Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	250,912	G→C	8.7%	A97A (GCC→GCG)	nfeD ←	membrane bound peptidase NefD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	250,912	0	G	C	8.7%	176.2 / 6.2	57	A97A (GCC→GCG)	nfeD	membrane bound peptidase NefD
Reads supporting (aligned to +/- strand):  ref base G (22/30);  new base C (3/2);  total (25/32)
Fisher's exact test for biased strand distribution p-value = 6.45e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.87e-01

ATCGTCGCCGCCTTTGGCTTTATCGTCACTGGGCGTGCCAGGCGCGCCGCCGATCCGCACCGGCGTGGCGGCGCCCAGGTTGGTCCCGGGCGCCATCGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGTACGGTGCTGGAGAGAATTGCCTTGATCATCTGGCGCATGGCACTGTCCAGCCCGCCCGGGGTATCCATGCGGATAACCACCAGTTGCGCGCCTTGCGCCTGGGCCTG  >  NC_002947/250765‑251052                                                                                                                                                    |                                                                                                                                             aTCGTCGCCGCCTTTGGCTTTATCGTCACTGGGCGTGCCAGGCGCGCCGCCGCTCCGCACCGGCGTGGCGGCGCCCAGGTTGGTCCCGGGCGCCATCGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGgc                                                                                                                                            >  1:455381/1‑150 (MQ=255)   cgtcgCCGCCTTTGGCTTTATCGTCACTGGGCGTGCCAGGCGCGCCGCCGATCCGCACCGGCGTGGCGGCGCCCAGGTTGGTCCCGGGCGCCATCGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGgcgc                                                                                                                                          <  2:413712/150‑1 (MQ=255)      cgcctcCTTTTGTGTGATCGTCACTGGGCGTGCCAGGCGCGCCGCCGATCCGCACCGGCGTGGCGGCGCCCAGGTTGGTCCCGGGCGCCATCGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGcgccgc                                                                                                                                       <  2:373902/150‑1 (MQ=255)        ccgccTTTGGCTTTATCGTCACTGGGCGTGCCAGGCGCGCCGCCGATCCGCACCGGCGTGGCGGCGCCCAGGTTGGTCCCGGGCGCCATCGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCCCGcgccgcca                                                                                                                                     <  2:414791/150‑3 (MQ=255)         cgccTTTGGCTTTATCGTCACTGGGCGTGCCAGGCGCGCCGCCGATCCGCACCGGCGTGGCGGCGCCCAGGTTGGTCCCGGGCGCCATCGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTgg                                                                                                                                    <  1:743035/150‑1 (MQ=255)         cgccTTTGGCTTTATCGTCACTGGGCGTGCCAGGCGCGCCGCCGATCCGCACCGGCGTGGCGGCGCCCAGGTTGGTCCCGGGCGCCATCGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTgg                                                                                                                                    <  2:195476/150‑1 (MQ=255)         cgccTTTGGCTTTATCGTCACTGGGCGTGCCAGGCGCGCCGCCGATCCGCACCGGCGTGGCGGCGCCCAGGTTGGTCCCGGGCGCCATCGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTgg                                                                                                                                    <  1:160793/150‑1 (MQ=255)           ccTTTGGCTTTATCGTCACTGGGCGTGCCAGGCGCGCCGCCGATCCGCACCGGCGTGGCGGCGCCCAGGTTGGTCCCGGGCGCCATCGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTgggg                                                                                                                                  <  2:273251/150‑1 (MQ=255)               tGGCTTTATCGTCACTGGGCGTGCCAGGCGCGCCGCCGATCCGCACCGGCGTGGCGGCGCCCAGGTTGGTCCCGGGCGCCATCGCTGCAATATGGCTAGCGTTGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCaa                                                                                                                              <  1:328986/150‑1 (MQ=255)                  cTTTATCGTCACTGGGCGTGCCAGGCGCGCCGCCGATCCGCACCGGCGTGGCGGCGCCCAGGTTGGTCCCGGGCGCCATCGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGt                                                                                                                           >  1:1020084/1‑150 (MQ=255)                   tttATCGTCACTGGGCGTGCCAGGCGCGCCGCCGATCCGCACCGGCGTGGCGGCGCCCAGGTTGGTCCCGGGCGCCATCGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTa                                                                                                                          >  1:1129729/1‑150 (MQ=255)                   gtgagggTCACGGGGCGGGCCAGGCGAGCCGCCGATCCGCCACGGCTTGGCGGCGCCCAGGTTGGTCCCGGGCGCCATCGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTa                                                                                                                          <  2:197999/144‑1 (MQ=255)                         gTCACTGGGCGTGCCAGGCGCGCCGCCGATCCGCACCGGCGTGGCCGCGCCTAGGTTGGTCCCGGGCGCCATCGCTGCAATATGGCTAGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTGGc                                                                                                                    >  2:168143/1‑150 (MQ=255)                            aCTGGGCGTGCCAGGCGCGCCGCCGATCCGCACCGGCGTGGCGGCGCCCAGGTTGGTCCCGGGCGCCATCGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTGGCGAc                                                                                                                 >  2:1101412/1‑150 (MQ=255)                                    tGCCAGGCGCGCCGCCGATCCGCACCGGCGTGGCGGCGCCCAGGTTGGTCCCGGGCGCCATCGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGTACgg                                                                                                         <  1:1141890/150‑1 (MQ=255)                                      ccAGGCGCGCCGCCGATCCGCACCGGCGTGGCGGCGCCCAGGTTGGTCCCGGGCGCCATCGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTg                                                                                                                      <  2:852688/135‑1 (MQ=255)                                      ccAGGCGCGCCGCCGATCCGCACCGGCGTGGCGGCGCCCAGGTTGGTCCCGGGCGCCATCGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTg                                                                                                                      >  1:852688/1‑135 (MQ=255)                                         ggCGCGCCGCCGATCCGCACCGGCGTGGCGGCGCCCAGGTTGGTCCCGGGCGCCAGCGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGTACGGTGCTg                                                                                                    <  1:20525/150‑1 (MQ=255)                                         ggCGCGCCGCCGATCCGCACCGGCGTGGCGGCGCCCAGGTTGGTCCCGGGCACCATCGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGTACGGTGCTg                                                                                                    <  1:992454/150‑1 (MQ=255)                                                  ccgATCCGCACCGGCGTGGCGGCGCCCAGGTTGGTCCCGGGCGCCATCGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGTACGGTGCTGGAGAGAAtt                                                                                           <  1:426197/150‑1 (MQ=255)                                                            tcGGCGTGGCGGCGCCCAGGTTGGTCCCGGGCGCCATCGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGTACGGTGCTGGAGAGAATTGCCTTGatca                                                                                 <  2:907047/149‑1 (MQ=255)                                                                 gTGGCGGCGCCCAGGTTGGTCCCGGGCGCCATCGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGTACGGTGCTg                                                                                                    <  2:460286/126‑1 (MQ=255)                                                                 gTGGCGGCGCCCAGGTTGGTCCCGGGCGCCATCGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGTACGGTGCTg                                                                                                    >  1:460286/1‑126 (MQ=255)                                                                      ggcgCCCAGGTTGGTCCCGGGCGCCATCGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGTACGGTGCTGGAGAGAATTGCCTTGATCATCTGGCGCAt                                                                       <  2:623800/150‑1 (MQ=255)                                                                             aGGTTGGTCCCGGGCGCCATCGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGTACGGTGCTGGAGAAAATTGCCTTGATCATCTGGCGCATGGCACTg                                                                >  2:1095151/1‑150 (MQ=255)                                                                               gTTGGTCCCGGGCGCCATCGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGTACGGTGCTGGAGAGAATTGCCTTGATCATCTGGCGCATGGCACTGTc                                                              <  1:593426/150‑1 (MQ=255)                                                                                  ggTCCCGGGCGCCATCGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGTACGGTGCTGGAGAGAATTGCCTTGATCATCTGGCGCATGGCACTGTCCAg                                                           <  1:713744/150‑1 (MQ=255)                                                                                    tCCCGGGCGCCATCGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTGGc                                                                                                                    <  1:614897/91‑1 (MQ=255)                                                                                    tCCCGGGCGCCATCGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTGGc                                                                                                                    >  2:614897/1‑91 (MQ=255)                                                                                    tCCCGGGCGCCATCGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGTACGGTGCTGGAGAGAATTGCCtt                                                                                      <  1:1062982/121‑1 (MQ=255)                                                                                    tCCCGGGCGCCATCGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGTACGGTGCTGGAGAGAATTGCCtt                                                                                      >  2:1062982/1‑121 (MQ=255)                                                                                    tCCCGGGCGCCATCGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGTACGGTGCTGGAGAGAATTGCCTTGATCATCTGGCGCATGGCACTGTCCAgcc                                                         >  1:1018978/1‑150 (MQ=255)                                                                                            gcCATCGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGt                                                                                                             >  1:331387/1‑90 (MQ=255)                                                                                            gcCATCGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGt                                                                                                             <  2:331387/90‑1 (MQ=255)                                                                                               aTCGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGTCCGGTGCTCGAGCATCGAGGCCAAATCATTGGGCGCATGGCACTGTCCAGCCCGCCCGGGGTa                                              >  1:570585/1‑150 (MQ=255)                                                                                               aTCGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGTACGGTGCTGGAGAGAATTGCCTTGATCATCTGGCGCATGGCACTGTCCAGCCCGCCCGGGGTa                                              >  2:1134556/1‑150 (MQ=255)                                                                                               aTCGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGTACGGTGCTGGAGAGAATTGCCTTGATCATCTGGCGCATGGCACTGTCCAGCCCGCCCGGGGTa                                              >  1:219290/1‑150 (MQ=255)                                                                                                 cGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGTACGGTGCTGGAGAGAAtt                                                                                           >  1:381655/1‑103 (MQ=255)                                                                                                 cGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGTACGGTGCTGGAGAGAAtt                                                                                           <  2:381655/103‑1 (MQ=255)                                                                                                    tGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGTACGGTGCTGGAGAGAATTGcc                                                                                        >  2:867031/1‑103 (MQ=255)                                                                                                    tGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGTACGGTGCTGGAGAGAATTGcc                                                                                        <  1:867031/103‑1 (MQ=255)                                                                                                                      gagaATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGTACGGTGCTGGAGAGAATTGCCTTGATCATCTGGCGCATGGCACTGTCCAGCCCGCCCGGGGGATCCATGCGGATAACCACCAGTTg                       >  1:786762/1‑150 (MQ=255)                                                                                                                         aaTATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGTACGGTGCTGGAGAGAATTGCCTTGATCATCTGGCGCATGGCACTGTCCAGCCCGCCCGGGGTATCCATGCGGATAACCACCAGTTgcgc                    >  1:256963/1‑150 (MQ=255)                                                                                                                           tataGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGTACGGTGCTGGAGAAAATTGCCTTGATCATCTGGCGCATGGCACTGTCCAGCCCGCCCGGGGTATCCATGCGGATAACCACCAGTTgcgcgc                  <  1:1095151/150‑1 (MQ=255)                                                                                                                             taGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGTACGGTGCTGGAGAGAATTGCCTTGATCATCTGGCGCATGGCACTGTCCAGCCCGCCCGGGGTATCCATGCGGATAACCACCAGTTGCGCGCCt                <  1:982252/150‑1 (MQ=255)                                                                                                                                gTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGTACGGTGCTGGAGAGAATTGCCTTGATCATCTGGCGCATGGCACTGTCCAGCCCGCCCGGGGTATCCATGCGGATAACCACCAGTTGCGCGCCTTgc             <  2:1020084/150‑1 (MQ=255)                                                                                                                                gTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGTACGGTGCTGGAGAGAATTGCCTTGATCATCTGGCGCATGGCACTGTCCAGCCCGCCCGGGGTATCCATGCGGATAACCACCAGTTGCGCGCCTTgc             >  2:857157/1‑150 (MQ=255)                                                                                                                                    cGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGTACGGTGCTGGAGAGAATTGCCTTGATCATCTGGCGCATGGCACTGTCCAGCCCGCCCGGGGTATCCATGCGGATAACCACCAGTTGCGCGCCTTGCgcct         >  1:561060/1‑150 (MQ=255)                                                                                                                                      gcgcTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGTACGGTGCTGGAGAGAATTGCCTTGATCATCTGGCGCATGGCACTGTCCAGCCCGCCCGGGGTATCCATGCGGATAACCACCAGTTGCGCGCCTTGCgcctgg       <  1:168143/150‑1 (MQ=255)                                                                                                                                      gcgcTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGTACGGTGCTGGAGAGAATTGCCTTGATCATCTGGCGCATGGCACTGTCCAGCCCGCCCGGGGTATCCATGCGGATAACCACCAGTTGCGCGCCTTGCgcctgg       <  2:256963/150‑1 (MQ=255)                                                                                                                                       ccccagcggcgCCCGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGTACGGTGCTGGAGAGAATTGCCTTGATCATCTGGCGCATGGCACTGTCCAGCCCGCCCGGGGTATCCATGc                                       <  1:167250/112‑1 (MQ=255)                                                                                                                                       ccccagcggcgCCCGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGTACGGTGCTGGAGAGAATTGCCTTGATCATCTGGCGCATGGCACTGTCCAGCCCGCCCGGGGTATCCATGc                                       >  2:167250/6‑117 (MQ=255)                                                                                                                                         ccagcggcgCCCGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGTACGGTGCGGGAGAGAATTGCCTTGATCATCTGGCGCATGGCACTGTCCAGCCCGCCCGGGGTATCCATGCGGATAACCACCAGTTGCGGGCCTTGCgcctggtcc    >  2:1194919/4‑150 (MQ=255)                                                                                                                                          cagcggcgCCCGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGTACGGTGCTGGAGAGAATTGCCTTGATCATCTGGCGCATGGCACTGTCCAGCCCGCCCGGGGTATCCATGCGGATAACCACCAGTTGCGCGCCTTGCgcctgggcct   >  2:484394/3‑150 (MQ=255)                                                                                                                                           ggcggcGCGGGGGCCGCTGGGGGCAACGTAGCTGGCGACGGGTACGGTGCTGGAGAGAATTGCCTTGAGCATCTGGCGCATGGCACTGTCCAGCCCGCCCGGGGTATCCATGCGGATAACCACCAGTTGCGCGCCTTGCgcctgggcctg  <  2:455381/150‑1 (MQ=255)                                                                                                                                              ggcgCGGGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGTACGGTGCTGGAGAGAATTGCCTTGATCATCTGGCGCATGGCACTGTCCAGCCCGCCCGGGGTATCCATGCGGa                                    >  2:741768/1‑113 (MQ=255)                                                                                                                                              ggcgCGGGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGTACGGTGCTGGAGAGAATTGCCTTGATCATCTGGCGCATGGCACTGTCCAGCCCGCCCGGGGTATCCATGCGGa                                    <  1:741768/113‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                             ATCGTCGCCGCCTTTGGCTTTATCGTCACTGGGCGTGCCAGGCGCGCCGCCGATCCGCACCGGCGTGGCGGCGCCCAGGTTGGTCCCGGGCGCCATCGCTGCAATATGGCTGGCGTAGAGAATATAGGTGCCGGCGCTGGCGGCGCGGGCGCCGCTGGGGGCAACGTAGCTGGCGACGGGTACGGTGCTGGAGAGAATTGCCTTGATCATCTGGCGCATGGCACTGTCCAGCCCGCCCGGGGTATCCATGCGGATAACCACCAGTTGCGCGCCTTGCGCCTGGGCCTG  >  NC_002947/250765‑251052

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑