Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,079,126	T→A	11.1%	intergenic (‑371/+26)	mgtE ← / ← PP_t56	magnesium transporter/tRNA‑Arg

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,079,126	0	T	A	11.1%	136.9 / 8.4	54	intergenic (‑371/+26)	mgtE/PP_t56	magnesium transporter/tRNA‑Arg
Reads supporting (aligned to +/- strand):  ref base T (25/23);  new base A (3/3);  total (28/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.71e-01

TGCGACGATTGTTGTGGATGGGAAAGCACATTTGATTTTTGAGGCCGCTCAGCGGCTCCAAACTACACCGCAATCATTACAGAAGAGCGTAGATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGCCCGCTCTATTGAGCGGGCTTTTTGATGGGGTATGGCGGACTCAGCAGGATTCGAA‑CCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGATGGTAGTTTTAGACCAGGTTACCACTGGCTTACTGAAATGGC  >  NC_002947/5078987‑5079274                                                                                                                                            |                                                                                                                                                      tGCGACGATTGTTGTGGATGGGAAAGCACATTTGATTTTTGAGGCCGCTCAGCGGCTCCAAACTACACCGCAATCATTACAGAAGAGCGTAGATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGCCCGCTCTATTGAGCgg                                                                                                                                              <  5:87028/149‑1 (MQ=255)   cgacgaTTGTTGTGGATGGGAAAGCACATTTGATTTTTGAGGCCGCTCAGCGGCTCCAAACTACACCGCAATCATTACAGAAGAGCGTAGATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGCCCGCTCTATTGAGCGGGc                                                                                                                                            >  1:218489/1‑149 (MQ=255)    gacgaTTGTTGTGGATGGGAAAGCACATTTGATTTTTGAGGCCGCTCAGCGGCTCCAAACTACACCGCAATCATTACAGAAGAGCGTAGATCGACAGGCTCAAGGATTCATTGGCGCACAAACAAAAAGCCCGCTCTATTGAGCGGGCt                                                                                                                                           >  5:146973/1‑149 (MQ=255)    gacgaTTGTTGTGGATGGGAAAGCACATTTGATTTTTGAGGCCGCTCAGCGGCTCCAAACTACACCGCAATCATTACAGAAGAGCGTAGATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGCCCGCTCTATTGAGCGGGCt                                                                                                                                           >  2:180260/1‑149 (MQ=255)    gacgaTTGTTGTGGATGGGAAAGCACATTTGATTTTTGAGGCCGCTCAGCGGCTCCAAACTACACCGCAATCATTACAGAAGAGCGTAGATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGCCCGCTCAATAGAGCGGGCt                                                                                                                                           <  4:223054/149‑1 (MQ=255)     acgaTTGTTGTGGATGGGAAAGCACATTTGATTTTTGAGGCCGCTCAGCGGCTCCAAACTACACCCCAATCCTTACAGAAGAGCCTAGATCGACAGGCTCAAGAATTCGTTGCCGCACAAACAAAAAGCCCGCGCTATTGAGCGGGCtt                                                                                                                                          <  8:238801/149‑1 (MQ=255)      cgaTTGTTGTGGATGGGAAAGCACATTTGATTTTTGAGGCCGCTCAGCGGCTCCAAACTACACCGCAATCATTACAGAAGAGCGTAGATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGCCCGCTCTATTGAGCGGGCttt                                                                                                                                         <  2:313806/149‑1 (MQ=255)             tgtgGATGGGAAAGCACATTTGATTTTTGAGGCCGCTCAGCGGCTCCAAACTACACCGCAATCATTACAGAAGAGCGTAGATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGCCCGCTCTATTGAGCGGGCTTTTTGATg                                                                                                                                   <  2:62417/148‑1 (MQ=255)              gtgGATGGGAAAGCACATTTGATTTTTGAGGCCGCTCAGCGGCTCCAAACTACACCGCAATCATTACAGAAGAGCGTAGATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGCCCGCTCTATTGAGCGGGCTTTTTGATggg                                                                                                                                 >  5:137728/1‑149 (MQ=255)               tgGATGGGAAAGCACATTTGATTTTTGAGGCCGCTCAGCGGCTCCAAACTACACCGCAATCATTACAGAAGAGCGTAGATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGCCCGCTCAATAGAGCGGGCTTTTTgtttgt                                                                                                                                 <  6:62294/148‑6 (MQ=255)                 gATGGGAAAGCACATTTGATTTTTGAGGCCGCTCAGCGGCTCCAAACTACACCGCAATCATTACAGAAGAGCGTAGATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGCCCGCTCTATTGAGCGGGCTTTTTGATGGGGTa                                                                                                                              >  3:189246/1‑149 (MQ=255)                 gATGGGAAAGCACATTTGATTTTTGAGGCCGCTCAGCGGCTCCAAACTACACCGCAATCATTACAGAAGAGCGTAGATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGCCCGCTCAATAGAGCGGGc                                                                                                                                            >  7:138482/1‑135 (MQ=255)                 gATGGGAAAGCACATTTGATTTTTGAGGCCGCTCAGCGGCTCCAAACTACACCGCAATCATTACAGAAGAGCGTAGATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGCCCGCTCAATAGAGCGGGc                                                                                                                                            <  8:138482/135‑1 (MQ=255)                    gggAAAGCACATTTGATTTTTGAGGCCGCTCAGCGGCTCCAAACTACACCGCAATCATTACAGAAGAGCGTAGATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGACCGCTGTATTGAGCGGGCTTTATGATGGGGTATgg                                                                                                                           >  6:175414/1‑149 (MQ=255)                      gAAAGCACATTTGATTTTTGAGGCCGCTCAGCGGCTCCAAACTACACCGCAATCATTACAGAAGAGCGTAGATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGCCCGCTCTATTGAGCGGGCTTTTTGATGGGGTATGGCg                                                                                                                         >  3:274733/1‑149 (MQ=255)                      gAAAGCACATTTGATTTTTGAGGCCGCTCAGCGGCTCCAAACTACACCGCAATCATTAAAGAAGAGCGTAGATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGCCAGCTCTATTGAGCGGTCTTTTTGATGGGTTATgtc                                                                                                                          >  5:176269/1‑146 (MQ=255)                      gAAAGAACATTTGATTTTTGAGGCCGCTCAGCGGCTCCAAACTACACCGCAATCATTACAGAAGAGCGTAGATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAATCACGCTCTATTGAGCGGGATTTTTGATTGGGTTTGGCg                                                                                                                         >  1:244370/1‑149 (MQ=255)                               tttGATTTTTGAGGCCGCTCAGCGGCTCCAAACTACACCGCAATCATTACAGAAGAGCGTAGATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGCCCGCTCTATTGAGCGGGCtttt                                                                                                                                        <  7:287584/125‑1 (MQ=255)                               tttGATTTTTGAGGCCGCTCAGCGGCTCCAAACTACACCGCAATCATTACAGAAGAGCGTAGATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGCCCGCTCTATTGAGCGGGCtttt                                                                                                                                        >  8:287584/1‑125 (MQ=255)                               tttGATTTTTGAGGCCGCTCAGCGGCTCCAAACTACACCGCAATCATTACAGAAGAGCGTAGATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGCCCGCTCTATTGAGCGGGCTTTTTGATGGGGTATGGCGGACTcagca                                                                                                                <  4:140367/149‑1 (MQ=255)                                  gATTTTTGAGGCCGCTCAGCGGCTCCAAACTACACCGCAATCATTACAGAAGAGCGTAGATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGACCGCTCTATTGAGCGGGCTTTTTGATGGGGTGGAACGGACTCAGCAGGa                                                                                                             >  1:109361/1‑149 (MQ=255)                                    tttttGAGGCCGCTCAGCGGCTCCAAACTACACCGCAATCATTACAGAAGAGCGTAGATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGCCCGCTCTATTGAGCGGGCttt                                                                                                                                         <  2:221302/119‑1 (MQ=255)                                    tttttGAGGCCGCTCAGCGGCTCCAAACTACACCGCAATCATTACAGAAGAGCGTAGATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGCCCGCTCTATTGAGCGGGCttt                                                                                                                                         >  1:221302/1‑119 (MQ=255)                                    tttttGAGGCCGCTCAGCGGCTCCAAACTACACCGCAATCATTACAGAAGAGCGTAGATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGCCCGCTCTATTGAGCGGGCTTTTTGATGGGGTATGGc                                                                                                                          >  2:173959/1‑134 (MQ=255)                                    tttttGAGGCCGCTCAGCGGCTCCAAACTACACCGCAATCATTACAGAAGAGCGTAGATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGCCCGCTCTATTGAGCGGGCTTTTTGATGGGGTATGGc                                                                                                                          <  1:173959/134‑1 (MQ=255)                                    tttttGAGGCCGCTCAGCGGCTCCAAACTACACCGCAATCATTACAGAAGAGCGTAGATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGCCCGCTCTATTGAGCGGGCTTTTTGATGGGGTATGGCGGACTCAGCAGGAt                                                                                                            <  5:270861/148‑1 (MQ=255)                                                cTCAGCGGCTCCAAACTACACCGCAATCATTACAGAAGAGCGTAGATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGCCCGCTCTATTGAGCGGGCTTTTTGATGGGGTATGGCGGACTCAGCAGG‑TTCGAATCCTGctga                                                                                              <  4:222914/149‑4 (MQ=255)                                                       gCTCCAAACTACACCGCAATCATTACAGAAGAGCGTAGATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGCCCGCTCTATTGAGCGGGCTTTTTGATGGGGTATGGCGGACTCAGCAGGATTCGAA‑CCTGCGACCGCTCgg                                                                                       >  4:51486/1‑149 (MQ=255)                                                                     cGCAATCATTACAGAAGAGCGTAGATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGCCCGCTCTATTGAGCGGGCTTTTTGATGGGGTATGGCGGACTCAGCAGGATTCGAA‑CCTGCGACCGCTCGGTTCGTAGCCGAGTa                                                                         >  3:246908/1‑149 (MQ=255)                                                                       cAATCATTACAGAAGAGCGTAGATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGCCCGCTCTATTGAGCGGGCTTTTTGATGGGGTATGGCGGACTCAGCAGGATTCGAA‑CCTGCGACCGCTCGGTTCGTAGCCGAGTAct                                                                       <  4:189246/149‑1 (MQ=255)                                                                        aaTCATTACAGAAGAGCGTAGATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGCCCGCTCTATTGAGCGGGCTTTTTGATGGGGTATGGCGGACTCAGCAGGATTCGAA‑CCTGCGACCGCTCGGTTc                                                                                    <  7:295203/135‑1 (MQ=255)                                                                        aaTCATTACAGAAGAGCGTAGATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGCCCGCTCTATTGAGCGGGCTTTTTGATGGGGTATGGCGGACTCAGCAGGATTCGAA‑CCTGCGACCGCTCGGTTc                                                                                    >  8:295203/1‑135 (MQ=255)                                                                          tCATTACAGAAGAGCGTAGATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGCCCGCTCTATTGAGCGGGCTTTTTGATGGGGTATGGCGGACTCAGCAGGATTCGAA‑CCTg                                                                                                  >  7:28961/1‑119 (MQ=255)                                                                          tCATTACAGAAGAGCGTAGATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGCCCGCTCTATTGAGCGGGCTTTTTGATGGGGTATGGCGGACTCAGCAGGATTCGAA‑CCTg                                                                                                  <  8:28961/119‑1 (MQ=255)                                                                            aTTACAGAAGAGCGTAGATCGACAGGCTCAAGGATTCATTGGCGCACAAACAAAAAGCCCGCTCTATTGAGCGGGCTTTTTGATGGGGTATGGCGGACTCAGCAGGATTCGAA‑CCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATc                                                                  <  6:146973/149‑1 (MQ=255)                                                                             ttACAGAAGAGCGTAGATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGCCCCGTCTATTGAGCGGGCTTTTTGATGGGGTATGGCGGACTCAGCAGGATTCGAA‑CCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATcc                                                                 <  5:175414/149‑1 (MQ=255)                                                                                 agaagaGCGTAGATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGCCCGCTCTATTGAGCGGGCTTTTTGATGGGGTATGGCGGACTCAGCAGGATTCGAA‑CCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCt                                                             <  1:180260/149‑1 (MQ=255)                                                                                         gTAGATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGCCCGCTCTATTGAGCGGGCTTTTTGATGGGGTATGGCGGACTCAGCAGGATTCGAA‑CCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTAt                                                      >  3:61545/1‑148 (MQ=255)                                                                                          tAGATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGCCCGCTCTATTGAGCGGGCTTTTTGATGGGGTATGGCGGACTCAGCAGGATTCGAA‑CCTGCGACCGCTCGGTTCGTAGcc                                                                              >  1:126105/1‑123 (MQ=255)                                                                                            gATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGCCCGCTCTATTGAGCGGGCTTTTTGATGGGGTATGGCGGACTCAGCAGGATTCGAA‑CCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGt                                                  >  6:275647/1‑149 (MQ=255)                                                                                                gACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGCCCCCTCTATTGAGCGGGCTTTTTGATGGGGTATGGCGGACTCAGCAGGATTCGAA‑CCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCg                                               <  5:275647/148‑1 (MQ=255)                                                                                                  cAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGCCCGCTCTATTGAGCGGGCTTTTTGATGGGGTATGGCGGACTCAGCAGGATTCGAA‑CCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGa                                            <  3:223857/149‑1 (MQ=255)                                                                                                       tCAAGAATTCATTGGCGCACAAACAAAAAGCCCGCTCTATTGAGCGGGCTTTTTGATGGGGTATGGCGGACTCAGCAGGATTCGAA‑CCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGAt                                           >  5:232831/1‑145 (MQ=255)                                                                                                       tCAAGAATTCATTGGCGCACAAACAAAAAGCCCGCTCTATTGAGCGGGCTTTTTGATGGGGTATGGCGGACTCAGCAGGATTCGAA‑CCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGAt                                           <  6:232831/145‑1 (MQ=255)                                                                                                       tCAAGAATTCATTGGCGCACAAACAAAAAGCCCGCTCTATTGAGCGGGCTTTTTGATGGGGTATGGCGGACTCAGCAGGATTCGAA‑CCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGATgg                                         >  3:224858/1‑147 (MQ=255)                                                                                                             aTTCATTGGCGCACAAACAAAAAGCCCGCTCTATTGAGCGGGCTTTTTGATGGGGTATGGCGGACTCAGCAGGATTCGAA‑CCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGATGGTAGTTTTa                                 <  4:61545/149‑1 (MQ=255)                                                                                                              ttCATTGGCGCACAAACAAAAAGCCCGCTCTATTGAGCGGGCTTTTTGATGGGGTATGGCGGACTCAGCAGGATTCGAA‑CCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGATGGTAGTTTTAg                                <  3:51486/149‑1 (MQ=255)                                                                                                                         cccatcaaaAAGCCCGCTCAATAGAGCGGGCTTTTTGATGGGGTATGGCGGACTCAGCAGGATTCGAA‑CCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGATGGTAGTTTTAGACCAGGTTAc                      >  4:233581/6‑148 (MQ=255)                                                                                                                           aaacaaaAAGCCCGCTCTATTGAGCGGGCTTTTTGATGGGGTATGGCGGACTCAGCAGGATTCGAA‑CCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGATGGTAGTTTTAGACCAGGTTACCAc                   >  1:281499/1‑149 (MQ=255)                                                                                                                             tcaaaAAGCCCGCTCAATAGAGCGGGCTTTTTGATGGGGTATGGCGGACTCAGCAGGATTCGAA‑CCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGATGGTAGTTTTAGACCAGGTTACCACTg                 >  8:117249/2‑149 (MQ=255)                                                                                                                                aaaaGCCCGCTCTATTGAGCGGGCTTTTTGATGGGGTATGGCGGACTCAGCAGGATTCGAA‑CCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGATGGTAGTTTTAGACCAGGTTACCACTGGCt              >  5:314011/1‑149 (MQ=255)                                                                                                                                    gCCCGCTCTATTGAGCGGGCTTTTTGATGGGGTATGGCGGACTCAGCAGGATTCGAA‑CCTGCGACCGCTCGGTTCGTAGc                                                                               <  2:310547/80‑1 (MQ=255)                                                                                                                                    gCCCGCTCTATTGAGCGGGCTTTTTGATGGGGTATGGCGGACTCAGCAGGATTCGAA‑CCTGCGACCGCTCGGTTCGTAGc                                                                               >  1:310547/1‑80 (MQ=255)                                                                                                                                     cccGCTATATTGAGCGGGATTTTTGATGGGGTATGGCGGACTCAGCAGGATTCGAA‑CCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGATGGTAGTTTTAGACCAGGTTACCACTGGCTTACTg         <  6:176269/149‑1 (MQ=255)                                                                                                                                            tATTGAGCGGGCTTTTTGATGGGGTATGGCGGACTCAGCAGGATTCGAA‑CCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGATGGTAGTTTTa                                 <  4:44232/118‑1 (MQ=255)                                                                                                                                            tATTGAGCGGGCTTTTTGATGGGGTATGGCGGACTCAGCAGGATTCGAA‑CCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGATGGTAGTTTTAGACCAGGTTACCACTGGCTTACTGAAATGGc  >  2:149903/1‑149 (MQ=255)                                                                                                                                            |                                                                                                                                                      TGCGACGATTGTTGTGGATGGGAAAGCACATTTGATTTTTGAGGCCGCTCAGCGGCTCCAAACTACACCGCAATCATTACAGAAGAGCGTAGATCGACAGGCTCAAGAATTCATTGGCGCACAAACAAAAAGCCCGCTCTATTGAGCGGGCTTTTTGATGGGGTATGGCGGACTCAGCAGGATTCGAA‑CCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGATGGTAGTTTTAGACCAGGTTACCACTGGCTTACTGAAATGGC  >  NC_002947/5078987‑5079274

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: ‑