Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,944,028	G→A	7.5%	T101T (ACG→ACA)	PP_5673 →	D‑alanine‑‑D‑alanine ligase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,944,028	0	G	A	7.5%	152.2 / 2.2	53	T101T (ACG→ACA)	PP_5673	D‑alanine‑‑D‑alanine ligase
Reads supporting (aligned to +/- strand):  ref base G (26/23);  new base A (2/2);  total (28/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.06e-01

CTCGCTAAATTCACCAGAGTCTTTTTGGCGCTTCATGGCGGTTTCGGTGAAAACGGGATGGCACAAGCATATTTAGAAGGACTAGGGATCCCATATAATGGCCCTTCTCCTCAGGCCAGCGCAATCTGCATGGACAA‑GCTTCTAACGAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTCGAAAAACGGTGATGACGTTTGTTTTGAAGAG‑ATCAGTGAACGTCTAGGAACACCCTGCATCGTCAAACCTAACCGTGAAGGATGTAGCTTCGGTGTGT  >  NC_002947/4943882‑4944176                                                                                                                                                    |                                                                                                                                                      cTCGCTAAATTCACCAGAGTCTTTTTGGCGCTTCATGGCGGTTTCGGTGAAAACGGGATGGCACAAGCATATTTAGAAGGACTAGGGATCCCATATAATGGCCCTTCTCCTCAGGCCAGCGCAATCTGCATGGACAA‑GCTTCTAACGaa                                                                                                                                                     <  3:223134/149‑1 (MQ=255) cTCGCTAAATTCACCAGAGTCTTTTTGGCGCTTCATGGCGGTTTCGGTGAAAACGGGATGGCACAAGCATATTTAGAAGGACTAGGGATCCCATATAATGGCCCTTCTCCTCAGGCCAGCGCAATCTGCATGGACAA‑GCTTCTAACGaa                                                                                                                                                     <  2:10987/149‑1 (MQ=255)    gCTAAATTCACCAGAGTCTTTTTGGCGCTTCATGGCGGTTTCGGTGAAAACGGGATGGCACAAGCATATTTAGAAGGACTAGGGATCCCATATAATGGCCCTTCTCCTCAGGCCAGCGCAATCTGCATGGACAA‑GCTTCTAACGAAGCa                                                                                                                                                  <  3:302100/149‑1 (MQ=255)          ttCACCAGAGTCTTTTTGGCGCTTCATGGCGGTTTCGGTGAAAACGGGATGGCACAAGCATATTTAGAAGGACTAGGGATCCCATATAATGGCCCTTCTCCTCAGGCCAGCGCAATCTGCATGGACAA‑GCTTCTAACGAAGCATATTg                                                                                                                                             >  2:243848/1‑148 (MQ=255)             aCCAGAGTCTTTTTGGCGCTTCATGGCGGTTTCGGTGAAAACGGGATGGCACAAGCATATTTAGAAGGACTAGGGATCCCATATAATGGCCCTTCTCCTCAGGCCAGCGCAATCTGCATGGACAA‑GCTTCTAACGAAGCATATTGCaa                                                                                                                                          >  4:344080/1‑148 (MQ=255)              ccAGAGTCTTTTTGGCGCTTCATGCCGGTTTCGGTGAAAACGGGATGGCACAAGCATATTTAGTATGACTAGGGATCCCATATAATGGCCCTTCTCCTCAGGCCAGCGCAATCTGCATGGACAA‑GCTTCTAACGAAGCATATTGCaaca                                                                                                                                        <  2:343108/149‑3 (MQ=255)               cAGAGTCTTTTTGGCGCTTCATGGCGGTTTCGGTGAAAACGGGATGGCACAAGCATATTTAGAAGGACTAGGGATCCCATATAATGGCCCTTCTCCTCAGGCCAGCGCAATCTGCATGGACAA‑GCTTCCAACGAAGCATATTGCAagag                                                                                                                                       >  7:186845/1‑149 (MQ=255)                    tCTTTTTGGCGCTTCATGGCGGTTTCGGTGAAAACGGGATGGCACAAGCATATTTAGAAGGACTAGGGATCCCATATAATGGCCCTTCTCCTCAGGCCAGCGCAATCTGCATGGACAA‑GCTTCTAACGAAGCATATTGCAAGAGGACtt                                                                                                                                  >  6:6464/1‑149 (MQ=255)                            gcgcTTCATGGCGGTTTCGGTGAAAACGGGATTGCACAAGCATATTTAGAAGGACTAGGGATCCCATATAATGGCCCTTCTCCTCAGGCCAGCGCAATCTGCATGGACAA‑GCTTCCAACGAAGCATATTGCAAGAGGACTTGGAATaaa                                                                                                                          <  8:186845/149‑1 (MQ=255)                            gcgcTTCATGGCGGTTTCGGTGAAAACGGGATGGCACAAGCATATTTAGAAGGACTAGGGATCCCATATAATGGCCCTTCTCCTCAGGCCAGCGCAATCTGCATGGACAA‑GCTTCTAACGAAGCATATTGCAAGAGGACTTGGAATaaa                                                                                                                          <  3:111023/149‑1 (MQ=255)                                  cATGGCGGTTTCGGTGAAAACGGGATGGCACAAGCATATTTAGAAGGACTAGGGATCCCATATAATGGCCCTTCTCCTCAGGCCAGCGCAATCTGCATGGACAA‑GCTTCTAACGAAGCATATTGCAAGAGGACTTGGAATAAATGTc                                                                                                                      <  5:324228/147‑1 (MQ=255)                                              ggTGAAAACGGGATGGCACAAGCATATTTAGAAGGACTAGGGATCCCATATAATGGCCCTTCTCCTCAGGCCAGCGCAATCTGCATGGACAA‑GCTTCTAACGAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTa                                                                                                        >  7:230516/1‑149 (MQ=255)                                               gTGAAAACGGGATGGCACAAGCATATTTAGAAGGACTAGGGATCCCATATAATGGCCCTTCTCCTCAGGCCAGCGCAATCTGCATGGACAA‑GCTTCTAACGAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTAc                                                                                                       >  2:140010/1‑149 (MQ=255)                                                  aaaaCGGGATGGCACAAGCATATTTAGAAGGACTAGGGATCCCATATAATGGCCCTTCTCCTCAGGCCAGCGCAATCTGCATGGACAA‑GCTTCTAACAAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTc                                                                                                     >  5:252308/1‑148 (MQ=255)                                                  aaaaCGGGATGGCACAAGCATATTTAGAAGGACTAGGGATCCCATATAATGGCCCTTCTCCTCAGGCCAGCGCAATCTGCATGGACAA‑GATTCTAACAAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTAc                                                                                                       >  5:78565/1‑146 (MQ=255)                                                    aaCGGGATGGCACAAGCATATTTAGAAGGACTAGGGATCCCATATAATGGCCCTTCTCCTCAGGCCAGCGCAATCTGCATGGACAA‑GCTTCTAACGAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTCGa                                                                                                   >  3:260663/1‑148 (MQ=255)                                                      cGGGATGGCACAAGCATATTTAGAAGGACTAGGGATCCCATATAATGGCCCTTCTCCTCAGGCCAGCGCAATCTGCATGGACAA‑GCTTCTAACGAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTCGaaa                                                                                                 >  6:196573/1‑148 (MQ=255)                                                       gggATGGCACAAGCATATTTAGAAGGACTAGGGATCCCATATAATGGCCCTTCTCCTCAGGCCAGCGCAATCTGCATGGACAA‑GCTTCTAACGAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTCGaaaaa                                                                                               <  7:197478/149‑1 (MQ=255)                                                         gATGGCACAAGCATATTTAGAAGGACTAGGGATCCCATATAATGGCCCTTCTCCTCAGGCCAGCGCAATCTGCATGGACAA‑GCTTCTAAAGAAGCATATTGCAAGAGGACTTGTAATAAATGTCGCAAACTATCTTTAATCGAAAAACg                                                                                             >  2:354638/1‑149 (MQ=255)                                                                caAGCATATTTAGAAGGACTAGGGATCCCATATAATGGCCCTTCTCCTCAGGCCAGCGCAATCTGCATGGACAA‑GCTTCTAACGAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTCGAAAAACGGtgatga                                                                                      >  3:111967/1‑149 (MQ=255)                                                                   gCATATTTAGAAGGACTAGGGATCCCATATAATGGCCCTTCTCCTCAGGCCAGCGCAATCTGCATGGACAA‑GCTTCTAACGAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTCGAAAAACGGTGATGACgt                                                                                   >  7:187341/1‑149 (MQ=255)                                                                             taGGACTAGGGATCCCATTTAATGGCCCATCTCCACAGCCCAGCGCAATCTGCATGGACAA‑GCTTCTAACGAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTCGAAAAACGGTGATGACGTTTGTTTTGaa                                                                         <  8:358899/148‑1 (MQ=255)                                                                              aGGACTAGGGATCCCATATAATGGCCCTTCTCCTCAGGCCAGCGCAATCTGCATGGACAA‑GCTTCTAACGAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTCGAAAAACGGTGATGACGTTTGTTTTGaa                                                                         <  1:243848/148‑1 (MQ=255)                                                                                 aCTAGGGATCCCATATAATGGCCCTTCTCCTCAGGCCAGCGCAATCTGCATGGACAA‑GCTTCTAACGAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTCGAAAAACGGTGATGACGTTTGTTTTGAAgag‑a                                                                    <  1:370233/149‑1 (MQ=255)                                                                                 aCTAGGGATCCCATATAATGGCCCTTCTCCTCAGGCCAGCGCAATCTGCATGGACAA‑GCTTCTAACGAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTCGAAAAACGGTGATGACGTTTGTTTTGAAgag‑a                                                                    <  5:6464/149‑1 (MQ=255)                                                                                  cTAGGGATCCCATATAATGGCCCTTCTCCTCAGGCCAGCGCAATCTGCATGGACAA‑GCTTCTAACGAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTCGAAAAACGGTGATGACGTTTGTTTTGAAgag‑a                                                                    <  4:111967/148‑1 (MQ=255)                                                                                   tAGGGATCCCATATAATGGCCCTTCTCCTCAGGCCAGCGCAATCTGCATGGACAA‑GCTTCTAACGAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTCGAAAAACGGTGATGACGTTTGTTTTGAAGAG‑At                                                                   >  5:369915/1‑148 (MQ=255)                                                                                     gggATCCCATATAATGGCCCTTCTCCTCAGGCCAGCGCAATCTGCATGGACAA‑GCTTCTAACGAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTCGAAAAACGGTGATGACGTTTGTTTTGAAGAG‑ATCAg                                                                <  3:344080/149‑1 (MQ=255)                                                                                      ggATCCCATATAATGGCCCTTCTCCTCAGGCCAGCGCAATCTGCATGGACAA‑GCTTCTAACGAAGCAGATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATATATACTCGAAAAACGGTGATGACGTTAGTTTTGAAGAG‑ATCAGt                                                               >  4:266170/1‑149 (MQ=255)                                                                                       gATCCAATATAATGGCCCTTCTCCTCAGGCCAGCGCAATCTGAATGGACAA‑TCTTCTTACGAAGCATATTGCAAGAGGAGGTGGATTAAATGTGGCAAAATTTCTTTACTCGATATACTGGGATGAGGTTTGTTTTGATGAT‑ATCAggg                                                              >  4:269834/1‑147 (MQ=255)                                                                                            cATATAATGGCCCTTCTCCTCAGGCCAGCGCAATCTGCATGGACAA‑GCTTCTAACGAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTCGAAAAACGGTGATGACGTTTGTTTTGAAGAG‑ATCAGTGAACGt                                                         >  8:149645/1‑149 (MQ=255)                                                                                             atatAATGGCCCTTCTCCTCAGGCCAGCGCAATCTGCATGGACAA‑GCTTCTAACGAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTCGAAAAACGGTGATGACGTTTGTTTTGAAGAG‑ATCAGTGAACGTc                                                        >  2:321261/1‑149 (MQ=255)                                                                                                taATGGCCCTTCTCCTCAGGCCAGCGCAATCTGCATGGACAA‑GCTTCTAACGAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTCGAAAAACGGTGATGACGTTTGTTTTGAAGAG‑ATCAGTGAACGTCTa                                                      <  7:222414/148‑1 (MQ=255)                                                                                                taATGGCCCTTCTCCTCAGGCCAGCGCAATCTGCATGGACAA‑GCTTCTAACGAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTCGAAAAACGGTGATGACGTTTGTTTTGAAGAG‑ATCAGTGAACGTCTAg                                                     <  8:230516/149‑1 (MQ=255)                                                                                                  aTGGCCCTTCTCCTCAGGCCAGCGCAATCTGCATGGACAA‑GCTTCTAACGAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTCGAAAAACGGTGATGACGTTTGTTTTGAAGAG‑ATCAGTGAACGTCTAgg                                                    >  1:184187/1‑148 (MQ=255)                                                                                                       ccTTCTCCTCAGGCCAGCGCAATCTGCATGGACAAGGCTTCTAACGAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTCGAAAAACGGTGATGACGTTTGTTTTGAAGAG‑ATCAGTGAACGTCTAGGAacac                                               >  1:64184/1‑149 (MQ=255)                                                                                                       ccTTCTCCTCAGGCCAGCGCAATCTGCATGGACAA‑GCTTCTAACGAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTCGAAAAACGGCGATGACGTTTGTTTTGAAGAG‑ATCAGTGAACGTCTAGGAACAcc                                              <  4:260663/149‑1 (MQ=255)                                                                                                       ccTTCTCCTCAGGCCAGCGCAATCTGCATGGACAA‑GCTTCTAACAAAGCATATTGCAAGATGACTTGGAATAAATGTCGCAAACTATCTTTACTCGAAAAACGGTGATGACGTTTGTTTTGAAGAG‑ATCAGTGAACGTCTAGGAACAcc                                              <  6:78565/149‑1 (MQ=255)                                                                                                       ccTTCTCCTCAGGCCAGCGCAATCTGCATGGACAA‑GCTTCTAACAAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTCGAAAAACGGTGATGACGTTTGTTTTGAAGAG‑ATCAGTGAACGTCTAGGAACAcc                                              <  6:252308/149‑1 (MQ=255)                                                                                                              ctcAGGCCAGCGCAATCTGCATGGACAA‑GCTTCTAACGAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTCGAAAAACGGTGATGACGTTTGTTTTGAAGAG‑ATCAGTGAACGTCTAGGAACACCCTGCATc                                       >  5:56065/1‑149 (MQ=255)                                                                                                                     cAGCGCAATCTGCATGGACAA‑GCTTCTAACGAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTCGAAAAACGGTGATGACGTTTGTTTTGAAGAG‑ATCAGTGAACGTCTAGGAACACCCTGCATCGTCAAAc                                >  4:54374/1‑149 (MQ=255)                                                                                                                         gcAATCTGCATGGACAA‑GCTTCTAACGAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTCGAAAAACGGTGATGACGTTTGTTTTGAAGAG‑ATCAGTGAACGTCTAGGAACACCCTGCATCGTCAAACCTaa                            <  2:184187/149‑1 (MQ=255)                                                                                                                                 cATGGACAA‑GCTTCTAACGAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTCGAAAAACGGTGATGACGTTTGTTTTGAAGAGCATCAGTGAACGTCTAGGAACACCCTGCATCGTCAAACCTAACCGTGaa                     <  1:289561/149‑1 (MQ=255)                                                                                                                                 cATGGACAA‑GCTTCTAACGAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTCGAAAAACGGTGATGACGTTTGTTTTGAAGAG‑ATCAGTGAACGTCTAGGAACACCCTGCATCGTCAAACCTAACCGTGaa                     <  8:187341/148‑1 (MQ=255)                                                                                                                                      aCAA‑GCTTCTAACGAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTCGAAAAACGGTGATGACGTTTGTTTTGAAGAG‑ATCAGTGAACGTCTAGGAACACCCTGCATCGTCAAACCTAACCGTGAAGGATg                >  7:298960/1‑148 (MQ=255)                                                                                                                                      aCAA‑GCTTCTAACGAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTCGAAAAACGGTGATGACGTTTGTTTTGAAGAG‑ATCAGTGAACGTCTAGGAACACCCTGCATCGTCAAACCTAACCGTGAAGGATg                <  3:54374/148‑1 (MQ=255)                                                                                                                                        aa‑GCTTCTAACGAAGCTTATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTCGAAAAACGGTGATGACGTTTGTTTTGAAGAG‑ATCAGTGAACGTCTAGGAACACCCTGCATCGTCAAACCTAACCGTGAAGGATGTAg             >  6:4801/1‑149 (MQ=255)                                                                                                                                           gCTTCTAACGAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTCGAAAAACGGTGATGACGTTTGTTTTGAAGAG‑ATCAGTGAACGTCTAGGAACACCCTGCATCGTCAAACCTAACCGTGAAGGATGTAGCt           >  8:175203/1‑149 (MQ=255)                                                                                                                                           gCTTCTAACGAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTCGAAAAACGGTGATGACGTTTGTTTTGAAGAG‑ATCAGTGAACGTCTAGGAACACCCTGCATCGTCAAACCTAACCGTGAAGGATGTAGCt           >  8:180425/1‑149 (MQ=255)                                                                                                                                                 aaCGAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTCGAAAAACGGTGATGACGTTTGTTTTGAAGAG‑ATCAGTGAACGTCTAGGAACACCCTGCATCGTCAAACCTAACCGTGAAGGATGTAGCTTCGgtg     >  3:59704/1‑149 (MQ=255)                                                                                                                                                  aCGAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTCGAAAAACGGTGATGACGTTTGTTTTGAAGAG‑ATCAGTGAACGTCTAGGAACACCCTGCATCGTCAAACCTAACCGTGAAGGATGTAGCTTCgg       <  6:369915/146‑1 (MQ=255)                                                                                                                                                  aCGAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTCGAAAAACGGTGATGACGTTTGTTTTGAAGAG‑ATCAGTGAACGTCTAGGAACACCCTGCATCGTCAAACCTAACCGTGAAGGATGTAGCTTCGgtgt    >  8:74682/1‑149 (MQ=255)                                                                                                                                                  aCGAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTCGAAAAACGGTGATGACGTTTGTTTTGAAGAG‑ATCAGTGAACGTCTAGGAACACCCTGCATCGTCAAACCTAACCGTGAAGGATGTAGCTTCGgtgt    <  6:56065/149‑1 (MQ=255)                                                                                                                                                    gAAGCTTATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTCGAAAAACGGTGATGACGTTTGTTTTGAAGAG‑ATCAGTGAACGTCTAGGAACACCCTGCATCGTCAAACCTAACCGTGAAGGATGTAGCTTCGgtgtgt  <  5:4801/149‑1 (MQ=255)                                                                                                                                                    gAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTCGAAAAACGGTGATGACGTTTGTTTTGAAGAG‑ATCAGTGAACGTCTAGGAACACCCTGCATCGTCAAACCTAACCGTGAAGGATGTAGCTTCGgtgtgt  <  5:305335/149‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                      CTCGCTAAATTCACCAGAGTCTTTTTGGCGCTTCATGGCGGTTTCGGTGAAAACGGGATGGCACAAGCATATTTAGAAGGACTAGGGATCCCATATAATGGCCCTTCTCCTCAGGCCAGCGCAATCTGCATGGACAA‑GCTTCTAACGAAGCATATTGCAAGAGGACTTGGAATAAATGTCGCAAACTATCTTTACTCGAAAAACGGTGATGACGTTTGTTTTGAAGAG‑ATCAGTGAACGTCTAGGAACACCCTGCATCGTCAAACCTAACCGTGAAGGATGTAGCTTCGGTGTGT  >  NC_002947/4943882‑4944176

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: ‑