Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,491,228	A→C	7.7%	L55V (TTG→GTG)	clpV ←	protein ClpV1

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,491,228	0	A	C	7.7%	156.9 / 4.3	52	L55V (TTG→GTG)	clpV	protein ClpV1
Reads supporting (aligned to +/- strand):  ref base A (26/22);  new base C (2/2);  total (28/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.91e-01

GTAATGTGCGGCGACAGCGCCGGGGTGCGGGTATTACCTTTCTTGAAGGTGCCCAGGGCGGTGACCAGCTGCGCTTGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGGTCGCTGTCGTTGTTGTC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGAACAGAGACTTCAGGTTCACAAGGCGACCCCATCGTAAGGAATG  >  NC_002947/3491083‑3491375                                                                                                                                                   |                                                                                                                                                    gTAATGTGCGGCGACAGCGCCGGGGTGCGGGTATTACCTTTCTTGAAGGTGCCCAGGGCGGTGACCAGCTGCGCTTGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGGTCGCTGTCGTTGTTGTC‑GAGCAACTg                                                                                                                                                  >  3:324086/1‑149 (MQ=255)        gcggcgACAGCGCCGGGGTGCGGGTATTACCTTTCTTGAAGGTGCCCAGGGCGGTGACCAGCTGCGCTTGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGGTCGCTGTCGTTGTTGTC‑GAGCAACTgcagcag                                                                                                                                            >  4:218537/1‑148 (MQ=255)         cggcgACAGCGCCGGGGTGCGGGTATTACCTTTCTTGAAGGTGCCCAGGGCGGTGACCAGCTGCGCTTGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGGTCGCTGTCGTTGTTGTC‑GAGCAACTgcagcagca                                                                                                                                          <  4:324086/149‑1 (MQ=255)             gACAGCGCCGGGGTGCGGGTATTACCTTTCTTGAAGGTGCCCAGGGCGGTGACCAGCTGCGCTTGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGGTCGCTGTCGTTGTTGTC‑GAGCAACTGCAGCAGCAGGTg                                                                                                                                      >  2:166880/1‑149 (MQ=255)                           gCGGGTATTACCTTTCTTGAAGGTGCCCAGGGCGGTGACCAGCTGCGCTTGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGGTCGCTGTCGTTGTTGTC‑GAGCAACTGCAGCAGCAGGTGCTCCAc                                                                                                                                <  2:307634/141‑1 (MQ=255)                           gCGGGTATTACCTTTCTTGAAGGTGCCCAGGGCGGTGACCAGCTGCGCTTGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGGTCGCTGTCGTTGTTGTC‑GAGCAACTGCAGCAGCAGGTGCTCCAc                                                                                                                                >  1:307634/1‑141 (MQ=255)                                    aCCTTTCTTGAAGGTGCCCAGGGCGGTGACCAGCTGCGCTTGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGGTCGCTGTCGTTGTTGTC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATgg                                                                                                                <  3:214854/148‑1 (MQ=255)                                    aCCTTTCTTGAAGGTGCCCAGGGCGGTGACCAGCTGCGCTTGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGGTCGCTGTCGTTGTTGTC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGt                                                                                                               >  8:43744/1‑149 (MQ=255)                                     ccTTTCTTGAAGGTGCCCAGGGCGGTGACCAGCTGCGCTTGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGGTCGCTGTCGTTGTTGTC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTg                                                                                                              <  2:95613/149‑1 (MQ=255)                                      cTTTCTTGAAGGTGCCCAGGGCGGTGACCAGCTGCGCTTGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGGTCGCTGTCGTTGTTGTC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGc                                                                                                             >  3:332238/1‑149 (MQ=255)                                       tttCTTGAAGGTGCCCAGGGCGGTGACCAGCTGCGCTTGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGGTCGCTGTCGTTGTTGTC‑GAGCAACTGCAGCAGCAGGTGCTCCa                                                                                                                                 <  5:95560/128‑1 (MQ=255)                                       tttCTTGAAGGTGCCCAGGGCGGTGACCAGCTGCGCTTGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGGTCGCTGTCGTTGTTGTC‑GAGCAACTGCAGCAGCAGGTGCTCCa                                                                                                                                 >  6:95560/1‑128 (MQ=255)                                       tttCTTGAAGGTGCCCAGGGAGGTGACCAGCTGCGCTTGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGCATCGGCGCCAGGTCGCTGTCGTTGTTGTC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGc                                                                                                             >  5:129952/1‑148 (MQ=255)                                                       aGGGCGATGACCAGCTGCGCTTGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGGTCGCTGTCGTTGTTGTC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGgc                                                                                            >  6:355218/1‑149 (MQ=255)                                                                    gCTGCGCTTGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGGTCGCTGTCGTTGTTGTC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCg                                                                                                                      >  1:293710/1‑110 (MQ=255)                                                                    gCTGCGCTTGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGGTCGCTGTCGTTGTTGTC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCg                                                                                                                      <  2:293710/110‑1 (MQ=255)                                                                        cgcTTGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGGTCGCTGTCGTTGTTGTC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTg                                                                            <  3:218537/148‑1 (MQ=255)                                                                          cTTGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGGTCGCTGTCGTTGTTGTC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGcc                                                                         <  7:43744/149‑1 (MQ=255)                                                                          cTTGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGGTCGCTGTCGTTGTTGTC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGcc                                                                         <  1:140023/149‑1 (MQ=255)                                                                           ttGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGGTCGCTGTCGTTGTTGTC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGcaca                                                                                                <  1:153203/125‑1 (MQ=255)                                                                           ttGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGGTCGCTGTCGTTGTTGTC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGcaca                                                                                                >  2:153203/1‑125 (MQ=255)                                                                               aGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGGTCGCTGTCGTTGTTGTC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCg                                                                    >  5:12006/1‑149 (MQ=255)                                                                               aGGCGTTCGGCGACGACCTGGAAGTGGCGCAGGATCGGCGCCAGGTCGCTGTCGTTGTTGTC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCg                                                                    >  3:53736/1‑149 (MQ=255)                                                                                    ttCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGGTCGCTGTCGTTGTTGTC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTgg                                                               <  4:332238/149‑1 (MQ=255)                                                                                       ggCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGGTCGCTGTCGTTGTTGTC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGttt                                                            >  1:279047/1‑149 (MQ=255)                                                                                       ggCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGGTCGCTGTCGTTGTTGTC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGttt                                                            >  1:283263/1‑149 (MQ=255)                                                                                        gCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGGTCGCTGTCGTTGTTGTC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTc                                                           >  5:5823/1‑149 (MQ=255)                                                                                           acgacCTGGTAGTGGCGCAGGATCGGCGCCAGGTCGCTGTCGTTGTTGTC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGtt                                                        <  4:53736/149‑1 (MQ=255)                                                                                                cTGGTAGTGGCGCAGGATCGGCGCCAGGTCGCTGTCGTTGATGTC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTg                                                                >  3:38579/1‑136 (MQ=255)                                                                                                cTGGTAGTGGCGCAGGATCGGCGCCAGGTCGCTGTCGTTGATGTC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTg                                                                <  4:38579/136‑1 (MQ=255)                                                                                                         gcgcAGGATCGGCGCCAGGTCGCTGTCGTTGTTGTC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGAACa                                          <  8:287667/149‑1 (MQ=255)                                                                                                               gATCGGCGCCAGGTCGCTGTCGTTGTTGTCTGAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCg                                                                                                                      >  1:214287/1‑68 (MQ=255)                                                                                                                     cgcCAGGTCGCTGTCGTTGTTGTC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGAACAGAGACTTCAGGt                              <  2:279047/149‑1 (MQ=255)                                                                                                                     cgcCAGGTCGCTGTCGTTGTTGTC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGAACAGAGACTTCAGGt                              <  2:283263/149‑1 (MQ=255)                                                                                                                         aGGTCGCTGTCGTTGTTGTC‑GAGCAACTGCAGGAGCAGGTGCTGCACTTCCACCTCGTAATGGTGCTCGGACAGTCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTGGAGCTTGGCGAACAGAGACTTCAGGTTcac                          <  7:151824/149‑1 (MQ=255)                                                                                                                         aGGTCGCTGTCGTTGTTGTC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGAACAGAGACTTCAGGTTca                           >  3:154715/1‑148 (MQ=255)                                                                                                                                tGTCGTTGTTGTC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTATTGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGAACAGAGACtt                                   >  3:252914/1‑133 (MQ=255)                                                                                                                                tGTCGTTGTTGTC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCcgccgc                                                                                      <  1:292247/82‑1 (MQ=255)                                                                                                                                tGTCGTTGTTGTC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCcgccgc                                                                                      >  2:292247/1‑82 (MQ=255)                                                                                                                                tGTCGTTGTTGTC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGAACAGAGACTTCAGGTTCACAAGGCGa                   >  5:63147/1‑149 (MQ=255)                                                                                                                                tGTCGTTGTTGTC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGAACAGAGACTTCAGGTTCACAAGGCGa                   >  7:161351/1‑149 (MQ=255)                                                                                                                                    gttgttGTC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCAACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGAACAGAGAATTCAGGTTCACAAGGCGAccc                >  2:249146/1‑148 (MQ=255)                                                                                                                                      tgttgtC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGAACaga                                        <  5:20970/122‑1 (MQ=255)                                                                                                                                      tgttgtC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGAACaga                                        >  6:20970/1‑122 (MQ=255)                                                                                                                                        ttgtC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGAACAGAGACTTCAGGTTCACAAGGCGACCCCATCg           <  5:355218/149‑1 (MQ=255)                                                                                                                                         tgtC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGAACAGAGACTTCAGGTTCACAAGGCGACCCCATCg           >  3:60466/1‑148 (MQ=255)                                                                                                                                           tC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGAACAGAGACTTCAGGTTCACAAGGCGACCCCATCGTaa        <  6:12006/149‑1 (MQ=255)                                                                                                                                            c‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGAACAGAGACTTCAGGTTCACAAGGCGACCCCATCGTAAg       <  1:166880/149‑1 (MQ=255)                                                                                                                                              gAGCACCTGCTGCTGCAGTTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGa                                             <  7:176671/110‑1 (MQ=255)                                                                                                                                              gAGCACCTGCTGCTGCAGTTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGa                                             >  8:176671/1‑110 (MQ=255)                                                                                                                                                gCACCTGCTGCTGCAGTTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGAACAGAGACTTc                                  >  1:344493/1‑119 (MQ=255)                                                                                                                                                gCACCTGCTGCTGCAGTTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGAACAGAGACTTc                                  <  2:344493/119‑1 (MQ=255)                                                                                                                                                  aaCTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGAACAGAGACTTCAGGTTCACAAGGCGACCCCATCGTAAGGAAtg  <  4:154715/149‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                                    GTAATGTGCGGCGACAGCGCCGGGGTGCGGGTATTACCTTTCTTGAAGGTGCCCAGGGCGGTGACCAGCTGCGCTTGCAGGCGTTCGGCGACGACCTGGTAGTGGCGCAGGATCGGCGCCAGGTCGCTGTCGTTGTTGTC‑GAGCAACTGCAGCAGCAGGTGCTCCACTTCCACCTCGTAATGGTGCTCCGACAGGCACAGGGCCGCCGCGCTTTCGGTGGCCGTGCGGCTGGTTTCGTTGAGCTTGGCGAACAGAGACTTCAGGTTCACAAGGCGACCCCATCGTAAGGAATG  >  NC_002947/3491083‑3491375

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: ‑