Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,758,227	A→T	9.4%	intergenic (+195/+323)	PP_5050 → / ← PP_5051	transposase/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,758,227	0	A	T	9.4%	159.8 / 5.4	53	intergenic (+195/+323)	PP_5050/PP_5051	transposase/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (24/24);  new base T (2/3);  total (26/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGGGGAGAAATTCTCTGGCACGCTGACTCGTACCTCGAGGTTGCTGAGAGAGGCCGATGGCGTTTTTACTGAAAATTTGCCTCCGGCCATAGAATCTCCTACCCCAATCCTGTGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCGGCCCCAGCCATTTCAGTCGTCTGAATGCACCGTTCCTGTGCCCGCTGCACCTCTGGAAGGCACAAATCCCCTCAAAATCCGGCCAAATCACCCGCAAAGCCCAGTATTCACGGCTTTTGCAAAACTGGCACGCCCCCTGCAATAAG  >  NC_002947/5758083‑5758376                                                                                                                                                  |                                                                                                                                                      tGGGGAGAAATTCTCTGGCACGCTGACTCGTACCTCGAGGTTGCTGAGAGAGGCCGATGGCGTTTTTACTGAAAATTTGCCTCCGGCCATAGAATCTCCTACCCCAATCCTGTGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCGGc                                                                                                                                                  <  1:1122563/150‑1 (MQ=255) tGGGGAGAAATTCTCTGGCACGCTGACTCGTACCTCGAGGTTGCTGAGAGAGGCCGATGGCGTTTTTACTGAAAATTTGCCTCCGGCCATAGAATCTCCTACCCCAATCCTGTGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCGGc                                                                                                                                                  <  1:13167/150‑1 (MQ=255)      agaAATTCTCTGGCACGCTGACTCGTACCTCGAGGTTGCTGAGAGAGGCCGATGGCGTTTTTACTGAAAATTTGCCTCCGGCCATAGAATCTCCTACCCCAATCCTGTGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCGGCCCCAg                                                                                                                                             >  2:222651/1‑150 (MQ=255)       ggcgtgccagttttgcaaaagccgtgaatactgggctttgcgggtgatttggccggattttgaggggatttgtgccttccagaggtgcagcgggcacaggaacggtgcattcagacgactgaaatggcTGGGGC‑GCAAAGCGGCCCCAGc                                                                                                                                            >  2:61733‑M1/129‑150 (MQ=255)              tctGGCACGCTGACTCGTACCTCGAGGTTGCTGAGAGAGGCCGATGGCGTTTTTACTGAAAATTTGCCTCCGGCCATAGAATCTCCTACCCCAATCCTGTGGGAGCGGCCTTGTGTCGAGATGGGGC‑GCAAAGCGGCCCCAGCCATTTCa                                                                                                                                     <  2:742052/150‑1 (MQ=255)                gttttgcaaaagccgtgaatactgggctttgcgggtgatttggccggattttgaggggatttgtgccttccagaggtgcagcgggcacaggaacggtgcattcagacgactgaaatggcTGGGGC‑GCAAAGCGGCCCCa                                                                                                                                              >  1:607943‑M1/120‑139 (MQ=255)                gttttgcaaaagccgtgaatactgggctttgcgggtgatttggccggattttgaggggatttgtgccttccagaggtgcagcgggcacaggaacggtgcattcagacgactgaaatggcTGGGGC‑GCAAAGCGGCCCCa                                                                                                                                              <  2:607943‑M1/20‑1 (MQ=255)                   cACGCTGACTCGTACCTCGAGGTTGCTGAGAGAGGCCGATGGCGTTTTTACTGAAAATTTGCCTCCGGCCATAGAATCTCCTACCCCAATCCTGTGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCGGCCCCAGCCATTTCAgtcgt                                                                                                                                <  2:1052585/150‑1 (MQ=255)                    aCGCTGACTCGTACCTCGAGGTTGCTGAGAGAGGCCGATGGCGTTTTTACTGAAAATTTGCCTCCGGCCATAGAATCTCCTACCCCAATCCTGTGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCGGCCCCAGCCATTTCAgtcgtc                                                                                                                               <  1:222651/150‑1 (MQ=255)                    aCGCTGACTCGTACCTCGAGGTTGCTGAGAGAGGCCGATGGCGTTTTTACTGAAAATTTGCCTCCGGCCATAGAATCTCCTACCCCAATCCTGTGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCGGCCCCAGCCATTTCAgtcgtc                                                                                                                               <  2:1081934/150‑1 (MQ=255)                     cGCTGACTCGTACCTCGAGGTTGCTGAGAGAGGCCGATGGCGTTTTTACTGAAAATTTGCCTCCGGCCATAGAATCTCCTACCCCAATCCTGTGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCGGCCCCAGCCATTTCAGTCGTCt                                                                                                                              >  2:308056/1‑150 (MQ=255)                         gACTCGTACCTCGAGGTTGCTGAGAGAGGCCGATGGCGTTTTTACTGAAAATTTGCCTCCGGCCATAGAATCTCCTACCCCAATCCTGTGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCGGCCCCAGCCATTTCAGTCGTCTGAAt                                                                                                                          <  1:769805/150‑1 (MQ=255)                            tCGTACCTCGAGGTTGCTGAGAGAGGCCGATGGCGTTTTTACTGAAAATTTGCCTCCGGCCATAGAATCTCCTACCCCAATCCTGTGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCgg                                                                                                                                                   >  1:71674/1‑122 (MQ=255)                            tCGTACCTCGAGGTTGCTGAGAGAGGCCGATGGCGTTTTTACTGAAAATTTGCCTCCGGCCATAGAATCTCCTACCCCAATCCTGTGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCgg                                                                                                                                                   <  2:71674/122‑1 (MQ=255)                            tCGTACCTCGAGGTTGCTGAGAGAGGCCGATGGCGTTTTTACTGAAAATTTGCCTCCGGCCATAGAATCTCCTACCCCAATCCTGTGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCGGCCCCAGCCATTTCAGTCGTCt                                                                                                                              <  1:236024/143‑1 (MQ=255)                            tCGTACCTCGAGGTTGCTGAGAGAGGCCGATGGCGTTTTTACTGAAAATTTGCCTCCGGCCATAGAATCTCCTACCCCAATCCTGTGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCGGCCCCAGCCATTTCAGTCGTCt                                                                                                                              >  2:236024/1‑143 (MQ=255)                                  cTCGAGGTTGCTGAGAGAGGCCGATGGCGTTTTTACTGAAAATTTGCCTCCGGCCATAGAATCTCCTACCCCAATCCTGTGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCGGCCCCAGCCATTTCAGTCGTCTGAATGCACCGTTc                                                                                                                 >  2:878593/1‑150 (MQ=255)                                  cTCGAGGTTGCTGAGAGAGGCCGATGGCGTTTTTACTGAAAATTTGCCTCCGGCCATAGAATCTCCTACCCCAATCCTGTGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCGGCCCCAGCCATTTCAGTCGTCTGAATGCACCGTTc                                                                                                                 >  1:553245/1‑150 (MQ=255)                                  cTCGAGGTTGCTGAGAGAGGCCGATGGCGTTTTTACTGAAAATTTGCCTCCGGCCATAGAATCTCCTACCCCAATCCTGTGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCGGCCCCAGCCATTTCAGTCGTCTGAATGCACCGTTc                                                                                                                 >  2:688218/1‑150 (MQ=255)                                   tCGAGGTTGCTGAGAGAGGCCGATGGCGTTTTTACTGAAAATTTGCCTCCGGCCATAGAATCTCCTACCCCAATCCTGTGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCGGCCCCAGCCATTTCAgtcgtc                                                                                                                               <  2:361175/135‑1 (MQ=255)                                   tCGAGGTTGCTGAGAGAGGCCGATGGCGTTTTTACTGAAAATTTGCCTCCGGCCATAGAATCTCCTACCCCAATCCTGTGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCGGCCCCAGCCATTTCAgtcgtc                                                                                                                               >  1:361175/1‑135 (MQ=255)                                    cGAGGTTGCTGAGAGAGGCCGATGGCGTTTTTACTGACAATTTGCCTCCGGCCATAGAATCTCCTACCCCAATCCTGTGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCGGCCCCAGCCATTTCAGTCGTCTGAATGCACCGTTCCt                                                                                                               <  1:1157118/150‑1 (MQ=255)                                             tGAGAGAGGCCGATGGCGTTTTTACTGAAAATTTGCCTCCGGCCATAGAATCTCCTACCCCAATCCTGTGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCGGCCCCAGCCATTTCAgtcgt                                                                                                                                >  2:1078826/1‑124 (MQ=255)                                             tGAGAGAGGCCGATGGCGTTTTTACTGAAAATTTGCCTCCGGCCATAGAATCTCCTACCCCAATCCTGTGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCGGCCCCAGCCATTTCAgtcgt                                                                                                                                <  1:1078826/124‑1 (MQ=255)                                                   agGCCGATGGCGTTTTTACTGAAAATTTGCCTCCGGCCATAGAATCTCCTACCCCAATCCTGTGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCGGCCCCAGCCATTTCAGTCGTCTGAATGCACCGTTCCTGTGCCCGCTGCACct                                                                                                >  1:846348/1‑150 (MQ=255)                                                       cGATGGCGTTTTTACTGAAAATTTGCCTCCGGCCATAGAATCTCCTACCCCAATCCTGTGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCGGCCCCAGCCATTTCAGTCGTCTGAATGCACCGTTCCTGTGCCCGCTGCACCTCTgg                                                                                            >  1:668302/1‑150 (MQ=255)                                                         aTGGCGTTTTTACTGAAAATTTGCCTCCGGCCATAGAATCTCCTACCCCAATCCTGTGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCGGCCCCAGCCATTTCAGTCGTCTGAATGCACCGTTCCTGTGCCCGCTGCACCTCTGGaa                                                                                          <  2:553245/150‑1 (MQ=255)                                                                        aaaaTTTGCCTCCGGCCATAGAATCTCCTACCCCAATCCTGTGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCGGCCCCAGCCATTTCAGTCGTCTGAATGCACCGTTCCTGTGCCCGCTGCACCTCTGGAAGGCACAAATCCCCTc                                                                           >  1:656490/1‑150 (MQ=255)                                                                                 cTCCGGCCATAGAATCTCCTACCCCAATCCTGTGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCGGCCCCAGCCATTTCAGTCGTCTGAAt                                                                                                                          >  1:590912/1‑94 (MQ=255)                                                                                 cTCCGGCCATAGAATCTCCTACCCCAATCCTGTGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCGGCCCCAGCCATTTCAGTCGTCTGAAt                                                                                                                          <  2:590912/94‑1 (MQ=255)                                                                                  tCCGGCCATAGAATCTCCTACCCCAATCCTGTGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCGGCCCCAGCCATTTCAGTCGTCTGAATGCACCGTTCCTGTGCCCGCTGCACCTCTGGAAGGCACAAATCCCCTCAAAATCCGGc                                                                 >  2:369679/1‑150 (MQ=255)                                                                                  tCCGGCCATAGAATCTCCTACCCCAATCCTGTGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCGGCCCCAGCCATTTCAGTCGTCTGAATGCACCGTTCCTGTGCCCGCTGCACCTCTGGAAGGCACAAATCCCCTCAAAATCCGGc                                                                 <  2:268662/150‑1 (MQ=255)                                                                                       ccATAGAATCTCCTACCCCAATCCTGTGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCGGCCCCAGCCATTTCAGTCGTCTGAATGCACCGTTCCTGTGCCCGCTGCACCTCTGGAAGGCACAAATCCCCTCAAAATCCGGCCAAAt                                                            <  2:656490/150‑1 (MQ=255)                                                                                          tAGAATCTCCTACCCCAATCCTGTGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCGGCCCCAGCCATTTCAGTCGTCTGAATGCACCGTTCCTGTGCCCGCTGCACCTCTGGAAGGCACAAATCCCCTCAAAATCCGGCCAAATCAc                                                         >  1:234951/1‑150 (MQ=255)                                                                                                     ccccgAATCCTGTGGGAGCGGCCTTCTGTCGCGATGGGGC‑GCAAATCGGCCCCAGCCATTTCAGTCGTCTGAATGCACCGTTCCTGTGCCCGCTGCACCTCTGGGAGGCACAAATCCCCTCAAAATCCGGCCAAATCACCCGCAAAGccc                                              <  2:574824/149‑1 (MQ=255)                                                                                                       cccAATCCTGTGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCGGCCGCAGCCATTTCAGTCGTCTGAATGCACCGTTCCTGTGCCCGCTGCACCTCTGGAAGGCACAAATCCCCTCAAAATCCg                                                                   >  1:1124302/1‑127 (MQ=255)                                                                                                       cccAATCCTGTGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCGGCCCCAGCCATTTCAGTCGTCTGAATGCACCGTTCCTGTGCCCGCTGCACctct                                                                                              >  1:716782/1‑100 (MQ=255)                                                                                                       cccAATCCTGTGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCGGCCCCAGCCATTTCAGTCGTCTGAATGCACCGTTCCTGTGCCCGCTGCACctct                                                                                              <  2:716782/100‑1 (MQ=255)                                                                                                       cccAATCCTGTGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCGGCCCCAGCCATTTCAGTCGTCTGAATGCACCGTTCCTGTGCCCGCTGCACCTCTGGAAGGCACAAATCCCCTCAAAATCCg                                                                   <  2:1124302/127‑1 (MQ=255)                                                                                                        ccAATCCTGGGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGGGGGCGCACATACTTTAGACGACTGAATGCACCGTTCCTGTGCCCGCTGCACCTCTGGAAGGCACAAATCCTCTCAACATCCGGCCAAATCACCCGCAAAGCCCAGt                                           >  2:644764/1‑150 (MQ=255)                                                                                                         cAATCCTGTGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCGGCCCCAGCCATTTCAGTCGTCTGAATGCACCGTTCCTGTGCCCGCTGCACCTCTGGAAGGCACAAATCCCCTCAAAATCCGGCCAAATCACCCGCAAAGCCCAGTa                                          >  1:927334/1‑150 (MQ=255)                                                                                                             ccTGTGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCGGCCCCAGCCATTTCAGTCGTCTGAATGCACCGTTCCTGTGCCCGCTGCACCTCTGGAAGGCACAAATCCCCTCAAAATCCGGCCAAATCACCCGCAAAGCCCAGTATTCa                                      <  1:878593/150‑1 (MQ=255)                                                                                                                   attcagacgactgaaatggcTGGGGCCGCTTTGCG‑CCCCAGCCATTTCAGTCGTCTGAATGCACCGTTCCTGTGCCCGCTGCACCTCTGGAAGGCACAAATCCCCTCAAAATCCGGCCAAATCACCCGCAAAGCCCa                                             >  2:1085226‑M1/21‑137 (MQ=255)                                                                                                                   attcagacgactgaaatggcTGGGGCCGCTTTGCG‑CCCCAGCCATTTCAGTCGTCTGAATGCACCGTTCCTGTGCCCGCTGCACCTCTGGAAGGCACAAATCCCCTCAAAATCCGGCCAAATCACCCGCAAAGCCCa                                             <  1:1085226‑M1/117‑1 (MQ=255)                                                                                                                     aGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCGGCCCCAGCCATTTCAGTCGTCTGAATGCACCGTTCCTGTGCCCGCTGCACCTCTGGAAGGCACAAATCCCCTCAAAATCCGGCCAAATCACCCGCAAAGCCCAGTATTCACGGCtttt                              <  2:927334/150‑1 (MQ=255)                                                                                                                      gCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCGGCCCCAGCCATTTCAGTCGTCTGAATGCACCGTTCCTGTGCCCGCTGCACCTCTGGAAGGCACAAATCCCCTCAAAATCCGGCCAAATCACCCGCAAAGCCCAGTATTCACGGCTTTTg                             <  2:668302/150‑1 (MQ=255)                                                                                                                          ccTTGTGTCGCGATGGGGC‑GCAAAGCGGCCCCAGCCATTTCAGTCGTCTGAATGCACCGTTCCTGTGCCCGCTGCACCTCTGGAAGGCACAAATCCCCTCAAAATCCGGCCAAATCACCCGCAAAGCCCAGTATTCACGGCTTTTGCaaa                         >  2:1050075/1‑150 (MQ=255)                                                                                                                           gactgaaatggcTGGGGCCGCTTTGCG‑CCCCAGCCATTTCAGTCGTCTGAATGCACCGTTCCTGTGCCCGCTGCACCTCTGGAAGGCACAAATCCCCTCAAAATCCGGCCAAATCACCCGCAAAGCCCa                                             <  2:307823‑M1/117‑1 (MQ=255)                                                                                                                           gactgaaatggcTGGGGCCGCTTTGCG‑CCCCAGCCATTTCAGTCGTCTGAATGCACCGTTCCTGTGCCCGCTGCACCTCTGGAAGGCACAAATCCCCTCAAAATCCGGCCAAATCACCCGCAAAGCCCa                                             >  1:307823‑M1/13‑129 (MQ=255)                                                                                                                              tgaaatggcTGGGGCCGCTTTGCG‑CCCCATCCATTTCAGTCGTCTGAATGCACCGTTCCTGTGCCCGCTGCACCTCTGGAAGGCACAAATCCCCTCAAAATCCGGCCAAATCACCCGCAAAGCCCAGTATTCACGGCTTTTGCAAAACTg                     <  2:1183810‑M1/141‑1 (MQ=255)                                                                                                                                 tCGCGATGGGGC‑GCAAAGCGGCCCCAGCCATTTCAGTCGTCTGAATGCACCGTTCCTGTGCCCGCTGCACCTCTGGAAGGCACAAATCCCCTCAAAATCCGGCCAAATCACCCGCAAAGCCCAGTATTCACGGCTTTTGCAAAACTGGCa                  >  1:1023855/1‑150 (MQ=255)                                                                                                                                            C‑GCAAAGCGGCCCCAGCCATTTCAGTCGTCTGAATGCACCGTTCCTGTGCCCGCTGCACCTCTGGAAGGCACAAATCCCCTCAAAATCCGGCCAAATCAc                                                         <  2:184810‑M1/100‑1 (MQ=255)                                                                                                                                            C‑GCAAAGCGGCCCCAGCCATTTCAGTCGTCTGAATGCACCGTTCCTGTGCCCGCTGCACCTCTGGAAGGCACAAATCCCCTCAAAATCCGGCCAAATCAc                                                         >  1:184810‑M1/1‑100 (MQ=255)                                                                                                                                                  aGCGGCCCCAGCCATTTCAGTCGTCTGAATGCACCGTTCCTGTGCCCGCTGCACCTCTGGAAGGCACAAATCCCCTCAAAATCCGGCCAAATCACCCGCAAAGCCCAGTATTCACGGCTTTTGCAAAACTGGCACGCCCCCTGCAATAAg  <  2:846348/150‑1 (MQ=255)                                                                                                                                                  aGCGGCCCCAGCCATTTCAGTAGTCTGAATGCACAGTTCCTAAGACCGCTGCACCGGAAGAAGGCACAAAACGGCTCAAAATCCGGCCAAATCACCCGCAAAGCCCAGTATTCACGGCTTTTGCAAAACTGGCACGCCCCCTGCAATAAg  >  2:740179/1‑150 (MQ=255)                                                                                                                                                  |                                                                                                                                                      TGGGGAGAAATTCTCTGGCACGCTGACTCGTACCTCGAGGTTGCTGAGAGAGGCCGATGGCGTTTTTACTGAAAATTTGCCTCCGGCCATAGAATCTCCTACCCCAATCCTGTGGGAGCGGCCTTGTGTCGCGATGGGGC‑GCAAAGCGGCCCCAGCCATTTCAGTCGTCTGAATGCACCGTTCCTGTGCCCGCTGCACCTCTGGAAGGCACAAATCCCCTCAAAATCCGGCCAAATCACCCGCAAAGCCCAGTATTCACGGCTTTTGCAAAACTGGCACGCCCCCTGCAATAAG  >  NC_002947/5758083‑5758376

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑