Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,541,263	A→T	7.5%	intergenic (‑278/+38)	PP_4872 ← / ← dnaB	hypothetical protein/replicative DNA helicase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,541,263	0	A	T	7.5%	156.4 / 3.5	53	intergenic (‑278/+38)	PP_4872/dnaB	hypothetical protein/replicative DNA helicase
Reads supporting (aligned to +/- strand):  ref base A (25/24);  new base T (2/2);  total (27/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.52e-01

AAATCGAGCGCCGCCCGCGCGGCGCATCGCGACGCAAGGCCGCTCCCACATTTGTTGCAACGTGCCAAAACTGCAAGGCCATGGTTGCCCGTTGCCCGCCTTGGCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAGGGCCCCTGCTAACGCAATTAGTTATTCATCATCATCAAAGTTGTACATCCCCGGCGCCAAGTTCTCGAACCGGGTGTACTTGCCGATAAACGCCAAACGCACGAAGCCGATGGGGCCGTTACGCTGTTTGC  >  NC_002947/5541117‑5541410                                                                                                                                                    |                                                                                                                                                    aaaTCGAGCGCCGCCCGCGCGGCGCATCGCGACGCAAGGCCGCTCCCACATTTGTTGCAACGTGCCAAAACTGCAAGGCCATGGTTGCCCGTTGCCCGCCTTGGCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCaaa                                                                                                                                                   <  7:275800/149‑1 (MQ=255)      atgcgcCGCCCGCGCGGCGCATCGCGACGCAAGGCCGCTCCCACATTTGTTGCAACGTGCCAAAACTGCAAGGCCATGGTTGCCCGTTGCCCGCCTTGGCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCAAagcagc                                                                                                                                              >  7:255187/3‑149 (MQ=255)       tgcgcCGCGCGGGCGGCGCATCGCGACGCAAGGCCGCTCCCACATTTGTTGCAACGTGCCAAAACTGCAAGGCCATGGTTGCCCGTTGCCCGCCTTGGCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCAAAGCAGcc                                                                                                                                             >  6:183205/2‑149 (MQ=255)        gcgcCGCCCGCGCGGCGCATCGCGACGCAAGGCCGCTCCCACATTTGTTGCAACGTGCCAAAACTGCAAGGCCATGGTTGCCCGTTGCCCGCCTTGGCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCAAAGCAGccc                                                                                                                                            >  8:252971/1‑149 (MQ=255)           ccgcccgcGCGGCGCATCGCGACGCAAGGCCGCTCCCACATTTGTTGCAACGTGCCAAAACTGCAAGGCCATGGTTGCCCGTTGCCCGCCTTGGCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCaaa                                                                                                                                                   >  6:98816/1‑139 (MQ=255)           ccgcccgcGCGGCGCATCGCGACGCAAGGCCGCTCCCACATTTGTTGCAACGTGCCAAAACTGCAAGGCCATGGTTGCCCGTTGCCCGCCTTGGCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCaaa                                                                                                                                                   <  5:98816/139‑1 (MQ=255)             gcccgcGCGGCGCATCGCGACGCAAGGCCGCTCCCACATTTGTTGCAACGTGCCAAAACTGCAAGGCCATGGTTGCCCGTTGCCCGCCTTGGCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCTTTGCAGcccat                                                                                                                                          <  6:232509/146‑3 (MQ=255)              cccgcGCGGCGCATCGCGACGCAAGGCCGCTCCCACATTTGTTGCAACGTGCCAAAACTGCAAGGCCATGGTTGCCCGTTGCCCGCCTTGGCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCAAAGCAGCCCCTACaa                                                                                                                                      <  8:255187/149‑1 (MQ=255)                cgcgcgGCGCATCGCGACGCAAGGCCGCTCCCACATTTGTTTCAACGTGCAAAAACTGCAAGGCCATGGTTGCCCGTTGCCCGCCTTGGCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAgg                                                                                                                                    <  5:360429/149‑1 (MQ=255)                 gcgcgGCGCATCGCGCCGCAAGGCCGCTACCACATTTGGTGCAACGTGCCAAAACTGCAAGGCCTTGGTGGCCCGTTGGCCGCCTTGGCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAggg                                                                                                                                   <  7:242080/149‑1 (MQ=255)                       cgcATCGCGACGCAAGGCCGCTCCCACATTTGTTGCAACGTGCCAAAACTGCAAGGCCATGGTTGCCCGTTGCCCGCCTTGGCCGAGTTGAACACGAATGTGGGCCTTGCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAGGGCCCCt                                                                                                                              <  1:270846/149‑1 (MQ=255)                              cgACGCAAGGCCGCTCCCACATTTGTTGCAACGTGCCAAAACTGCAAGGCCATGGTTGCCCGTTGCCCGCCTTGGCCGAGTTGAA‑ACGAATGTGGGCTTTGCGTCGCGATGGGCTGCTTTGCAGcccatc                                                                                                                                         <  4:86436/130‑4 (MQ=255)                              cgACGCAAGGCCGCTCCCACATTTGTTGCAACGTGCCAAAACTGCAAGGCCATGGTTGCCCGTTGCCCGCCTTGGCCGAGTTGAA‑ACGAATGTGGGCTTTGCGTCGCGATGGGCTGCTTTGCAGcccatc                                                                                                                                         >  3:86436/1‑127 (MQ=255)                                           cTCCCACATTTGTTGCAACGTGCCAAAACTGCAAGGCCATGGTTGCCCGTTGCCCGCCTTGGCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAGGGCCCCTGCTAACGCAATTAGTTATtca                                                                                                         >  4:100117/1‑149 (MQ=255)                                            tCCCACATTTGTTGCAACGTGCCAAAACTGCAAGGCCATGGTTGCCCGTTGCCCGCCTTGGCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAggg                                                                                                                                   >  2:99747/1‑122 (MQ=255)                                              ccACATTTGTTGCAACGTGCCAAAACTGCAAGGCCATGGTTGCCCGTTGCCCGCCTTGGCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAGGGCCCCTGCTAACGCAATTAg                                                                                                                >  5:162830/1‑139 (MQ=255)                                              ccACATTTGTTGCAACGTGCCAAAACTGCAAGGCCATGGTTGCCCGTTGCCCGCCTTGGCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAGGGCCCCTGCTAACGCAATTAg                                                                                                                <  6:162830/139‑1 (MQ=255)                                              ccACATTTGTTGCAACGTGCCAAAACTGCAAGGCCATGGTTGCCCGTTGCCCGCCTTGGCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAGGGCCCCTGCTAACGCAATTAGTTATtcatca                                                                                                      >  1:137002/1‑149 (MQ=255)                                              ccACATTTGTTGCAACGTGCCAAAACTGCAAGGCCATGGTTGCCCGTTGCCCGCCTTGGCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAGGGCCCCTGCTAACGCAATTAGTTATtcatca                                                                                                      <  7:252971/149‑1 (MQ=255)                                              ccACATTTGTTGCAACGTGCCAAAACTGCAAGGCCATGGTTGCCCGTTGCCCGCCTTGGCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAGGGCCCCTGCTAACGCAATTAGTTATtcatca                                                                                                      >  1:250785/1‑149 (MQ=255)                                               cacaTTTGTTGCAACGTGCCAAAACTGCAAGGCCATGGTTGCCCGTTGCCCGCCTTGGCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAGGGCCCCTGCTAACGCAATTa                                                                                                                 >  5:25877/1‑137 (MQ=255)                                               cacaTTTGTTGCAACGTGCCAAAACTGCAAGGCCATGGTTGCCCGTTGCCCGCCTTGGCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAGGGCCCCTGCTAACGCAATTa                                                                                                                 <  6:25877/137‑1 (MQ=255)                                                acaTTTGTTGCAACGTGCCAAAACTGCAAGGCCATGGTTGCCCGTTGCCCGCCTTGGCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAgg                                                                                                                                    <  6:104917/117‑1 (MQ=255)                                                 caTTTGTTGCAACGTGCCAAAACTGCAAGGCCATGGTTGCCCGTTGCCCGCCTTGGCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAGGGCCCCTGCTAACGCAATTAGTTa                                                                                                             <  7:12392/139‑1 (MQ=255)                                                 caTTTGTTGCAACGTGCCAAAACTGCAAGGCCATGGTTGCCCGTTGCCCGCCTTGGCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAGGGCCCCTGCTAACGCAATTAGTTa                                                                                                             >  8:12392/1‑139 (MQ=255)                                                 caTTTGTTGCAACGTGCCAAAACTGCAAGGCCATGGTTGCCCGTTGACCGCCTTGGCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAGGGCCCCTGCTAACGCAATTAGTTATtaatcatc                                                                                                    >  8:247641/1‑148 (MQ=255)                                                      gttgCAACGTGCCAAAACTGCAAGGCCATGGTTGCCCGTTGCCCGCCTT‑GCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCAAagca                                                                                                                                                <  4:162839/98‑1 (MQ=255)                                                      gttgCAACGTGCCAAAACTGCAAGGCCATGGTTGCCCGTTGCCCGCCTT‑GCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCAAagca                                                                                                                                                >  3:162839/1‑98 (MQ=255)                                                       ttgCAACGTGCCAAAACTGCAAGGCCATGGTTGCCCGTTGCCCGCCTTGGCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAGGGCCCCTGCTAACGCAATTAGTTATTCATCATCATCaaa                                                                                              <  5:183205/148‑1 (MQ=255)                                                         gCAACGTGCCAAAACTGCAAGGCCATGGTTGCCCGTTTCCCGGCTTGGGCGAGTTGAA‑ACGAATGTGGGGCTTTGGTCGCGATGGGCTGCAAAGCAGCCCCGTCAAGGGCCCCTGCTAACGCAATTAGTTTTTGATGATCATCAAAGtt                                                                                           >  1:191895/1‑149 (MQ=255)                                                           aaCGTGCCAAAACTGCAAGGCCATGGTTGCCCGTTGCCCGCCTTGGCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCAAAGCAGCCCGTACAAGGGCCCCTGCTAACGCAATTAGTTATtc                                                                                                          >  7:189803/1‑132 (MQ=255)                                                           aaCGTGCCAAAACTGCAAGGCCATGGTTGCCCGTTGCCCGCCTTGGCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAGGGCCCCTGCTAACGCAATTAGTTATtc                                                                                                          <  8:189803/132‑1 (MQ=255)                                                             cGTGCCAAAACTGCAAGGCCATGGTTGCCCGTTGCCCGCCTTGGCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAGGGCCCCTGCTAACGCAATTAGTTATTCATCATCATCAAAGTTGTAc                                                                                       <  3:100117/149‑1 (MQ=255)                                                                 ccAAAACTGCAAGGCCATGGTTGCCCGTTGCCCGCCTTGGCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAGGGCCCCTGCTAACGCAATTAGTTATtcatcatc                                                                                                    >  7:85600/1‑132 (MQ=255)                                                                 ccAAAACTGCAAGGCCATGGTTGCCCGTTGCCCGCCTTGGCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAGGGCCCCTGCTAACGCAATTAGTTATtcatcatc                                                                                                    <  8:85600/132‑1 (MQ=255)                                                                   aaaaCTGCAAAGCCATGGTTGCCCGTTGCCCGCCTTGGCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAGGGCCCCTGCTAAc                                                                                                                        >  6:239653/1‑110 (MQ=255)                                                                   aaaaCTGCAAAGCCATGGTTGCCCGTTGCCCGCCTTGGCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAGGGCCCCTGCTAAc                                                                                                                        <  5:239653/110‑1 (MQ=255)                                                                          cAAGGCCATGGTTGCCCGTTGCCCGCCTTGGCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAGGGCCCCTGCTAACGCAATTAGTTATTCATCATCATCAAAGTTGTACATCCCCGgcgc                                                                            <  2:191895/147‑1 (MQ=255)                                                                              gCCATGGTTGCCCGTTGCCCGCCTTGGCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAGGGCCCCTGCTAACACAATTAGTTATTCATCATCATCAAAGTTGTACATCCCCGGCGCCAAGtt                                                                      >  4:245514/1‑149 (MQ=255)                                                                                              gcccgCCTTGGCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAGGGCCCCTGCTAACGCAATTAGTTATTCATCATCATCAAAGTTGTACATCCCCGGCGCCAAGTTCTCGAACCGGGTGTAc                                                      >  6:98539/1‑149 (MQ=255)                                                                                               cccgCCTTGGCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAGGGCCCCTGCTAACGCAATTAGTTATTCATCATCATCAAAGTTGTACATCCCCGGCGCCAAGTTCTCGAACCGGgt                                                          >  2:56136/1‑144 (MQ=255)                                                                                               cccgCCTTGGCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAGGGCCCCTGCTAACGCAATTAGTTATTCATCATCATCAAAGTTGTACATCCCCGGCGCCAAGTTCTCGAACCGGgt                                                          <  1:56136/144‑1 (MQ=255)                                                                                                        gCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAGGGCCCCTGCTAACGCAATTAGTTATTCATCATCATCAAAGTTGTACATCCCCGGCGCCAAGTTCTCGAACCGGGTGTACTTGCCGATaa                                            <  1:140865/149‑1 (MQ=255)                                                                                                                          gtgGGCCTTGCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAGGGCCCCTGCTAACGCAATTAGTTATTCATCATCATCAAAGTTGTACATCCCCGGCGCCAAGTTCTCGAACCGGGTGTACTTGCCGATAAACGCCAAACGCACGaaa                           >  8:234119/1‑148 (MQ=255)                                                                                                                               ccTTGCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAGGGCCCCTGCTAACGCAATTAGTTATTCATCATCATCAAAGTTGTACATCCCCGGCGCCAAGTTCTCGAACCGGGTGTACTTGCCGATAAACGCCAAACGCACGAAGCCGAt                      <  7:247641/149‑1 (MQ=255)                                                                                                                               ccTTGCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAGGGCCCCTGCTAACGCAATTAGTTATTCATCATCATCAAAGTTGTACATCCCCGGCGCCAAGTTCTCGAACCGGGTGTACTTGCCGATAAACGCCAAACGCACGAAGCCGAt                      >  4:36157/1‑149 (MQ=255)                                                                                                                                cTTGCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAGGGCCCCTGCTAACGCAATTAGTTATTCATCATCATCAAAGTTGTACATCCCCGGCGCCAAGTTCTCGAACCGGGTGTACTTGCCGATAAACGCCAAACGCACGAAGCCGATg                     >  7:229723/1‑149 (MQ=255)                                                                                                                                 ttGCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAGGGCCCCTGCTAACGCAATTAGTTATTCATCATCATCAAAGTTGTACATCCCCGGCGCCAAGTTCTCGAACCGGGTGTACTTGCCGATAAACGCCAAACGCa                                <  2:221163/137‑1 (MQ=255)                                                                                                                                 ttGCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAGGGCCCCTGCTAACGCAATTAGTTATTCATCATCATCAAAGTTGTACATCCCCGGCGCCAAGTTCTCGAACCGGGTGTACTTGCCGATAAACGCCAAACGCa                                >  1:221163/1‑137 (MQ=255)                                                                                                                                   gCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAGGGCCCCTGCTAACGCAATTAGTTATTCATCATCATCAAAGTTGTACATCCCCGGCGCCAAGTTCTCGAACCGGGTGTACTTGCCGATAAACGCCAAACGCACGAACCCGATggg                   <  7:234119/148‑1 (MQ=255)                                                                                                                                   gCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAGGGCCCCTGCTAACACAATTAGTTATTCATCATCATCAAAGTTGTACATCCCCGGCGCCAAGTTCTCGAACCGGGTGTACTTGCCGATAAACGCCAAACGCACGAAGCCGATgg                    <  3:245514/147‑1 (MQ=255)                                                                                                                                      tCGCGATGGGCTGCAAAGCAGCCCCTACAAGGGCCCCTGCTAACGCAATTAGTTATTCATCATCATCAAAGTTGTACATCCCCGGCGCCAAGTTCTCGAACCGGGTGTACTTGCCGATAAACGCCAAACGCACGAAGCCGATggg                   >  2:32734/1‑145 (MQ=255)                                                                                                                                      tCGCGATGGGCTGCAAAGCAGCCCCTACAAGGGCCCCTGCTAACGCAATTAGTTATTCATCATCATCAAAGTTGTACATCCCCGGCGCCAAGTTCTCGAACCGGGTGTACTTGCCGATAAACGCCAAACGCACGAAGCCGATggg                   <  1:32734/145‑1 (MQ=255)                                                                                                                                        gcgATGGGCTGCAAAGCAGCCCCTACAAGGGCCCCTGCTAACGCAATTAGTTATTCATCATCATCAAAGTTGTACATCCCCGGCGCCAAGTTCTCGAACCGGGTGTACTTGCCGATAAACGCCAAACGCACGAAGCCGATGGGGCCGt              <  8:229723/148‑1 (MQ=255)                                                                                                                                           aggggCTGCTTTGCAGCCCCTACAAGGGCCCCTGCTAACGCAATTAGTTATTGATCATCATCAAAGTTGTACATCCCCGGCGCCAAGTTCTCGAACCGGGTGTACTTGACGATAAACGCCAAACGCACGAAGCCGATGGGGCCGTTACg          >  5:18977/3‑149 (MQ=255)                                                                                                                                                   cAAAGCAGCCCCTACAAGGGCCCCTGCTAACGCAATTAGTTATTCATCATCATCAAAGTTGTACATCCCCGGCGCCAAGTTCTCGAACCGGGTGTACTTGCCGATAAACGCCAAACGCACGAAGCCGATGGGGCCGTTACGCTGTTTGc  >  7:27798/1‑149 (MQ=255)                                                                                                                                                    |                                                                                                                                                    AAATCGAGCGCCGCCCGCGCGGCGCATCGCGACGCAAGGCCGCTCCCACATTTGTTGCAACGTGCCAAAACTGCAAGGCCATGGTTGCCCGTTGCCCGCCTTGGCCGAGTTGAA‑ACGAATGTGGGCCTTGCGTCGCGATGGGCTGCAAAGCAGCCCCTACAAGGGCCCCTGCTAACGCAATTAGTTATTCATCATCATCAAAGTTGTACATCCCCGGCGCCAAGTTCTCGAACCGGGTGTACTTGCCGATAAACGCCAAACGCACGAAGCCGATGGGGCCGTTACGCTGTTTGC  >  NC_002947/5541117‑5541410

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑