Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,941,390	T→G	7.4%	F208V (TTT→GTT)	PP_2574 →	LysR family transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,941,390	0	T	G	7.4%	163.3 / 3.3	54	F208V (TTT→GTT)	PP_2574	LysR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base T (25/25);  new base G (2/2);  total (27/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.29e-01

TCGAGGCCGAGCCGCTGATGCCGCCGCAGAAGCCCTATGTGCTGCTACCCGAGAACCACCGCTTTGCCAGCCAGGCCCAGGTCTCGCTGCGCGACCTGTGCCCGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCAGTTCACCGTCGATCGAGATGGTGCGCGGCATGGTCGGTCAGGGTTTCGGTTTTTCGTTGCTGGTAACCCGTCCGCACTCGGAATACACCTAT  >  NC_002947/2941244‑2941530                                                                                                                                                   |                                                                                                                                              tCGAGGCCGAGCCGCTGATGCCGCCGCAGAAGCCCTATGTGCTGCTACCCGAGAACCACCGCTTTGCCAGCCAGGCCCAGGTCTCGCTGCGCGACCTGTGCCCGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACttt                                                                                                                                             <  3:20545/149‑1 (MQ=255) tCGAGGCCGAGCCGCTGATGCCGCCGCAGAAGCCCTATGTGCTGCTACCCGAGAACCACCGCTTTGCCAGCCAGGCCCAGGTCTCGCTGCGCGACCTGTGCCCGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACtt                                                                                                                                              <  4:225614/148‑1 (MQ=255)           gCCGCTGATGCCGCCGCAGAAGCCCTATGTGCTGCTACCCGAGAACCACCGCTTTGCCAGCCAGGCCCAGGTCTCGCTGCGCGACCTGTGCCCGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGt                                                                                                                                   <  4:176967/149‑1 (MQ=255)             cGCTGATGCCGCCGCAGAAGCCCTATGTGCTGCTACCCGAGAACCACCGCTTTGCCAGCCAGGCCCAGGTCTCGCTGCGCGACCTGTGCCCGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGtt                                                                                                                                  >  1:180289/1‑148 (MQ=255)                  aTGCCGCCGCAGAAGCCCTATGTGCTGCTACCCGAGAACCACCGCTTTGCCAGCCAGGCCCAGGTCTCGCTGCGCGACCTGTGCCCGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAAc                                                                                                                              >  6:66797/1‑147 (MQ=255)                      cgccgcAGAAGCCCTATGTGCTGCTACCCGAGAACCACCGCTTTGCCAGCCAGGCCCAGGTCTCGCTGCGCGACCTGTGCCCGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATg                                                                                                                        <  5:66797/149‑1 (MQ=255)                       gccgcAGAAGCCCTATGTGCTGCTACCCGAGAACCACCGCTTTGCCAGCCAGGCCCAGGTCTCGCTGCGCGACCTGTGCCCGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATgg                                                                                                                       >  3:144305/1‑149 (MQ=255)                                gCCCTATGTGCTGCTACCCGAGAACCACCGCTTTGCCAGCCAGGCCCAGGTCTCGCTGCGCGACCTGTGCCCGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAc                                                                                                              >  2:320025/1‑149 (MQ=255)                                      tgtcCTGATACCCGAGAACCACCGCTTTGCCAGCCAGGCCCAGGTCTCGCTGCGCGACCTGTGACCGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACCTACTTTGACAGCTTGTTCAACGAGATGCGCCTGGCAC‑CGAACa                                                                                                       >  4:160664/1‑149 (MQ=255)                                             ctACCCGAGAACCACCGCTTTGCCAGCCAGGCCCAGGTCTCGCTGCGCGACCTGTGCCCGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTc                                                                                                  <  5:113228/147‑1 (MQ=255)                                             ctACCCGAGAACCACCGCTTTGCCAGCCAGGCCCAGGTCTCGCTGCGCGACCTGTGCCCGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCtt                                                                                                <  4:282220/149‑1 (MQ=255)                                               aCCCGAGAACCACCGCTTTGCCAGCCAGGCCCAGGTCTCGCTGCGCGACCTGTGCCCGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCtt                                                                                                >  2:151255/1‑147 (MQ=255)                                                cccGAGAACCACCGCTTTGCCAGCCAGGCCCAGGTCTCGCTGCGCGACCTGTGCCCGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCAg                                                                                             <  3:160664/149‑1 (MQ=255)                                                   gagaACCACCGCTTTGCCAGCCAGGCCCAGGTCTCGCTGCGCGACCTGTGCCCGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCAGTTc                                                                                          <  5:94562/149‑1 (MQ=255)                                                    agaACCACCGCTTTGCCAGCCAGGCCCAGGTCTCGCTGCGCGACCTGTGCCCGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCAGTTCa                                                                                         >  7:156208/1‑149 (MQ=255)                                                       accaccGCTTTGCCAGCCAGGCCCAGGTCTCGCTGCGCGACCTGTGCCCGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCAGTTCACCg                                                                                      <  8:142014/149‑1 (MQ=255)                                                          accGCTTTGCCAGCCAGGCCCAGGTCTCGCTGCGCGACCTGTGCCCGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCCCGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCAGTTCACCGtcg                                                                                   >  5:28373/1‑149 (MQ=255)                                                            cGCTTTGCCAGCCAGGCCCAGGTCTCGCTGCGCGACCTGTGCCCGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCa                                                                                              >  2:74898/1‑136 (MQ=255)                                                            cGCTTTGCCAGCCAGGCCCAGGTCTCGCTGCGCGACCTGTGCCCGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGCCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCa                                                                                              <  1:74898/136‑1 (MQ=255)                                                              cTTTGCCAGCCAGGCCCAGGTCTCGCTGCGCGACCTGTGCCCGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCAGTTCACCGtcgatcg                                                                               <  8:72248/149‑1 (MQ=255)                                                                   ccagccagGCCCAGGTCTCGCTGCGCGACCTGTGCCCGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCAGTTCACCGTCGATCGAGATg                                                                          <  2:180289/149‑1 (MQ=255)                                                                    cagccagGCCCAGGTCTCGCTGCGCGACCTGTGCCCGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCAGTTCACCGtcgatcga                                                                              <  4:71279/144‑1 (MQ=255)                                                                    cagccagGCCCAGGTCTCGCTGCGCGACCTGTGCCCGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCAGTTCACCGtcgatcga                                                                              >  3:71279/1‑144 (MQ=255)                                                                     agccagGCCCAGGTCTCGCTGCGCGACCTGTGCCCGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATg                                                                                                                        <  8:164258/102‑1 (MQ=255)                                                                     agccagGCCCAGGTCTCGCTGCGCGACCTGTGCCCGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATg                                                                                                                        >  7:164258/1‑102 (MQ=255)                                                                         agGCCCAGGTCTCGCTGCGCGACCTGTGCCCGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCAGTTCACCGTCGATCGAGATGGTgcgc                                                                    <  1:320025/149‑1 (MQ=255)                                                                           gCCCAGGTCTCGCTGCGCGACCTGTGCCCGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCAGTTCACCGTCGATCGAGATGGTGCGCgg                                                                  >  8:207517/1‑149 (MQ=255)                                                                            cccAGGTCTCGCTGCGCGACCTGTGCCCGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGa                                                                                                          <  2:170611/108‑1 (MQ=255)                                                                            cccAGGTCTCGCTGCGCGACCTGTGCCCGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGa                                                                                                          >  1:170611/1‑108 (MQ=255)                                                                            cccAGGTCTCGCTGCGCGACCTGTGCCCGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCAGTTCACCGTCGATCGAGATGGTGCGCgg                                                                  >  3:49003/1‑148 (MQ=255)                                                                             ccAGGTCTCGCTGCGCGACCTGTGCCCGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCAGTTCACCGTCGATCGAGATGGTGCACGGCa                                                                >  4:88911/1‑149 (MQ=255)                                                                                                cTGTGCCCGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCAGTTCACCGTCGATCGAGATGGTGCGCGGCATggt                                                            <  3:97148/134‑1 (MQ=255)                                                                                                cTGTGCCCGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCAGTTCACCGTCGATCGAGATGGTGCGCGGCATggt                                                            >  4:97148/1‑134 (MQ=255)                                                                                                     cccGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCAGTTCACCGTCGATCGAGATGGTGCGCGGCATGGTCGGTCAGGGTTTCGGttttt                                        >  7:141911/1‑149 (MQ=255)                                                                                                     cccGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCAGTTCACCGTCGATCGAGATGGTGCGCGGCATGGTCGGTCAGGGTTTCGGtttt                                         <  4:49003/148‑1 (MQ=255)                                                                                                      ccGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCAGTTCACCGTCGATCGAGATGGTGCGCGGCATGGTCGGTCAGGGTTTCGGttttt                                        >  3:312993/1‑148 (MQ=255)                                                                                                      ccGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCAGTTCACCGTCGATCGAGATGGTGCGCGGCATGGTCGGTCAGGGTTTCGGttttt                                        <  4:312993/148‑1 (MQ=255)                                                                                                      ccGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCAGTTCACCGTCGATCGAGATGGTGCGCGGCATGGTCGGTCAGGGTTTCGGTTTTTc                                       >  1:45305/1‑149 (MQ=255)                                                                                                       cGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACGTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCAGTTCACCGTCGATCGAGATGGTGCGCGGCATGGTCGGTCAGGGTTTCGGTTTTTCg                                      >  3:205563/1‑149 (MQ=255)                                                                                                       cGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACGTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCAGTTCACCGTCGATCGAGATGGTGCGCGGCATGGTCGGTCAGGGTTTCGGTTTTTCg                                      >  3:201022/1‑149 (MQ=255)                                                                                                             cGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCAGTTCACCGTCGATCGAGATGGTGCGCGGCATGGTCGGTCAGGGTTTCGGTTTTTCGTTGCTg                                <  8:141911/149‑1 (MQ=255)                                                                                                              gatgatCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCAGTTCACCGtg                                                                                    >  1:291243/1‑95 (MQ=255)                                                                                                              gatgatCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCAGTTCACCGtc                                                                                    <  2:291243/96‑1 (MQ=255)                                                                                                                  atCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCAGTTCACCGTCGATCGAGATGGTGCGCGGCATGGTCGGTCAGGGTTTCGGTTTTTCGTTGCTGGTaa                            <  2:45305/148‑1 (MQ=255)                                                                                                                  atCCTGCAGTACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCAGTTCACCGTCGATCGAGATGGTGCGCGGCATGGTCGGTCAGGGTTTCGGTTTTTCGTTGCTGGTAAc                           <  8:156208/149‑1 (MQ=255)                                                                                                                    ccTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCAGTTCACCGTCGATCGAGATGGTGCGCGGCATGGTCGGTCAGGGTTTCGGTTTTTCGTTGCTGGTAAccc                         >  5:34017/1‑149 (MQ=255)                                                                                                                              gtcgCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCAGTTCACCGTCGATCGAGATGGTGCGCGGCATGGTCGGTCAGGGTTTCGGTTTTTCGTTGCTGGTAACCCGTCCGCACTc               >  2:47177/4‑149 (MQ=255)                                                                                                                              ggggCCCCTAGCCGCACGTTCTTTGTCAGGGTGTTGAACGTTCTGGGCCTGGCAC‑CGAACATCGTCTTCAGTTCACCGTCGATCGAGATGGTGCGCGGCATGGTCGGTCAGGGTTTCGGTTTTTCGTTGCTGGTAACCCGTCCGCACTc               <  3:19449/147‑1 (MQ=255)                                                                                                                              gTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCACGCGAACATCGTCTTCAGTTCACCGTCGATCGAGATGGTGCGCGGCATGGTCGGTCAGGGTTTCGGTTTTTCGTTGCTGGTAACCCGTCCGCACt                >  1:99004/1‑149 (MQ=255)                                                                                                                                 gCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCAGTTCACCGTCGATCGAGATGGTGCGCGGCATGGTCGGTCAGGGTTTCGGTTTTTCGTTGCTGGTAACCCGTCCGCACTCGGa            <  6:34017/149‑1 (MQ=255)                                                                                                                                 gCCCCTAGCCGCACGTACGTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCAGTTCACCGTCGATCGAGATGGTGCGCGGCATGGTCGGTCAGGGTTTCGGTTTTTCGTTGCTGGTAACCCGTCCGCACTCGGa            <  4:201022/149‑1 (MQ=255)                                                                                                                                 gCCCCTAGCCGCACGTACGTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCAGTTCACCGTCGATCGAGATGGTGCGCGGCATGGTCGGTCAGGGTTTCGGTTTTTCGTTGCTGGTAACCCGTCCGCACTCGGa            <  4:205563/149‑1 (MQ=255)                                                                                                                                    ccTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCAGTTCACCGTCGATCGAGATGGTGCGCGGCATGGTCGGTCAGGGTTTCGGTTTTTCGTTGCTGGTAACCCGTCCGCACTCGGAAt          >  5:94016/1‑148 (MQ=255)                                                                                                                                     cTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCAGTTCACCGTCGATCGAGATGGTGCGCGGCATGGTCGGTCAGGGTTTCGGTTTTTCGTTGCTGGTAACCCGTCCGCACTCGGAATac        <  4:144305/149‑1 (MQ=255)                                                                                                                                        gCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCAGTTCACCGTCGATCGAGATGGTGCGCGGCATGGTCGGTCAGGGTTTCGGTTTTTCGTTGCTGGTAACCCGTCCGCACTCGGAATacac      <  1:47177/148‑1 (MQ=255)                                                                                                                                           gCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCAGTTCACCGTCGATCGAGATGGTGCGCGGCATGGTCGGTCAGGGTTTCGGTTTTTCGTTGCTGGTAACCCGTCCGCACTCGGAATACACCTAt  >  4:194816/1‑149 (MQ=255)                                                                                                                                                   |                                                                                                                                              TCGAGGCCGAGCCGCTGATGCCGCCGCAGAAGCCCTATGTGCTGCTACCCGAGAACCACCGCTTTGCCAGCCAGGCCCAGGTCTCGCTGCGCGACCTGTGCCCGGAGCCGATGATCCTGCTGGACGTGGCCCCTAGCCGCACGTACTTTGTCAGCTTGTTCAACGAGATGGGCCTGGCAC‑CGAACATCGTCTTCAGTTCACCGTCGATCGAGATGGTGCGCGGCATGGTCGGTCAGGGTTTCGGTTTTTCGTTGCTGGTAACCCGTCCGCACTCGGAATACACCTAT  >  NC_002947/2941244‑2941530

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: ‑