Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,548,181	G→A	14.3%	S7S (AGC→AGT)	rhtA ←	threonine/homoserine exporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,548,181	0	G	A	14.3%	61.7 / 3.5	28	S7S (AGC→AGT)	rhtA	threonine/homoserine exporter
Reads supporting (aligned to +/- strand):  ref base G (12/12);  new base A (2/2);  total (14/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.27e-01

ATGATGCTGGCGAAGATCAGGCGCAGGGTGGTAGTGCCTTGTGCGCCGACGATCGGGAACATGCTTTTGGCCAGGGAGGCGCCGGACTGAATCGATGCCATGGCGATAAGC‑AGTAGGCCGATCGGGAAGAGGGTGGCGGCCAG‑GCTGCGGGGTTGGGTGTTCATTTAAGTGCGGCAATCCTTGGGCGGGGGAGATGGTGAGCAATATAGTGCGCAATTGGTGGGGGAGGTGGTAGCCCTCAAGCGGCTTCACCAGCAATATTTCAAATCATTGAAATTAAAGGTTGACCTTC  >  NC_002947/2548038‑2548329                                                                                                                                                  |                                                                                                                                                     atgatgCTGGCGAAGATCAGGCGCAGGGTGGTAGTGCCTTGTGCGCCGACGATCGGGAACATGCTTTTGGCCAGGGAGGCGCCGGACTGAATCGATGCCATGGCGATAAGC‑AGTAGGCCGATCGGGAAGAGGGTGGCGGCCAG‑GCTGc                                                                                                                                                  <  6:157300/148‑1 (MQ=255)        tGGCGAAGATCAGGCGCAGGGTGGTAGTGCCTTGTGCGCCGACGATCGGGAACATGCTTTTGGCCAGGGAGGCGCCGGACTGAATCGATGCCATGGCGATAAGC‑AGTAGGCCGATCGGGAAGAGGGTGGCGGCCAG‑GCTGCGGGGTTgg                                                                                                                                          >  5:59492/1‑149 (MQ=255)               gATCAGGCGCAGGGTGGTAGTGCCTTGTGCGCCGACGATCGGGAACATGCTTTTGGCCAGGGAGGCGCCGGACTGAATCGATGCCATGGCGATAAGC‑AGTAGGCCGATCGGGAAGAGGGTGGCGGCCAG‑GCTGCGGGGTTGGGTGTTCa                                                                                                                                   >  6:251004/1‑149 (MQ=255)                 tCAGGCGCAGGGTGGTAGTGCCTTGTGCGCCGACGATCGGGAACATGCTTTTGGCCAGGGAGGCGCCGGACTGAATCGATGCCATGGCGATAAGC‑AGTAGGCCGAGCGGGAAGAGGGTGGCGGCCAG‑GCTGCGGGGTTGGGTGTTCAtt                                                                                                                                 <  8:78263/149‑1 (MQ=255)                          gggTGGTAGTGCCTTGTGCGCCGACGATCGGGAACATGCTTTTGGCCAGGGAGGCGCCGGACTGAATCGATGCCATGGCGATAAGC‑AGTAGGCCGATCGGGAAGAGGGTGGCGGCCAGTGCTGCGGGGTTGGGTGTTCATTTAAGTGCg                                                                                                                         <  1:27765/149‑1 (MQ=255)                                     ccTTGTGCGCCGACGATCGGGAACATGCTTTTGGCCAGGGAGGCGCCGGACTGAATCGATGCCATGGCGATAAGC‑AGTAGGCCGATCGGGAAGAGGGTGGCGGCCAG‑GCTGCGGGGTTGGGTGTTCAttt                                                                                                                                <  7:139717/130‑1 (MQ=255)                                     ccTTGTGCGCCGACGATCGGGAACATGCTTTTGGCCAGGGAGGCGCCGGACTGAATCGATGCCATGGCGATAAGC‑AGTAGGCCGATCGGGAAGAGGGTGGCGGCCAG‑GCTGCGGGGTTGGGTGTTCAttt                                                                                                                                >  8:139717/1‑130 (MQ=255)                                      cTTGTGCGCCGACGATCGGGAACATGCTTTTGGCCAGGGAGGCGCCGGACTGAATCGATGCCATGGCGATAAGC‑AGTAGGCCGATCGGGAAGAGGGTGGCGGCCAG‑GCTGCGGGGTTGGGTGTTCAttt                                                                                                                                <  7:223459/129‑1 (MQ=255)                                      cTTGTGCGCCGACGATCGGGAACATGCTTTTGGCCAGGGAGGCGCCGGACTGAATCGATGCCATGGCGATAAGC‑AGTAGGCCGATCGGGAAGAGGGTGGCGGCCAG‑GCTGCGGGGTTGGGTGTTCAttt                                                                                                                                >  8:223459/1‑129 (MQ=255)                                          tgCGCCGACGATCGGGAACATGCTTTTGGCCAGGGAGGCGCCGGACTGAATCGATGCCATGGCGATAAGC‑AGTAGGCCGATCGGGAAGAGGGTGGCAGCCAG‑GCTGCGGGGTTGGGTGTTCATTTAAGTGCGGCAATCCTTGGGCggg                                                                                                         <  3:91603/148‑1 (MQ=255)                                               cgacgaTCGGGAACATGCTTTTGGCCAGGGAGGCGCCGGACTGAATCGATGCCATGGCGATAAGC‑AGTAGGCCGATCGGGAAGAGGGTGGCGGCCAG‑GCTGCGGGGTTGGGTGTTCATTTAAGTGCGGCAATCCTTGGGCGGGGGAGAt                                                                                                   <  5:251004/149‑1 (MQ=255)                                                    aTCGGGAACATGCTTTTGGCCAGGGAGGCGCCGGACTGAATCGATGCCATGGCGATAAGC‑AGTAGGCCGATCGGGAAGAGGGTGGCGGCCAG‑GCTGCGGGGTTGGGTGTTCATTTAAGTGCGGCAATCCTTGGGCGGGGGAGATGGTGa                                                                                              <  6:59492/149‑1 (MQ=255)                                                     tCGGGAACATGCTTTTGGCCAGGGAGGCGCCGGACTGAATCGATGCCATGGCGATAAGC‑AGTAGGCCGATCGGGAAGAGGGTGGCGGCCAG‑GCTGCGGGGTTGGGTGTTCATTTAAGTGCGGCAATCCTTGGGCGGGGGAGATGGTGAg                                                                                             >  5:178348/1‑149 (MQ=255)                                                     tCGGGAACATGCTTTTGGCCAGGGAGGCGCCGGACTGAATCGATGCCATGGCGATAAGC‑AGTAGGCCGATCGGGAAGAGGGTGGCGGCCAG‑GCTGCGGGGTTGGGTGTTCATTTAAGTGCGGCAATCCTTGGGCGGGGGAGATGGTGAg                                                                                             <  6:178348/149‑1 (MQ=255)                                                       gggAACATGCTTTTGGCCAGGGAGGCGCCGGACTGAATCGATGCCATGGCGATAAGC‑AGTAGGCCGATCGGGAAGAGGGTGGCGGCCAG‑GCTGCGGGGTTGGGTGTTCATTTAAGTGCGGCAATCCTTGGGCGGGGga                                                                                                      >  4:242170/1‑138 (MQ=255)                                                       gggAACATGCTTTTGGCCAGGGAGGCGCCGGACTGAATCGATGCCATGGCGATAAGC‑AGTAGGCCGATCGGGAAGAGGGTGGCGGCCAG‑GCTGCGGGGTTGGGTGTTCATTTAAGTGCGGCAATCCTTGGGCGGGGga                                                                                                      <  3:242170/138‑1 (MQ=255)                                                             aTGCTTTTGGCCAGGGAGGCGCCGGACTGAATCGATGCCATGGCGATAAGCGAGTAGGCCGATCGGGAAGAGGGTGGCGGCCAG‑GCTGCGGGGTTGGGTGTTCATTTAAGTGCGGCAATCCTTGGGCGGGGGAGATGGTGAGCAAtata                                                                                      >  1:231040/1‑149 (MQ=255)                                                             aTGCTTTTGGCCAGGGAGGCGCCGGACTGAATCGATGCCATGGCGATAAGC‑AGTAGGCCGATCGGGAAGAGGGTGGCGGCCAG‑GCTGCGGGGTTGGGTGTTCATTTAAGTGCGGCAATCCTTGGGCGGGGGAGATGGTGAGCAATATAg                                                                                     >  4:42407/1‑149 (MQ=255)                                                                         aGGGAGGCGCCGGACTGAATCGATGCCATGGCGATAAGC‑AGTAGGCCGATCGGGAAGAGGGTGGCGGCCAG‑ACTGCGGGGTTGGGTGTTCATTTAAGTGCGGCAATCCTTGGGCGGGGGAGATGGTGAGCAATATAGt                                                                                    >  5:267557/1‑138 (MQ=255)                                                                         aGGGAGGCGCCGGACTGAATCGATGCCATGGCGATAAGC‑AGTAGGCCGATCGGGAAGAGGGTGGCGGCCAG‑ACTGCGGGGTTGGGTGTTCATTTAAGTGCGGCAATCCTTGGGCGGGGGAGATGGTGAGCAATATAGt                                                                                    >  5:272352/1‑138 (MQ=255)                                                                         aGGGAGGCGCCGGACTGAATCGATGCCATGGCGATAAGC‑AGTAGGCCGATCGGGAAGAGGGTGGCGGCCAG‑ACTGCGGGGTTGGGTGTTCATTTAAGTGCGGCAATCCTTGGGCGGGGGAGATGGTGAGCAATATAGt                                                                                    <  6:267557/138‑1 (MQ=255)                                                                         aGGGAGGCGCCGGACTGAATCGATGCCATGGCGATAAGC‑AGTAGGCCGATCGGGAAGAGGGTGGCGGCCAG‑ACTGCGGGGTTGGGTGTTCATTTAAGTGCGGCAATCCTTGGGCGGGGGAGATGGTGAGCAATATAGt                                                                                    <  6:272352/138‑1 (MQ=255)                                                                                        tGAATCGATGCCATGGCGATAAGC‑AGTAGGCCGATCGGGAAGAGGGTGGCGGCCAG‑GCTGCGGGAGTGGGTGTTAATTTAAATTCCGCCATACTTTGGCGGGGGAGTTGGTGCACAAATTAATGGGCAATTTGTGGGGGAGGTGGTAGc                                                          >  1:91012/1‑149 (MQ=255)                                                                                           aTCGTTGCCATGGCTATAAGG‑AGTCGTCGGAGGGGGAAGTGGGTGGCGGCCAG‑GCTGGGGGGTTGGGTGTTCATTTAAGTGCGGCAATCCTTGGGGGGGGGAGATGGTGAGCAATATAGTGCGCAATTGGTGGGGGAGGTGGTAGccc                                                        <  2:231040/148‑1 (MQ=255)                                                                                                       gCGATAAGC‑AGTAGGCCGATCGGGAAGAGGGTGGCGGCCAG‑GCTGCGGGGTTGGGTGTTCATTTAAGTGCGGCAATCCTTGGGCGGGGGAGATGGTGAGCAATATAGTGCGCAATTGGTGGGGGAGGTGGTAGCCCTCAAGCGGCTTCa                                           >  1:86132/1‑149 (MQ=255)                                                                                                        cGATAAGC‑AGTAGGCCGATCGGGAAGAGGGTGGCGGCCAG‑GCTGCGGGGTTGGGTGTTCATTTAAGTGCGGCAATCCTTGGGCGGGGGAGATGGTGAGCAATATAGTGCGCAATTGGTGGGGGAGGTGGTAGCCCTCAAGCGCCTTCAc                                          >  3:135840/1‑149 (MQ=255)                                                                                                               c‑AGTAGGCCGATCGGGAAGAGGGTGGCGGCCAG‑GCTGCGGGGTTGGGTGTTCATTTAAGTGCGGCAATCCTTGGGCGGGGGAGATGGTGAGCAATATAGTGCGCAATTGGTGGGGGAGGTGGTAGCCCTCAAGCGGCTTCACCAGCaa                                    >  3:117835/1‑148 (MQ=255)                                                                                                                                     ggTGGCGGCCAG‑GCGGCGGGGTTGGGTGTGCATTTAAGTGCGGCAATCCTTGGGCGGGGGAGATGGTGACCAATATAGTGCGCAATTGGGGCGGGAGGTGGTAGCCCTCAAGCGGCTTCACCAGCAATATTTCAAATCATTGAAATTaa              <  4:95986/149‑1 (MQ=255)                                                                                                                                                  gCTGGGTGGTGGGGTTTTCTATTAAGTGCGCCAAGCCTTGGGCGGGGTAGATGGTTATAAATATAGTGCGCAATTGGGGGGGCAGGTGGTAGCCCTCAAGCGGCTTCACCAGCAATATTTCAAATCATTGAAATTAAAGGTTGACCTtc  <  3:42407/149‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                     ATGATGCTGGCGAAGATCAGGCGCAGGGTGGTAGTGCCTTGTGCGCCGACGATCGGGAACATGCTTTTGGCCAGGGAGGCGCCGGACTGAATCGATGCCATGGCGATAAGC‑AGTAGGCCGATCGGGAAGAGGGTGGCGGCCAG‑GCTGCGGGGTTGGGTGTTCATTTAAGTGCGGCAATCCTTGGGCGGGGGAGATGGTGAGCAATATAGTGCGCAATTGGTGGGGGAGGTGGTAGCCCTCAAGCGGCTTCACCAGCAATATTTCAAATCATTGAAATTAAAGGTTGACCTTC  >  NC_002947/2548038‑2548329

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: ‑