Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,162,527	G→A	9.1%	intergenic (+474/‑106)	PP_2776 → / → PP_2777	homocysteine S‑methyltransferase family protein/acyl carrier protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,162,527	0	G	A	9.1%	117.1 / 2.4	44	intergenic (+474/‑106)	PP_2776/PP_2777	homocysteine S‑methyltransferase family protein/acyl carrier protein
Reads supporting (aligned to +/- strand):  ref base G (19/21);  new base A (2/2);  total (21/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.69e-01

GGAACTATCGTGCTGTTTCAAGCAATCGATTTTGTCATTTTACGACCCCTCTCCAAGCCCCATTGAGCTGCATGAATCAAAG‑‑GTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTATTCATTCAATGCGGCTTTTGTAGGGAAACACTCAATGAATAATCCGTTGGAATTGGACAGCGTCAT  >  NC_002947/3162384‑3162664                                                                                                                                                  |                                                                                                                                          ggAACTATCGTGCTGTTTCAAGCAATCGATTTTGTCATTTTAAGAACCCTCTGCAAGCCCCATTTAGCTGCATTAATCAAAGTAGTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAggg                                                                                                                                         <  1:261186/148‑1 (MQ=255)  gAACTATCGTGCTGTTTCAAGCAATCGATTTTGTCATTTTACGACCCCTCTCCAAGCCCCATTGAGCTGCATGAATCAAAG‑‑GTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAgggg                                                                                                                                        <  6:96279/146‑1 (MQ=255)   aaCTATCGTGCTGTTTCAAGCAATCGATTTTGTCATTTTACGACCCCTCTCCAAGCCCCATTGAGCTGCATGAATCAAAG‑‑GTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGgaga                                                                                                                                    <  7:206054/149‑1 (MQ=255)      tATCGTGCTGTTTCAAGCAATCGATTTTGTCATTTTACGACCCCTCTCCAAGCCCCATTGAGCTGCATGAATCAAAG‑‑GTTTCAGTGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCCTAAGGGgaga                                                                                                                                    <  7:117706/146‑1 (MQ=255)      tATCGTGCTGTTTCAAGCAATCGATTTTGTCATTTTACGACCCCTCTCCAAGCCCCATTGAGCTGCATGAATCAAAG‑‑GTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCCTAAGGGgaga                                                                                                                                    >  8:117706/1‑146 (MQ=255)      tATCGTGCTGTTTCAAGCAATCGATTTTGTCATTTTACGACCCCTCTCCAAGCCCCATTGAGCTGCATGAATCAAAG‑‑GTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTCACTCTCCGATTAGGGGGAGCCtt                                                                                                                                 >  8:249269/1‑149 (MQ=255)        tCGTGCTGTTTCAAGCAATCGATTTTGTCATTTTACGACCCCTCTCCAAGCCCCATTGAGCTGCATGAATCAAAG‑‑GTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACtt                                                                                                                                 <  1:51660/147‑1 (MQ=255)        tCGTGCTGTTTCAAGCAATCGATTTTGTCATTTTACGACCCCTCTCCAAGCCCCATTGAGCTGCATGAATCAAAG‑‑GTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTa                                                                                                                               >  7:228675/1‑149 (MQ=255)             cTGTTTCAAGCAATCGATTTTGTCATTTTACGACCCCTCTCCAAGCCCCATTGAGCTGCATGAATCAAAG‑‑GTTTCAGGGAGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGCCTCGACCCTTAGGGGGTCGCTTTAGACTc                                                                                                                          >  2:295344/1‑149 (MQ=255)              tGTTTCAAGCAATCGATTTTGTCATTTTACGACCCCTCTCCAAGCCCCATTGAGCTGCATGAATCAAAG‑‑GTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTcc                                                                                                                         >  3:217676/1‑149 (MQ=255)                tttCAAGCAATCGATTTTGTCATTTTACGACCCCTCTCCAAGCCCCATTGAGCTGCATGAATCAAAG‑‑GTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGTCTAAAGTCTccc                                                                                                                        <  4:179700/148‑1 (MQ=255)                tttCAAGCAATCGATTTTGTCATTTTACGACCCCTCTCCAAGCCCCATTGAGCTGCATGAATCAAAG‑‑GTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACtt                                                                                                                                 <  7:173707/139‑1 (MQ=255)                tttCAAGCAATCGATTTTGTCATTTTACGACCCCTCTCCAAGCCCCATTGAGCTGCATGAATCAAAG‑‑GTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACtt                                                                                                                                 >  8:173707/1‑139 (MQ=255)                  tCAAGCAATCGATTTTGTCATTTTACGACCCCTCTCCAAGCCCCATTGAGCTGCATGAATCAAAG‑‑GTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACttt                                                                                                                                >  2:253272/1‑138 (MQ=255)                  tCAAGCAATCGATTTTGTCATTTTACGACCCCTCTCCAAGCCCCATTGAGCTGCATGAATCAAAG‑‑GTTTCAGGGCGCGCTGGCATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACttt                                                                                                                                <  1:253272/138‑1 (MQ=255)                   cAAGCAATCGATTTTGTCATTTTACGACCCCTCTCCAAGCCCCATTGAGCTGCATGAATCAAAG‑‑GTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGTCTAAAGTCTccccct                                                                                                                     <  5:245135/148‑4 (MQ=255)                   cAAGCAATCGATTTTGTCATTTTACGACCCCTCTCCAAGCCCCATTGAGCTGCATGAATCAAAG‑‑GTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCACTTAGGGGGAGACTTTAGACTCCCGGcc                                                                                                                    >  4:87851/1‑149 (MQ=255)                         aTCGATTTTGTCATTTTACGACCCCTCTCCAAGCCCCATTGAGCTGCATGAATCAAAG‑‑GTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGa                                                                                                               >  6:111861/1‑148 (MQ=255)                          tCGATTTTGTCATTTTACGACCCCTCTCCAAGACCCATTGAGCTGCATGAATCAAAG‑‑GTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGa                                                                                                               >  6:151811/1‑147 (MQ=255)                                 tGTCATTTTACGACCCCTCTCCAAGCCCCATTGAGCTGCATGAATCAAAG‑‑GTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTg                                                                                                       <  3:29568/148‑1 (MQ=255)                                              ccccTCTCCAAGCCCCATTGAGCTGCATGAATCAAAG‑‑GTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCt                                                                                         >  2:182329/1‑149 (MQ=255)                                               cccTCTCCAAGCCCCATTGAGCTGCATGAATCAAAG‑‑GTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCtt                                                                                        >  8:2173/1‑149 (MQ=255)                                                      cAAGCCCCATTGAGCTGCATTAATCAAAG‑‑GTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTgg                                                                                 <  7:118796/149‑1 (MQ=255)                                                          ccccATTGAGCTGCATGAATCAAAG‑‑GTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCt                                                                                                        >  4:160962/1‑122 (MQ=255)                                                          ccccATTGAGCTGCATGAATCAAAG‑‑GTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCt                                                                                                        <  3:160962/122‑1 (MQ=255)                                                                   gCTGCATGAATCAAAG‑‑GTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGTGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTTGCCTGAAAACAGCTTTTTTTGGCCCGATGACTTTa                                                                    <  1:295344/149‑1 (MQ=255)                                                                    cTGCATGAATCAAAG‑‑GTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTat                                                                   <  5:111861/149‑1 (MQ=255)                                                                      gCATGAATCAAAG‑‑GTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGAGTTTattc                                                                 >  2:238557/1‑149 (MQ=255)                                                                         tGAATCAAAG‑‑GTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCAGGCACCCGATAGATATGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTattcatt                                                              >  2:40195/1‑149 (MQ=255)                                                                                       ttCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTATTCATTCAATGCGGCttt                                                  >  1:153246/1‑149 (MQ=255)                                                                                        tCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTATTCATTCAATGCGGCttt                                                  <  8:228675/148‑1 (MQ=255)                                                                                          aGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCTGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGAAGACTTTATTCATTCAATGCGGCTTTTGt                                               <  1:182329/149‑1 (MQ=255)                                                                                           gggCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTATTCATTCAATGCGGCTTTTGTa                                              <  6:158623/149‑1 (MQ=255)                                                                                             gggcgcTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTATTCATTCAATGCGGCTTTTGTAg                                             <  7:249269/146‑1 (MQ=255)                                                                                                              acaAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTATTCATTCAATGCGGCTTTTGTAGGGAAACACTCAATGaat                            >  3:210388/1‑148 (MQ=255)                                                                                                                 aaaaGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTATTCATTCAATGCGGCTTTTGTAGGGAAACACTCAATGAATAATc                        <  5:151811/149‑1 (MQ=255)                                                                                                                      cACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTATTCATTCAATGCGGCTTTTGTAGGGAAACACTCAATGAATAATCCGTTg                   <  3:87851/149‑1 (MQ=255)                                                                                                                            tGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTATTCATTCAATGCGGCTTTTGTAGGGAAACACTCAATGAATAATCCGTTGGAAtt              <  7:10850/148‑1 (MQ=255)                                                                                                                              gCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTATTCATTCAATGCGGCTTTTGTAgg                                            <  7:116268/116‑1 (MQ=255)                                                                                                                              gCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTATTCATTCAATGCGGCTTTTGTAgg                                            >  8:116268/1‑116 (MQ=255)                                                                                                                               cccGTTGCCTCGCCGCTGAGGGGGAGACTTTAGACTCCCGGCCACCTATAGATCTGGCCTCAAAACATCTTTTTTTGGCCCGATGACTTTATTCATTCAATGCGGCTTTTGTAGGGAAACACTCAATGAATAATCCGTTGGAATTGGAc          <  4:217676/147‑1 (MQ=255)                                                                                                                                  gTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTATTCATTCAATGCGGCTTTTGTAGGGAAACACTCAATGAATAATCCGTTGGAATTGGACAGc       <  7:2173/149‑1 (MQ=255)                                                                                                                                   taaagtctcCCCCTAAGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTATTCATTCAATGCGGCTTTTGTAGGGAAacac                                     <  6:115606/113‑1 (MQ=255)                                                                                                                                   taaagtctcCCCCTAAGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTATTCATTCAATGCGGCTTTTGTAGGGAAacac                                     >  5:115606/6‑118 (MQ=255)                                                                                                                                        tctcCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTATTCATTCAATGCGGCTTTTGTAGGGAAACACTCAATGAATAATCCGTTGGAATTGGACAGCGtcat  >  5:207852/1‑148 (MQ=255)                                                                                                                                        tctcCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTGTTTTTGGCCCGATGACTTTATTCATTCAATGCGGCTTTTGTGGGGAAACACTCAATGAATAATCCGTTGGAAGTGGAGAGGGtcat  >  4:55070/1‑148 (MQ=255)                                                                                                                                                  |                                                                                                                                          GGAACTATCGTGCTGTTTCAAGCAATCGATTTTGTCATTTTACGACCCCTCTCCAAGCCCCATTGAGCTGCATGAATCAAAG‑‑GTTTCAGGGCGCGCTGGGATTTCTCACAAAAAGCACTGATGGCACGTTGACTCTCCCCTTAGGGGGAGACTTTAGACTCCCGGCCCCCGATAGATCTGGCCTCAAAACAGCTTTTTTTGGCCCGATGACTTTATTCATTCAATGCGGCTTTTGTAGGGAAACACTCAATGAATAATCCGTTGGAATTGGACAGCGTCAT  >  NC_002947/3162384‑3162664

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: ‑