Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,180,099	C→A	7.8%	T154K (ACG→AAG)	PP_5610 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,180,099	0	C	A	7.8%	177.4 / 2.7	59	T154K (ACG→AAG)	PP_5610	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (27/27);  new base A (2/3);  total (29/30)
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

GCTAAGAGTGGCCTTCTTGGAATCGCACATTATTTCTATGGCCTACTATGATCTTTTCAACTTCCTCAACTTACTAGCCGAACAAAAATCGCAAGATGCCAATCAAATACTCGCAAGCATCGATTTAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGAACTTAAAGCTTATCCAAGGAGGAAAAACAAGTGACTAAACAGCTTTATTCAATCTATGAATCAGAAATCATTCCTGACGCAGCCCAACCAAACCATA  >  NC_002947/4179956‑4180246                                                                                                                                                |                                                                                                                                                    gcTAAGAGTGGCCTTCTTGGAATCGCACATTATTTCTATGGCCTACTATGATCTTTTCAACTTCCTCAACTTACTAGCCGAACAAAAATCGCAAGATGCCAATCAAATACTCGCAAGCATCGATTTAAAGATCAAAACATCGACGGCTaa                                                                                                                                               >  2:1559235/1‑150 (MQ=255)   tAAGAGTGGCCTTCTTGGAATCGCACATTATTTCTATGGCCTACTATGATCTTTTCAACTTCCTCAACTTACTAGCCGAACAAAAATCGCAAGATGCCAATCAAATACTCGCAAGCATCGATTTAAAGATCAAAACATCGACGGCTAAAt                                                                                                                                             >  1:809388/1‑150 (MQ=255)    aaGAGTGGCCTTCTTGGAATCGCACATTATTTCTATGGCCTACTATGATCTTTTCAACTTCCTCAACTTACTAGCCGAACAAAAATCGCAAGATGCCAATCAAATACTCGCAAGCATCGATTTCCAGATCAAAACATCGACGGCTAAATa                                                                                                                                            <  2:1113656/150‑1 (MQ=255)     agagTGGCCTTCTTGGAATCGCACATTATTTCTATGGCCTACTATGATCTTTTCAACTTCCTCAACTTACTAGCCGAACAAAAATCGCAAGATGCCAATCCAATACTCGCAAGCATCGATTTAAAGATCAAAACATCGACGGCTAAATAc                                                                                                                                           <  1:190932/150‑1 (MQ=255)            ccTTCTTGGAATCGCACATTATTTCTATGGCCTACTATGATCTTTTCAACTTCCTCAACTTACTAGCCGAACAAAAATCGCAAGATGCCAATCAAATACTCGCAAGCATCGATTTAAAGATCAAAACATCGACGGCTAAATACCAGAAat                                                                                                                                    >  2:1110094/1‑150 (MQ=255)                  tGGAATCGCACATTATTTCTATGGCCTACTATGATCTTTTCAACTTCCTCAACTTACTAGCCGAACAAAAATCGCAAGGTGCCAATCAAATACTCGCAACCATCGATTTAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCttt                                                                                                                              <  2:1054447/150‑1 (MQ=255)                  tGGAATCGCACATTATTTCTATGGCCTACTATGATCTTTTCAACTTCCTCAACTTACTAGCCGAACAAAAATCGCAAGATGCCAATCAAATACTCGCAAGCATCGATTTAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCttt                                                                                                                              <  1:92070/150‑1 (MQ=255)                     aaTCGCACATTATTTCTATGGCCTACTATGATCTTTTCAACTTCCTCAACTTACTAGCCGAACAAAAATCGCAAGATGCCAATCAAATACTCGCAAGCATCGATTTAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCa                                                                                                                           <  2:323493/150‑1 (MQ=255)                         gCACATTATTTCTATGGCCTACTATGATCTTTTCAACTTCCTCAACTTACTAGCCGAACAAAAATCGCAAGATGCCAATCAAATACTCGCAAGCATCGATTTAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTca                                                                                                                       >  1:905756/1‑150 (MQ=255)                          cacaTTAGTTCTATGGCCTACTATGATCTTTTCAACTTCCCCAACTTACTAGCCGAACAAAAATCGCAAGATGCCAATCAAATACTCGCAAGCATCGATTTAAAGATCAAAACACCGACGGCTAAATACCAGAAATATCTTTGCACTcac                                                                                                                      >  2:1328655/1‑150 (MQ=255)                             attattTCTATGGCCTACTATGATCTTTTCAACTTCCTCAACTTACTAGCCGAACAAAAATCGCAAGATGCCAATCAAATACTCGCAAGCATCGATTTAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACaaa                                                                                                                   <  1:45731/150‑1 (MQ=255)                               tattTCTATGGCCTACTATGATCTTTTCAACTTCCTCAACTTACTAGCCGAACAAAAATCGCAAGATGCCAATCAAATACTCGCAAGCATCGATTTAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGc                                                                                                                 >  2:1912802/1‑150 (MQ=255)                                         gCCTACTATGATCTTTTCAACTTCCTCAACTTACTAGCCGAACAAAAATCGCAAGATGCCAATCAAATACTCGCAAGCATCGATTTAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCt                                                                                                       <  2:1660739/150‑1 (MQ=255)                                              ctaTGATCTTTTCAACTTCCTCAACTTACTAGCCGAACAAAAATCGCAAGATGCCAATCAAATACTCGCAAGCATCGATTTAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGaa                                                                                                  <  1:1014206/150‑1 (MQ=255)                                               taTGATCTTTTCAACTTCCTCAACTTACTAGCCGAACAAAAATCGCAAGATGCCAATCAAATACTCGCAAGCATCGATTTAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGAAc                                                                                                 >  1:580285/1‑150 (MQ=255)                                                 tGATCTTTTCAACTTCCTCAACTTACTAGCCGAACAAAAATCGCAAGATGCCAATCAAATACTCGCAAGCATCGATTTAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGAACtt                                                                                               >  2:1140602/1‑150 (MQ=255)                                                    tCTTTTCAACTTCCTCAACTTACTAGCCGAACAAAAATCGCAAGATGCCAATCAAATACTCGCAAGCATCGATTTAAAGATCAAAACATCGAAGGCTAAGAACCACAAATATCTTTTCACTCACAAAGCCACCTCCGCTGAGAACTTaaa                                                                                            <  1:331374/150‑1 (MQ=255)                                                    tCTTTGCAACTTCCTCAACTTACTAGCCGAACAAAAATCGCAAGATGCCAATCAAATACTCGCAAGCATCGATTTAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGAACTTaaa                                                                                            >  2:28102/1‑150 (MQ=255)                                                      ttttCAACTTCCTCAACTTACTAGCCGAACAAAAATCGCAAGATGCCAATCAAATACTCGCAAGCATCGATTTAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGAACTTAAAGc                                                                                          >  1:1748234/1‑150 (MQ=255)                                                               tCCTCAACTTACTAGCCGAACAAAAATCGCAAGATGCCAATCAAATACTCGCAAGCATCGATTTAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGAACTTAAAGCTTATCCAag                                                                                 <  2:1664490/150‑1 (MQ=255)                                                               tCCTCAACTTACTAGCCGAACAAAAATCGCAAGATGCCAATCAAATACTCGCAAGCATCGATTTAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGAACTTAAAGCTTATCCAag                                                                                 <  2:925078/150‑1 (MQ=255)                                                                 cTCAACTTACTAGCCGAACAAAAATCGCAAGATGCCAATCAAATACTCGCAAGCATCGATTTAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGAACTTAAAGCTTATCCAagga                                                                               <  1:1518955/150‑1 (MQ=255)                                                                  tCAACTTACTAGCCGAACAAAAATCGCAAGATGCCAATCAAATACTCGCAAGCATCGATTTAAAGATCAAAACATCGAAGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGaa                                                                                                  <  1:759284/130‑1 (MQ=255)                                                                  tCAACTTACTAGCCGAACAAAAATCGCAAGATGCCAATCAAATACTCGCAAGCATCGATTTAAAGATCAAAACATCGAAGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGaa                                                                                                  <  1:1729811/130‑1 (MQ=255)                                                                  tCAACTTACTAGCCGAACAAAAATCGCAAGATGCCAATCAAATACTCGCAAGCATCGATTTAAAGATCAAAACATCGAAGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGaa                                                                                                  >  2:759284/1‑130 (MQ=255)                                                                  tCAACTTACTAGCCGAACAAAAATCGCAAGATGCCAATCAAATACTCGCAAGCATCGATTTAAAGATCAAAACATCGAAGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGaa                                                                                                  >  2:1729811/1‑130 (MQ=255)                                                                           tAGCCGAACAAAAATCGCAAGATGCCAATCAAATACTCGCAAGCATCGATTTAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGAACTTAAAGCTTATCCAAGGAGGAAAAACaa                                                                     <  1:651831/150‑1 (MQ=255)                                                                               cGAACAAAAATCGCAAGATGCCAATCAAATACTCGCAAGCATCGATTTAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGAACTTAAAGCTTATCCAAGGAGGAAAAACAAGTGa                                                                 >  1:789218/1‑150 (MQ=255)                                                                                            cAAGATGCCAATCAAATACTCGCAAGCATCGATTTAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGAACTTAAAGCTTATCCAAGGAGGAAAAACAAg                                                                    <  1:650540/134‑1 (MQ=255)                                                                                            cAAGATGCCAATCAAATACTCGCAAGCATCGATTTAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGAACTTAAAGCTTATCCAAGGAGGAAAAACAAg                                                                    >  2:650540/1‑134 (MQ=255)                                                                                             aaGATGCCTATCAAATACTCGCAAGCATCGATTTAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGAACTTaaa                                                                                            >  2:1899087/1‑109 (MQ=255)                                                                                             aaGATGCCTATCAAATACTCGCAAGCATCGATTTAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGAACTTaaa                                                                                            <  1:1899087/109‑1 (MQ=255)                                                                                                  gCCAATCAAATACTCGCAAGCATCGATTTAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGAACTTAAAGCTTATCCAAGGAGGAAAAACAAGTGACTAAACAGCTTTATTCAAt                                              <  2:699287/150‑1 (MQ=255)                                                                                                    cAATCAAATACTCGCAAGCATCGATTTAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGAACTTAAAGCTTATCCAAGGAGGAAAAACAAGTGACTAAACAGCTTTATTCAATCt                                            >  1:1313413/1‑150 (MQ=255)                                                                                                    cAATCAAATACTCGCAAGCATCGATTTAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGAACTTAAAGCTTATCCAAGGAGGAAAAACAAGTGACTAAACAGCTTTATTCAATCt                                            >  2:1361369/1‑150 (MQ=255)                                                                                                          aaTACTCGCAAGCATCGATTTAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGAACTTAAAGCTTATCCAAGGAGGAAAAACAAGTGACTAAACAGCTTTATTCAATCTATGAAt                                      >  2:844428/1‑150 (MQ=255)                                                                                                          aaTACTCGCAAGCATCGATTTAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGAACTCACAAAGCCACCTCCGCTGAGAACTTAAAGCTTATCCAAGGAGGAAAAACAAGTGACTAAACAGCTTTATTCAATCTATGAAt                                      >  2:128714/1‑150 (MQ=255)                                                                                                           aTACTCGCAAGCATCGATTTAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGAACTTAAAGCTTATCCAAGGAGGAAAAACAAGTGACTAAACAGCTTTATTCAATCTATGAATc                                     >  2:595969/1‑150 (MQ=255)                                                                                                               tCGCAAGCATCGATTTAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGAACTTAAAGCTTATCCAAGGAGGAAAAACAAGTGACTAAACAGCTTTATTCAATCTATGAATCAGaa                                 <  1:1361369/150‑1 (MQ=255)                                                                                                               tCGCAAGCATCGATTTAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGAACTTAAAGCTTATCCAAGGAGGAAAAACAAGTGACTAAACAGCTTTATTCAATCTATGAATCAGaa                                 <  2:1313413/150‑1 (MQ=255)                                                                                                                cGCAAGCATCGATTTAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGAACTTAAAGCTTATCCAAGGAGGAAAAACAAGTGACTAAACAGCTTTATTCAATCTATGAATCAGaaa                                <  1:527199/150‑1 (MQ=255)                                                                                                                 gCAAGCATCGATTTAAAGATCGAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGAACTTAAAGCTTATCCAAGGAGGAAAAACAAGTGACTAAACAGCTTTATTCAATCTATGAATCAGAAAt                               >  1:141743/1‑150 (MQ=255)                                                                                                                 gCAAGCATCGATTTAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGAACTTAAAGCTTATCCAAGGAGGAAAAACAAGTGACTAAACAGCTTTATTCAATCTATGAATCAGAAAt                               >  2:1371066/1‑150 (MQ=255)                                                                                                                 gCAAGCATCGATTTAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGAACTTAAAGCTTATCCAAGGAGGAAAAACAAGTGACTAAACAGCTTTATTCAATCTATGAATCAGAAAt                               <  2:789218/150‑1 (MQ=255)                                                                                                                       aTCGATTTAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGAACTTGAAGCTTATCCAAGGAGGAAAAACAAGTGACTAAACAGCTTTATTCAATCTATGAATCAGAAATCATTcc                         <  1:1912802/150‑1 (MQ=255)                                                                                                                        tCGATTTAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGAACTTAAAGCTTATCCAAGGAGGAAAAACAAGTGACTAAACAGCTTTATTCAATCTATGAATCAGAAATCATTCCt                        >  2:295139/1‑150 (MQ=255)                                                                                                                         cGATTTAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCAACCTCCGCTGAGAACTTAAAGCTTATCCAAGGAGGAAAAACAATTGACTAAACAGCTTTATTCAATCTATAAATCAGAAATCATTCCTg                       <  2:905756/150‑1 (MQ=255)                                                                                                                            tttAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGAACTTAAAGCTTATCCAAGGAGGAAAAACaa                                                                     >  2:1306402/1‑101 (MQ=255)                                                                                                                            tttAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGAACTTAAAGCTTATCCAAGGAGGAAAAACaa                                                                     <  1:1306402/101‑1 (MQ=255)                                                                                                                               aaaGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAGAGCCACCTCCGCTGAGAACTTAAAGCTTATCCAAGGAGGAAAAAc                                                                       >  2:1051571/1‑96 (MQ=255)                                                                                                                               aaaGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGAACTTAAAGCTTATCCAAGGAGGAAAAAc                                                                       <  1:1051571/96‑1 (MQ=255)                                                                                                                               aaaGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGAACTTAAAGCTTATCCAAGGAGGAAAAACAAGTGACTAAACAGCTTTATTCAATCTATGAATCAGAAATCATTCCTGACGCAg                 >  1:1219552/1‑150 (MQ=255)                                                                                                                               aaaGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGACATCTTCCAGAGACGTCAGCTTATAACTTAAAGCTTATCCAAGGAGGAAAAACAAGTGACTAAACAGCTTTATTCAATCTATGAATCAGAAATCATTCCTGACGCAg                 >  1:514563/1‑150 (MQ=255)                                                                                                                                     cAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGAACTTAAAGCTTATCCAAGGAGGAAAAACAAGTGACt                                                               <  1:1016528/98‑1 (MQ=255)                                                                                                                                     cAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGAACTTAAAGCTTATCCAAGGAGGAAAAACAAGTGACt                                                               >  2:1016528/1‑98 (MQ=255)                                                                                                                                         aCATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGAACTTAAAGCTTATCCAAGGAGGAAAAACAAGTGACTAAACAGCTTTATTCAATCTATGAATCAGAAATCATTCCTGACGCAGCCCaaccaaa       <  1:238264/150‑1 (MQ=255)                                                                                                                                          cATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGAACTTAAAGCTTATCCAAGGAGGAAAAACAAGTGACTAAACAGCTTTATTCAATCTATGAATCAGAAATCATTCCTGACGCAGCCCaaccaaac      <  1:595969/150‑1 (MQ=255)                                                                                                                                            tCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGAACTTAAAGCTTATCCAAGGAGGAAAAACAAGTGACTAAACAGCTTTATTCAATCTATGAATCAGAAATCATTCCTGACGCAGCCCaaccaaacca    >  1:1836223/1‑150 (MQ=255)                                                                                                                                              gACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGAACTTAAAGCTTATCCAAGGAGGAAAAACAAGTGACTAAACAGCTTTATTCAATCTATGAATCAGAAATCATTCCTGACGCAGCCCAACCAAACCATa  <  1:295139/150‑1 (MQ=255)                                                                                                                                                |                                                                                                                                                    GCTAAGAGTGGCCTTCTTGGAATCGCACATTATTTCTATGGCCTACTATGATCTTTTCAACTTCCTCAACTTACTAGCCGAACAAAAATCGCAAGATGCCAATCAAATACTCGCAAGCATCGATTTAAAGATCAAAACATCGACGGCTAAATACCAGAAATATCTTTGCACTCACAAAGCCACCTCCGCTGAGAACTTAAAGCTTATCCAAGGAGGAAAAACAAGTGACTAAACAGCTTTATTCAATCTATGAATCAGAAATCATTCCTGACGCAGCCCAACCAAACCATA  >  NC_002947/4179956‑4180246

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑