Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,666,747	A→T	8.9%	intergenic (+21/‑45)	acnA‑II → / → prpF	aconitate hydratase/aconitate isomerase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,666,747	0	A	T	8.9%	156.6 / 5.6	56	intergenic (+21/‑45)	acnA‑II/prpF	aconitate hydratase/aconitate isomerase
Reads supporting (aligned to +/- strand):  ref base A (20/31);  new base T (3/2);  total (23/33)
Fisher's exact test for biased strand distribution p-value = 3.92e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.42e-01

CAATGGCGAGTGCCTGGAAGTACCGGTGACCTGCCGTCTGGACACCGCCGAGGAAGTGTCGATCTACGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAGGGTATTTCACCGGACTATCAGGATGCCCAAGAAAATGTCACATGTACCCCAGATCAAAATCCCCGCCACCTACATCCGCGGCGGCACCAGCAAAGGCGTGTTCTTCCGCCTGCAAGACCTGCCCGAGCAGGCGC  >  NC_002947/2666603‑2666891                                                                                                                                                 |                                                                                                                                                  cAATGGCGAGTGCCTGGAAGTACCGGTGACCTGCCGTCTGGACACCGCCGAGGAAGTGTCGATCTACGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCgg                                                                                                                                               <  4:328955/149‑1 (MQ=255)      gCGAGTGCCTGGAAGTACCGGTGACCTGCCGTCTGGACACCGCCGAGGAAGTGTCGATCTACGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCa                                                                                                                                         >  4:192709/1‑149 (MQ=255)       cGAGTGCCTGGAAGTACCGGTGACCTGCCGTCTGGACACCGCCGAGGAAGTGTCGATCTACGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAg                                                                                                                                        <  8:254893/149‑1 (MQ=255)        gAGTGCCTGGAAGTACCGGTGACCTGCCGTCTGGACACCGCCGAGGAAGTGTCGATCTACGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAgg                                                                                                                                       >  2:290699/1‑149 (MQ=255)        gAGTGCCTGGAAGTACCGGTGACCTGCCGCCTGGACACCGCCGAGGAAGTGTCGATCTACGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAgg                                                                                                                                       <  5:371286/149‑1 (MQ=255)              cTGGAAGTACCGGTGACCTGCCGTCTGGACACCGCCGAGGAAGTGTCGATCTACGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGc                                                                                                                                                 >  4:148434/1‑134 (MQ=255)              cTGGAAGTACCGGTGACCTGCCGTCTGGACACCGCCGAGGAAGTGTCGATCTACGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGc                                                                                                                                                 <  3:148434/134‑1 (MQ=255)              cTGGAAGTACCGGTGACCTGCCGTCTGGACACCGCCGAGGAAGTGTCGATCTACGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCCCAAACCGGC‑CCCAcgggaat                                                                                                                                  >  8:310805/1‑144 (MQ=255)              cTGGAAGTACCGGTGACCTGCCGTCTGGACACCGCCGAGGAAGTGTCGATCTACGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGACTGAGCATGAATCGGGGGCCGCAAAACGGC‑CCCCggggttt                                                                                                                                  >  8:351662/1‑144 (MQ=255)                   aGTACCGGTGACCTGCCGTCTGGACACCGCCGAGGAAGTGTCGATCTACGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGTCCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAGGGTATTTCACCg                                                                                                                            <  8:218637/149‑1 (MQ=255)                    tcggcGGTGTCCAGACGGCAGGTCACCGCCGAGGAAGTGTCGATCTACGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAGGGTATTTGACCgg                                                                                                                           >  2:14645/5‑149 (MQ=255)                    gTACCGGTGACCTGCCGTCTGGACACCGCCGAGGAAGTGTCGATCTACGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAGGGTATTTCACCg                                                                                                                            <  1:205717/148‑1 (MQ=255)                    gTACCGGTGACCTGCCGTCTGGACACCGCCGAGGAAGTGTCGATCTACGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAGGGTATTTCACCg                                                                                                                            <  1:199416/148‑1 (MQ=255)                        cGGTGACCTGCCGTCTGGACACCGCCGAGGAAGTGTCGATCTACGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAGGGTATTTCACCGGAcga                                                                                                                       >  7:182936/1‑147 (MQ=255)                         ggTGACCTGCCGTCTGGACACCGCCGAGGAAGTGTCGATCTACGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAGGGTATTTCACCGGACTAt                                                                                                                      <  7:310805/149‑1 (MQ=255)                              ccTGCCGTCTGGACACCGCCGAGGAAGTGTCGATCTACGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAGGGTATTTCACCGGACTATCAGGa                                                                                                                 <  5:107017/149‑1 (MQ=255)                                tGCCGTCTGGACACCGCCGAGGAAGTGTCGATCTACGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAGGGTATTTCa                                                                                                                               <  6:388926/133‑1 (MQ=255)                                tGCCGTCTGGACACCGCCGAGGAAGTGTCGATCTACGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAGGGTATTTCa                                                                                                                               >  5:388926/1‑133 (MQ=255)                                     tCTGGACACCGCCGAGGAAGTGTCGATCTACGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAGGGTATTTCACCGGACTATc                                                                                                                     <  7:276215/138‑1 (MQ=255)                                     tCTGGACACCGCCGAGGAAGTGTCGATCTACGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAGGGTATTTCACCGGACTATc                                                                                                                     >  8:276215/1‑138 (MQ=255)                                     tCTGGACACCGCCGAGGAAGTGTCGATCTACGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAGGGTATTTCACCGGACTATCAGGATGCCCaa                                                                                                          <  3:192709/149‑1 (MQ=255)                                         gACACCGCCGAGGAAGTGTCGATCTACGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAgg                                                                                                                                       <  1:288119/116‑1 (MQ=255)                                         gACACCGCCGAGGAAGTGGCGATCTACGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAACCGGC‑CCCAgg                                                                                                                                       >  2:288119/1‑116 (MQ=255)                                          acacCGCCGAGGAAGTGTCTATCTACGAAGCGGGCGGGGTGCTGCAGCTCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAGGGTATTTCACCGGACTATCACGATGCCCAAGaaaa                                                                                                     <  7:351662/149‑1 (MQ=255)                                           cacCGCCGAGGAAGTGTCGATCTACGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGCCCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAGGGTATTTCACCGGCCTATCAGGCTGCCCAAGAatat                                                                                                    >  8:306816/1‑149 (MQ=255)                                           cacCGCCGAGGAAGTGTCGATCTACGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAGGGTATTTCACCGGACTATCAGGATGCCCAAGAAAAt                                                                                                    <  8:182936/149‑1 (MQ=255)                                           cacCGCCGAGAAAGTGTCTATCTACGAAGCTGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAGGGTATTTCACCGGACTATCAGGATGCCCAAGAAAAt                                                                                                    <  3:186829/149‑1 (MQ=255)                                           cacCGCCGAGAAAGTGTCGATCTACGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAGGGTATTTCACCGGACTATCAGGATGCCCAAGAAAAt                                                                                                    <  3:180608/149‑1 (MQ=255)                                               gccgAGGAAGTGTCGATCTACGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAGGGTATTTCACCGGACTATCAGGATGCCCAAGAAAATGTca                                                                                                <  3:334523/149‑1 (MQ=255)                                               gccgAGGAAGTGTCGATCTACGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAGGGTATTTCACCGGACTATCAGGATGCCCAAGAAAATGTca                                                                                                <  6:153760/149‑1 (MQ=255)                                               gccgAGGAAGTGTCGATCTACGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAGGGTATTTCACCGGACTATCAGGATGCCCAAGAAAATGTca                                                                                                <  8:54578/149‑1 (MQ=255)                                                ccgAGGAAGTGTCGATCTACGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAGGGTATTTCACCGGACTATCAGGATGCCCAAGAAAATGTc                                                                                                 <  8:205772/147‑1 (MQ=255)                                                ccgAGGAAGTGTCGATCTACGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAGGGTATTTCACCGGACTATCAGGATGCCCAAGAAAATGTc                                                                                                 >  7:205772/1‑147 (MQ=255)                                                        gtgtCGATCTACGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAGGGTATTTCACCGGACTATCAGGATGCCCAAGAAAATGTCACATGTAccc                                                                                       <  2:342058/149‑1 (MQ=255)                                                          gtCGATCTACGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAGGGTATTTCACCGGACTATCAGGATGCCCAAGAAAATGTCACATGTAccc                                                                                       >  7:90205/1‑147 (MQ=255)                                                            cGATCTACGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAGGGTATTTCACCGGACTATCAGGATGCCCAAGAAAATGTCACATGTACCCCAGa                                                                                   <  8:90205/149‑1 (MQ=255)                                                             gATCTACGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAGGGTATTTCACCGGACTATCAGGATGCCCAAGAAAATGTCACATGTACCCCAGa                                                                                   <  5:196076/148‑1 (MQ=255)                                                                  aCGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGGCCCCAAACGGCGCCCCGGGGA‑TTGACCGGACTAAGAGGATTACCAAGAAAAAGTAAAAAGTAACCCCGaaaaaa                                                                              >  4:408174/1‑143 (MQ=255)                                                                   cGAAGGGGGCGGGGGGCTGCAGCGCTTTGCCCACGACTTCCTCGCAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAGGGTATTTCACCGGACTATCAGGATGCCCAAGAAAATGTCACATGTAccc                                                                                       <  8:392349/138‑1 (MQ=255)                                                                   cGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCCAAGCGGC‑CGCAGGGGATTTCACCGGCCTAACAGGATGCCCAAGAAAATGTCACAAGTAccc                                                                                       >  7:392349/1‑138 (MQ=255)                                                                           gcgggGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAGGGTATTTCACCGGACTATCAGGATGCCCAAGAAAATGTCACATGTACCCCAGATCAAAATCCCCGCCa                                                                    <  2:374181/149‑1 (MQ=255)                                                                                      cAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAGGGTATTTCACCGGACTATCAGGATGCCCAAGAAAATGTca                                                                                                >  7:222026/1‑110 (MQ=255)                                                                                      cAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAGGGTATTTCACCGGACTATCAGGATGCCCAAGAAAATGTca                                                                                                <  8:222026/110‑1 (MQ=255)                                                                                                               aaGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAGGGTATTTCACCGGACTATCAGGATGCCCAAGAAAATGTca                                                                                                <  6:216683/85‑1 (MQ=255)                                                                                                               aaGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAGGGTATTTCACCGGACTATCAGGATGCCCAAGAAAATGTca                                                                                                >  5:216683/1‑85 (MQ=255)                                                                                                                  cGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAGGGTATTTCACCGGACTATCAGGATGCCCAAGAAAATGTCACATGTACCCCAGATCAAAATCTCCGCCACCTACATCCGCGGCGGCACCAGCAAAGGCGTGTTCTTcc                             <  1:290699/149‑1 (MQ=255)                                                                                                                    aCCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAGGGTATTTCACCGGACTATCAGGATGCCCAAGAAAATGTCACATGTACCCCAGATAAAAATCCCCGCCCCCTACATACCCGGCGGCACCAGCAAAGGCGTGTTATTcccc                           >  7:179866/1‑147 (MQ=255)                                                                                                                     ccGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAGGGTATTTCACCGGACTATc                                                                                                                     <  7:134847/58‑1 (MQ=255)                                                                                                                                   ccctggggCCGCTTTGCGGC‑CCCCGGGTATTCCACCGGACTATCAGGATGCCCAAGAAAATGTCACATGTACCCCAGATCAAAATCCCCGCCACCTACATCCGCGGCGGCACCAGCAAAGGCGTGTTCTTCCGCCTGCAAGACCTGccc            >  3:158594/5‑149 (MQ=255)                                                                                                                                     ctggggCCGCTTTGCGGC‑CCCAGGGTATTTCACCGGACTATCAGGATGCCCAAGAAAATGTCACATGTACCCCAGATCAAAATCCCCGCCACCTACATCCGCGGCGGCACCAGCAAAGGCGTGTTCTTCCGc                           <  1:143330/130‑1 (MQ=255)                                                                                                                                     ctggggCCGCTTTGCGGC‑CCCAGGGTATTTCACCGGACTATCAGGATGCCCAAGAAAATGTCACATGTACCCCAGATCAAAATCCCCGCCACCTACATCCGCGGCGGCACCAGCAAAGGCGTGTTCTTCCGc                           >  2:143330/3‑132 (MQ=255)                                                                                                                                      tggggCCGCTTTGCGGC‑CCCAGGGTATTTCACCGGACTATCAGGATGCCCAAGAAAATGTCACATGTACCCCAGATCAAAATCCCCGCCACCTACATCCGCGGCGGCACCAGCAAAGGCGTGTTCTTCCGCCTGCAAGACCTGccc            >  6:97457/2‑146 (MQ=255)                                                                                                                                        gggCCGCTTTGCGGC‑CCCAGGGTATTTCACCGGACTATCAGGATGCCCAAGAAAATGTCACATGTACCCCAGATCAAAATCCCCGCCACCTACATCCGCGGCGGCACCAGCAAAGGCGTGTTCTTCCGCCTGCAAGACCTGCCCGa          <  5:97457/146‑1 (MQ=255)                                                                                                                                            cGCAAAGCGGC‑CCCAGGGTATTTCACCGGACTATCAGGATGCCCAAGAAAATGTCACATGTACCCCAGATCAAAATCCCCGCCACCTACATCCGCGGCGGCACCAGCAAAGGCGTGTTCTTCCGCCTGCAAGACCTGCCCGAGCAGgcg   >  6:267829/1‑149 (MQ=255)                                                                                                                                             gCAAAGCGGC‑CCCAGGGTATTTCACCGGACTATCAGGATGCCCAAGAAAATGTCACATGTACCCCAGATCAAAATCCCCGCCACCTACATCCGCGGCGGCACCAGCAAAGGCGTGTTCTTCCGCCTGCAAGACCTGCCCGAGCAGgcgc  <  1:14645/149‑1 (MQ=255)                                                                                                                                              cAAAGCGGC‑CCCAGGGTATTTCACCGGACTATCAGGATGCCCAAGAAAATGTCACATGTACCCCAGATCAAAATCCCCGCCACCTACATCCGCGGCGGCACCAGCAAAGGCGTGTTCTTCCGCCTGCAAGACCTGCCCGAGCAGgcgc  >  2:100805/1‑148 (MQ=255)                                                                                                                                                 |                                                                                                                                                  CAATGGCGAGTGCCTGGAAGTACCGGTGACCTGCCGTCTGGACACCGCCGAGGAAGTGTCGATCTACGAAGCGGGCGGGGTGCTGCAGCGCTTTGCCCAGGACTTCCTCGAAGCGACCGCCTGAGCATGAATCGGGGGCCGCAAAGCGGC‑CCCAGGGTATTTCACCGGACTATCAGGATGCCCAAGAAAATGTCACATGTACCCCAGATCAAAATCCCCGCCACCTACATCCGCGGCGGCACCAGCAAAGGCGTGTTCTTCCGCCTGCAAGACCTGCCCGAGCAGGCGC  >  NC_002947/2666603‑2666891

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑