Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,221,178	G→A	7.5%	R150* (CGA→TGA)	PP_1960 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,221,178	0	G	A	7.5%	148.1 / 2.5	53	R150* (CGA→TGA)	PP_1960	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (27/22);  new base A (2/2);  total (29/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.79e-01

AAAGCTACTGAGGTAGGTCCGAATCTCCGACTGATTTATAAGGGTGCGGCGTTGGGACTGTCGCGACTCCTTGTCCAGGGCGCGAACGTTTTTGGCATCGATTGTTACCCTTGCCTTTGCTTGAATGTAAGACAGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATCTCAACATTCGATTTATACCCTTTA‑ATGTTCAACCAGTGAAAATAGTTGAGGATAATCTTTAGGTCTTCATAGACT‑GTTTCTGAGGAAGGCTTAAGGCTCTGGGTCTC  >  NC_002947/2221032‑2221319                                                                                                                                                   |                                                                                                                                                aaaGCTACTGAGGTAGGTCCGAATCTCCGACTGATTTATAAGGGTGCGGCGTTGGGACTGTCGCGACTCCTTGTCCAGGGCGCGAACGTTTTTGGCATCGATTGTTACCCTTGCCTTTGCTTGAATGTAAGACAGTAATCTACTTCGAt                                                                                                                                               >  4:59863/1‑149 (MQ=255)  aaGCTACTGAGGTAGGTCCGAATCTCCGACTGATTTATAAGGGTGCGGCGTTGGGACTGTCGCGACTCCTTGTCCAGGGCGCGAACGTTTTTGGCATCGATTGTTACCCTTGCCTTTGCTTGAATGTAAGACAGTAATCTACTTCGAtt                                                                                                                                              <  1:221521/149‑1 (MQ=255)       aCTGAGGTAGGTCCGAATCTCCGACTGATTTATAAGGGTGCGGCGTTGGGACTGTCGCGACTCCTTGTCCAGGGCGCGAACGTTTTTGGCATCGATTGTTACCCTTGCCTTTGCTTGAATGTAAGACAGTAATCTACTTCGATTGAAg                                                                                                                                          >  3:17254/1‑148 (MQ=255)               aggtCCGAATCTCCGACTGATTTATAAGGGTGCGGCGTTGGGACTGTCGCGACTCCTTGTCCAGGGCGCGAACGTTTTTGGCATCGATTGTTACCCTTGCCTTTGCTTGAATGTAAGACAGTAATCTACTTCAATTGAAGTAAGcc                                                                                                                                    <  8:63890/146‑1 (MQ=255)               aggtCCGAATCTCCGACTGATTTATAAGGGTGCGGCGTTGGGACTGTCGCGACTCCTTGTCCAGGGCGCGAACGTTTTTGGCATCGATTGTTACCCTTGCCTTTGCTTGAATGTAAGACAGTAATCTACTTCAATTGAAGTAAGcc                                                                                                                                    >  7:63890/1‑146 (MQ=255)               aggtCCGAATCTCCGACTGATTTATAAGGGTGCGGCGTTGGGACTGTCGCGACTCCTTGTCCAGGGCGCGAACGTTTTTGGCATCGATTGTTACCCTTGCCTTTGCTTGAATGTAAGACAGTAATCTACTTCAATTGAAGTAAGcc                                                                                                                                    <  8:59537/146‑1 (MQ=255)               aggtCCGAATCTCCGACTGATTTATAAGGGTGCGGCGTTGGGACTGTCGCGACTCCTTGTCCAGGGCGCGAACGTTTTTGGCATCGATTGTTACCCTTGCCTTTGCTTGAATGTAAGACAGTAATCTACTTCAATTGAAGTAAGcc                                                                                                                                    >  7:59537/1‑146 (MQ=255)                          tcCGACTGATTTATAAGGGTGCGGCGTTGGGACTGTCGCGACTCCTTGTCCAGGGCGCGAACGTTTTTGGCATCGATTGTTACCCTTGCCTTTGCTTGAATGTAAGACATTAATCTAATTCGATAGAAGTAAGCCGTGGACCGAtt                                                                                                                         >  2:248825/1‑146 (MQ=255)                             gACTGATTTATAAGGGTGCGGCGTTGGGACTGTCGCGACTCCTTGTCCAGGGCGCGAACGTTTTTGGCATCGATTGTTACCCTTGCCTTTGCTTGAATGTAAGACAGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCt                                                                                                                    >  6:127974/1‑148 (MQ=255)                                  aTTTATAAGGGTGCGGCGTTGGGACTGTCGCGACTCCTTGTCCAGGGCGCGAACGTTTTTGGCATCGATTGTTACCCTTGCCTTTGCTTGAATGTAAGACAGTAATCTACTTCGATTg                                                                                                                                             >  7:295538/1‑118 (MQ=255)                                  aTTTATAAGGGTGCGGCGTTGGGACTGTCGCGACTCCTTGTCCAGGGCGCGAACGTTTTTGGCATCGATTGTTACCCTTGCCTTTGCTTGAATGTAAGACAGTAATCTACTTCGATTg                                                                                                                                             <  8:295538/118‑1 (MQ=255)                                                ggcgTTGGGACTGTCGCGACTCCTTGTCCAGGGCGCGAACGTTTTTGGCATCGATTGTTACCCTTGCCTTTGCTTGAATGTAAGACAGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATGTCAACATTCGATTta                                                                                                >  3:237121/1‑149 (MQ=255)                                                    ttGGGACTGTCGCGACTCCTTGTCCAGGGCGCGAACGTTTTTGGCATCGATTGTTACCCTTGCCTTTGCTTGAATGTAAGACAGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATCTCAACATTCGATTTATAcc                                                                                            <  1:55011/149‑1 (MQ=255)                                                      gggACTGTCGCGACTCCTTGTCCAGGGCGCGAACGTTTTTGGCATCGATTGTTACCCTTGCCTTTGCTTGAATGTAAGACAGTAATCTACTTCGATTg                                                                                                                                             >  3:65247/1‑98 (MQ=255)                                                      gggACTGTCGCGACTCCTTGTCCAGGGCGCGAACGTTTTTGGCATCGATTGTTACCCTTGCCTTTGCTTGAATGTAAGACAGTAATCTACTTCGATTg                                                                                                                                             <  4:65247/98‑1 (MQ=255)                                                          cTGTCGCGACTCCTTGTCCAGGGCGCGAACGTTTTTGGCATCGATTGTTACCCTTGCCTTTGCTTGAATGTAAGACAGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGc                                                                                                                     >  3:156489/1‑118 (MQ=255)                                                          cTGTCGCGACTCCTTGTCCAGGGCGCGAACGTTTTTGGCATCGATTGTTACCCTTGCCTTTGCTTGAATGTAAGACAGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGc                                                                                                                     <  4:156489/118‑1 (MQ=255)                                                           tGTCGCGACTCCTTGTCCAGGGCGCGAACGTTTTTGGCATCGATTGTTACCCTTGCCTTTGCTTGAATGTAAGACAGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATCTCAACATTCGATTTATACCCTTTA‑At                                                                                    >  2:302781/1‑149 (MQ=255)                                                            gTCGCGACTCCTTGTCCAGGGCGCGAACGTTTTTGGCATCGATTGTTACCCTTGCCTTTGCTTGAATGTAAGACAGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATCTCAACATTCGATTTATACCCTTTA‑ATg                                                                                   >  4:140310/1‑149 (MQ=255)                                                             tCGCGACTCCTTGTCCAGGGCGCGAACGTTTTTGGCATCGATTGTTACACTTGCCTTTGCTTGAATGTAAGACAGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATCTCAACATTCGATTTATACCCTTTA‑ATGt                                                                                  >  5:146267/1‑149 (MQ=255)                                                               gcgACTCCTTGTCCAGGGCGCGAACGTTTTTGGCATCGATTTTTACCCTTGCCTTTGCTTGAATGTAAGACAGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATCTCAACATTCGATTTATACCCTTTA‑ATGTTc                                                                                <  1:248825/149‑1 (MQ=255)                                                               gcgACTCCTTGTCCAGGGCGCGAACGTTTTTGGCATCGATTGTTACCCTTGCCTTTGCTTGAATGTAAGACAGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATCTCAACATTCGATTTATACCCTTTA‑ATGtt                                                                                 >  1:72703/1‑148 (MQ=255)                                                                 gACTCCTTGTCCAGGGCGCGAACGTTTTTGGCATCGATTGTTACCCTTGCCTTTGCTTGAATGTAAGACAGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATCTCAACATTCGATTTATACCCTTTA‑ATGTTCaa                                                                              <  3:140310/149‑1 (MQ=255)                                                                    tCCTTGTCCAGTGCGCGAACGTTTTTGGCATCGATTGTTACCCTTGCCTTTGCTTGAATGTAAGACAGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATCTCAACATTCGATTTATAc                                                                                             <  5:203672/132‑1 (MQ=255)                                                                    tCCTTGTCCAGGGCGCGAACGTTTTTGGCATCGATTGTTACCCTTGCCTTTGCTTGAATGTAAGACAGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATCTCAACATTCGATTTATAc                                                                                             >  6:203672/1‑132 (MQ=255)                                                                    tCCTTGTCCAGGGCGCGAACGTTTTTGGCATCGATTGTTACCCTTGCCTTTGCTTGAATGTAAGACAGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATCTCAACATTCGATTTATACCCTTTA‑ATGTTCAACCa                                                                           >  3:177455/1‑149 (MQ=255)                                                                      cTTGTCCAGGGCGCGAACGTTTTTGGCATCGATTGTTACCCTTGCCTTTGCTTGAATGTAAGACAGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATCTCAACATTCGATTTATACCCTTTA‑ATGTTCAACCAGt                                                                         >  4:41587/1‑149 (MQ=255)                                                                         gTCCAGGGCGCGAACGTTTTTGGCATCGATTGTTACCCTTGCCTTTGCTTGAATGTAAGACAGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATCTCAACATTCGATTTATACCCTTTA‑ATGTTCAACCAGTGa                                                                       <  1:252408/148‑1 (MQ=255)                                                                            catggCGCGAACGTTTTTGGCATCGATTGTTACCCTTGCCTTTGCTTGAATGTAAGACAGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATCTCAACATTCGATTTATACCCTTTA‑ATGTTCAACCAGTGAAAAt                                                                   <  4:17254/146‑1 (MQ=255)                                                                              gggCGCGAACGTTTTTGGCATCGATTGTTACCCTTGCCTTTGCTTGAATGTAAGACAGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATCTCAACATTCGATTTATAACCTTTA‑ATGTTCAACCAGTGAAAATAg                                                                 >  1:184713/1‑149 (MQ=255)                                                                                  gcgAACGTTTTTGGCATCGATTGTTACCCTTGCCTTTGCTTGAATGTAAGACAGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATCTCAACATTCGATTTATACCCTTTA‑ATGTTCAACCAGTGAAAATAGTTGa                                                             <  5:127974/149‑1 (MQ=255)                                                                                                         ttACCCTTTCCTTTGCTTGAATTTAATACAGTAATCTACTTTGATTTAACTAAGCCGTGGACCGCTTAATCTCAATCTAAACATTCGATTTATACCCTTTACATGTTCAACCAGTGAAAATAGTTGAGGATAATCTTTAGGTCTTCAt                                        <  1:232877/148‑1 (MQ=255)                                                                                                            cccTTGCCTTTGCTTGAATGTAAGACAGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATCTCAACATTCGATTTATACCCTTTA‑ATGTTCAACCAGTGAAAATAGTTGAGGATAATCTTTAGGTCTTCATAGACt                                   >  3:147797/1‑149 (MQ=255)                                                                                                                   cTTTGCTTGAATGTAAGACAGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATCTCAAGATTCGATTTATACCCTTTA‑ATGTTCAACCAGTGAAAATAGTTGAGGATAATCTTTAGGTCTTCATAGACT‑GTTTCTg                           <  6:146267/149‑1 (MQ=255)                                                                                                                   cTTTGCTTGAATGTAAGACAGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATCTCAACATTCGATTTATACCCTTTA‑ATGTTCAACCAGTGAAAATAGTTGAGGATAATCTTTAGGTCTTCATAGACT‑GTTTCt                            >  2:209975/1‑148 (MQ=255)                                                                                                                    tttGCTTGAATGTAAGACAGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATCTCAACATTCGATTTATACCCTTTA‑ATGTTCAACCAGTGAAAATAGTTGa                                                             <  3:269410/115‑1 (MQ=255)                                                                                                                    tttGCTTGAATGTAAGACAGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATCTCAACATTCGATTTATACCCTTTA‑ATGTTCAACCAGTGAAAATAGTTGa                                                             >  4:269410/1‑115 (MQ=255)                                                                                                                    tttGCTTGAATGTAAGACAGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATCTCAACATTCGATTTATACCCTTTA‑ATGTTCAACCAGTGAAAATAGTTGa                                                             >  4:274000/1‑115 (MQ=255)                                                                                                                    tttGCTTGAATGTAAGACAGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATCTCAACATTCGATTTATACCCTTTA‑ATGTTCAACCAGTGAAAATAGTTGa                                                             <  3:274000/115‑1 (MQ=255)                                                                                                                    tttGCTTGAATGTAAGACAGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATCTCAACATTCGATTTATACCCTTTA‑ATGTTCAACCAGTGAAAATAGTTGAGGATAATCTTTAGGTCTTCATAGACT‑GTTTCt                            >  2:201200/1‑147 (MQ=255)                                                                                                                      tGCTTGAATGTAAGACAGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATCTCAACATTCGATTTATACCCTTTA‑ATGTTCAACCAGTGAAAATAGTTGAGGATAATCTTTAGGTCTTCATAGACT‑GTTTCTGa                          <  2:72703/147‑1 (MQ=255)                                                                                                                       gCTTGAATGTAAGACAGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATCTCAACATTCGATTTATACCCTTTA‑ATGTTCAACCAGTGAAAATAGTTGAGGATAATCTTTAGGTCTTCATAGACT‑GTTTCTGAgg                        >  7:269246/1‑148 (MQ=255)                                                                                                                        cTTGAATGTAAGACAGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATCTCAACATTCGATTTATACCCTTTA‑ATGTTCAACCAGTGAAAATAGTTGAGGATAATCTTTAGGTCTTCATAGACT‑GTTTCTGAGGaa                      <  4:147797/149‑1 (MQ=255)                                                                                                                        cTTGAATGTAAGACAGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATCTCAACATTCGATTTATACCCTTTA‑ATGTTCAACCAGTGAAAATAGTTGAGGATAATCTTTAGGTCTTCATAGACT‑GTTTCTGAGGa                       <  4:177455/148‑1 (MQ=255)                                                                                                                              tGTAAGACAGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATCTCAACATTCGATTTATACCCTTTA‑ATGTTCAACCAGTGAAAATAGTTGAGGATAATCTTTAGGTCTTCATAGACT‑GTTTCTGAGGAAGGCtt                 >  8:60019/1‑148 (MQ=255)                                                                                                                                tAAGACAGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATCTCAACATTCGATTTATACCCTTTA‑ATGTTCAACCAGTGAAAATAGTTGAGGATAATCTTTAGGTCTTCATAGACT‑GTTTCTGa                          >  7:33897/1‑137 (MQ=255)                                                                                                                                tAAGACAGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATCTCAACATTCGATTTATACCCTTTA‑ATGTTCAACCAGTGAAAATAGTTGAGGATAATCTTTAGGTCTTCATAGACT‑GTTTCTGa                          <  8:33897/137‑1 (MQ=255)                                                                                                                                 aaGACAGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATCTCAACATTCGATTTATACCCTTTA‑ATGTTCAACCAGTGAAAATAGTTGAGGATAATCTTTAGGTCTTCATAGACT‑TTTTCTGAGGATGGATTAAgg             >  4:213288/1‑149 (MQ=255)                                                                                                                                      aGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATCTCAACATTCGATTTATACCCTTTA‑ATGTTCAACCAGTGAAAATAGTTGAGGATAATCTTTAGGTCTTCATAGACT‑GTTTCTGAGGAAGGCTTAAGGCTCTg        <  1:302781/149‑1 (MQ=255)                                                                                                                                      aGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATCTCAACATTCGATTTATACCCTTTA‑ATGTTCAACCAGTGAAAATAGTTGAGGATAATCTTTAGGTCTTCATAGACT‑GTTTCTGAGGAAGGCTTAAGGCTATg        >  3:129258/1‑149 (MQ=255)                                                                                                                                      aGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATCTCAACATTCAATTTATACCCTTTA‑ATGTTCAACCAGTGAAAATAGTTGAGGATAATCTTTAGGTCTTCATAGACT‑GTTTCTGAGGAAGGCTTAAGGCTCTg        <  3:59863/149‑1 (MQ=255)                                                                                                                                           tCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATCTCAACATTCGATTTATACCCTTTA‑ATGTTCAACCAGTGAAAATAGTTGAGGATAATCTTTAGGTCTTCGTAGACT‑GTTTCTGAGGAAGGCTTAAGGCTCTGGGtct   >  6:137877/1‑149 (MQ=255)                                                                                                                                             tACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATCTCAACATTCGATTTATACCCTTTA‑ATGTTCAACCAGTGAAAATAGTTGAGGATAATCTTTAGGTCTTCATAGACTCGTTTCTGAGGAAGGCTTAAGGCTCTGGGtctc  <  1:201200/149‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                                AAAGCTACTGAGGTAGGTCCGAATCTCCGACTGATTTATAAGGGTGCGGCGTTGGGACTGTCGCGACTCCTTGTCCAGGGCGCGAACGTTTTTGGCATCGATTGTTACCCTTGCCTTTGCTTGAATGTAAGACAGTAATCTACTTCGATTGAAGTAAGCCGTGGACCGCTTAAGCTCAATCTCAACATTCGATTTATACCCTTTA‑ATGTTCAACCAGTGAAAATAGTTGAGGATAATCTTTAGGTCTTCATAGACT‑GTTTCTGAGGAAGGCTTAAGGCTCTGGGTCTC  >  NC_002947/2221032‑2221319

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: ‑