Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,903,165	A→C	12.1%	intergenic (‑129/‑139)	PP_5175 ← / → PP_5176	HlyD family secretion protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,903,165	0	A	C	12.1%	104.7 / 4.1	47	intergenic (‑129/‑139)	PP_5175/PP_5176	HlyD family secretion protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (14/27);  new base C (2/4);  total (16/31)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.27e-01

GACGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGT‑GAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGC‑CTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGCCGAATGCCACCGA  >  NC_002947/5903021‑5903313                                                                                                                                                  |                                                                                                                                                      gACGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGT‑GAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGccc                                                                                                                                                   <  1:12092/149‑1 (MQ=255)    gCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGT‑GAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGa                                                                                                                                                       <  6:35891/142‑1 (MQ=255)    gCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGT‑GAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGa                                                                                                                                                       >  5:35891/1‑142 (MQ=255)      aTCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGT‑GAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGTGGGCGAGCCCGCGaa                                                                                                                                              >  7:92412/1‑149 (MQ=255)      aTCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGT‑GAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCTCGCCCGCGaa                                                                                                                                              <  7:125112/149‑1 (MQ=255)         aaCTCCTTGCTGGCTCCTTGCTTGTGCACAAATTATTTGTGGGATGCGACTGT‑GAGCGTACTTCAGGGTTCGTTAAACATCACTGACGGGGGCCCTGCTGGCATTTTTGGTGCCTGCTGTGGCCTCTTCGCGGGCTCGCCCGCGAagag                                                                                                                                           <  5:233059/149‑1 (MQ=255)         aaCGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGT‑GAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCTCGCCCGCGAagag                                                                                                                                           <  5:228617/149‑1 (MQ=255)         aaCGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGT‑GAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAaga                                                                                                                                            <  6:226197/148‑1 (MQ=255)         aaCGCCATGCTGGCGCCTTGCTTCTGCACAAATGATTTGTTGGATGCGACTGT‑GAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAagag                                                                                                                                           <  6:227365/149‑1 (MQ=255)                  cTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGT‑GAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTAATAGCGGGCGCGCCCGCGAATAAGG‑CTCccca                                                                                                                                 >  3:181031/1‑149 (MQ=255)                         cttgcttgTGCACAAATGATTTGTGGGATGCGACTGT‑GAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCcgcg                                                                                                                                                <  6:40246/128‑1 (MQ=255)                         cttgcttgTGCACAAATGATTTGTGGGATGCGACTGT‑GAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCcgcg                                                                                                                                                >  5:40246/1‑128 (MQ=255)                         cttgcttgTGCACAAATGATTTGTGGGATGCGACTGT‑GAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGC‑CTCCACAGCCATGt                                                                                                                          >  5:84397/1‑149 (MQ=255)                         cttgctggTGCACAATTGTTTTGTGGGAGGCCACTGT‑GAGCTTTGTTCAGGGTTCTATAAAAATCACTGACGGGGGCCATGCTGGCATTTTTGGGGCCTGGGGGGGCCTCTGCGCGGGCGAGCCCGCTAAGAGGC‑CTCCACAGCCATGt                                                                                                                          <  2:245263/149‑1 (MQ=255)                             cttgTGCACAAATGATTTGTGGGATGCGACTGT‑GAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGTGGGCGAGCCCGCGAAGAGGC‑CTCCACAGCCATGTATCa                                                                                                                      <  8:92412/149‑1 (MQ=255)                             ctgcgccacacaTGCTTGCTGGGATGCGACTGT‑GCGCGTCTTTCAGGGTTCGACAAACATCACGGACGGGGGCCATGCGGGCATTTTTGGGGCCTGCGGGGGCCTCTGCGCGGCCGCGCCCGCGAAGAGGC‑CTCCACAGCCATGTATc                                                                                                                       <  8:271243/142‑1 (MQ=255)                                   cacaAATGATTTGTGGGATGCGACTGT‑GAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGC‑CTCCACAGCCATGTATCa                                                                                                                      >  8:88567/1‑143 (MQ=255)                                   cacaAATGATTTGTGGGATGCGACTGT‑GAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGC‑CTCCACAGCCATGTATCa                                                                                                                      <  7:88567/143‑1 (MQ=255)                                     caAATGATTTGTGGGATGCGACTGT‑GAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGa                                                                                                                                                       <  7:73401/109‑1 (MQ=255)                                     caAATGATTTGTGGGATGCGACTGT‑GAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGa                                                                                                                                                       >  8:73401/1‑109 (MQ=255)                                      aaaTGATTTGTGGGATGCGACTGT‑GAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTACCCGGCGAGCCCGCGAAGAGGC‑CACCACACCCAAGTAACAGTATATGc                                                                                                              >  8:173594/1‑148 (MQ=255)                                            tttGTGGGATTCGACTGT‑GAGCTTTGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGC‑CTCCACAGCCATGTATCAGTATCTGCCATATc                                                                                                        <  7:173594/148‑1 (MQ=255)                                               gtgGGATGCGACTGT‑GAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGC‑CTCCACAGCCATGTATCAGTATCTGCCATATCCAg                                                                                                     <  7:186479/148‑1 (MQ=255)                                                tgGGATGCGA‑TGTGGAGCGTCGTGATGGGTGCGAAACACATCCCTGCCGGGGGCCATGCGGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGGGAGCCCGCTAAGAGGC‑CTCCACAGCCATGTATCAGTATCTGCCATATCCAGaa                                                                                                   <  8:110447/149‑1 (MQ=255)                                                       cGACTGT‑GAGCGTAGTTCAGGGTTCGATAAACATCACTGCCGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGC‑CGCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCa                                                                                            <  8:204333/149‑1 (MQ=255)                                                        gACTGT‑GAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGC‑CTCCACAGCCAt                                                                                                                            >  6:148247/1‑116 (MQ=255)                                                        gACTGT‑GAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGC‑CTCCACAGCCAt                                                                                                                            <  5:148247/116‑1 (MQ=255)                                                                 gCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGC‑CTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCgg                                                                                    <  6:84397/148‑1 (MQ=255)                                                                          aGGGTTCGATAACCATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCTAAGAGGC‑CTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGt                                                                          <  4:299298/149‑1 (MQ=255)                                                                           gggTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGC‑CTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGtt                                                                         <  5:1804/149‑1 (MQ=255)                                                                            ggTTCGTTAAACATCACTGAC‑GGGGCCATGCTGGCATTTTTGTTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGC‑CTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGtt                                                                         <  7:17204/147‑1 (MQ=255)                                                                                 gaaaaaCACCACTGACGGGGCCCATGCGGGAATTTTGGGCGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCTAAGAGGC‑CTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAAcc                                                                   <  7:113839/146‑1 (MQ=255)                                                                                    aaaCATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGC‑CTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCAt                                                                                >  7:7702/1‑133 (MQ=255)                                                                                    aaaCATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGC‑CTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCAt                                                                                <  8:7702/133‑1 (MQ=255)                                                                                                   gggCCATGGTGGAATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCTAAGAGGC‑CTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAg                                                 <  4:181031/149‑1 (MQ=255)                                                                                                        aTGCTGGCATTTTTGGGGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCTAAGAGGC‑CTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTca                                            <  7:126316/149‑1 (MQ=255)                                                                                                              gCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGC‑CTCCACAGCCATGTATAAGTATATGCCATATACAGAAACCATCAGGCAAAGGCCATCCCCGTTCCAACCGCTACCATTCACAGGGAGGCGAACAtta                                       >  8:75188/1‑147 (MQ=255)                                                                                                                    ttGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGC‑CTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTAc                                                              >  1:229701/1‑119 (MQ=255)                                                                                                                       gTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCTCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCGACCTTTCACAGGGAGGCTCACATTCAAgg                                   >  1:58121/1‑144 (MQ=255)                                                                                                                          ccTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGC‑CTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCaa                           <  7:75188/148‑1 (MQ=255)                                                                                                                                  ggCCTCTTCGCGGGCGAGCCCGCGAAGAGGC‑CTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGtt                  <  7:103816/149‑1 (MQ=255)                                                                                                                                     ctctTCGCGGGCGAGCCCGCGAAGAGGC‑CTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGc               >  4:47101/1‑149 (MQ=255)                                                                                                                                       ctTCGCGGGCGAGCCCGCGAAGAGGC‑CTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAg                                    <  3:70996/126‑1 (MQ=255)                                                                                                                                       ctTCGCGGGCGAGCCCGCGAAGAGGC‑CTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAg                                    >  4:70996/1‑126 (MQ=255)                                                                                                                                          cgcgGGCTCGCCCGCGAAGAGGC‑CTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGCCGAAt          >  5:144303/1‑149 (MQ=255)                                                                                                                                             gggCGAGCCCGCGAAGAGGC‑CTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGc                      >  6:147759/1‑134 (MQ=255)                                                                                                                                             gggCGAGCCCGCGAAGAGGC‑CTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGc                      <  5:147759/134‑1 (MQ=255)                                                                                                                                             gggCGAGCCCGCGAAGAGGC‑CTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGCCGAATGc        >  5:289991/1‑148 (MQ=255)                                                                                                                                              ggCGAGCCCGCGAAGAGGC‑CTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGCCGAATGCCa      <  3:258488/149‑1 (MQ=255)                                                                                                                                              ggCGAGCCCGCGAAGAGGC‑CTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGCCGAATGCCa      <  3:47101/149‑1 (MQ=255)                                                                                                                                               gCGAGCCCGCGAAGAGGC‑CTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGCCGAATGCCAc     <  2:58121/149‑1 (MQ=255)                                                                                                                                                  aGCCCGCGAAGAGGC‑CTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGCCGAATGCCACCGa  >  3:189207/1‑149 (MQ=255)                                                                                                                                                  |                                                                                                                                                      GACGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGT‑GAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGC‑CTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGCCGAATGCCACCGA  >  NC_002947/5903021‑5903313

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑