 (MQ=255)                                                                                                                                           ttcttggggcCGCTTTGCGGCCCCAATTACAAACACC‑AAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTAGTTGCTCTGCGCCTTGATCAGGTTTAc            <  7:266494‑M2/139‑1 (MQ=255)                                                                                                                                              ttggggcCGCAAAGCGGCCCCAATTACAAACACC‑AAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTAGTTGCTCTGCGCCTTGATCAGGTTTACCAg         >  4:259052‑M2/8‑149 (MQ=255)                                                                                                                                              ttggggcCGCAAAGCGGCCCCAATTACAAACACC‑AAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTAGTTGCTCTGCGCCTTGATCAGGTTTACCAg         >  4:167753‑M2/8‑149 (MQ=255)                                                                                                                                                ggggcCGCTTTGCGGCCCCAATTACAAACACC‑AAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTAGTTGCTCTGCGCCTTGATCAGGTTTACCAGCt       >  8:69037‑M2/6‑149 (MQ=255)                                                                                                                                                   gcCGCTTTGCGGCCCCAATTACAAACACC‑AAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTAGTTGCTCTGCGCCTTGATCAGGTTTACCAGCTCGc    >  4:181480‑M2/3‑149 (MQ=255)                                                                                                                                                     cgcTTTGCGGCCCCAATTACAAACACC‑AAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTAGTTGCTCTGCGCCTTGATCAGGTTTACCAGCTCGCCg  <  3:181480/149‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                      GGGCCGAACACAGGTAGCGGCCGGTGACCAGGCTTTGCCATTGATAGAACGGGGCGGGGGCAGCGGGGGCAGGCAGAACCAGCACCAGCAAGGGGAACAAGGCCAGTAACGACAGCCGCTTCATTCGCGTGAACCTTCACATTCTTGGCGCTTTGCGGCCCCAATTACAAACACC‑AAAGCCAATACAATCATCAGGTCATCTGAATGATGGTCTGCATGATGGTGCTTTCAGTGGAAATGGTCTTGGCATTGGCCTGGTAGTTGCTCTGCGCCTTGATCAGGTTTACCAGCTCGCCG  >  NC_002947/4980438‑4980734

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.