Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,045,549	G→A	8.9%	P42P (CCG→CCA)	pstA →	phosphate ABC transporter permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,045,549	0	G	A	8.9%	120.5 / 2.9	45	P42P (CCG→CCA)	pstA	phosphate ABC transporter permease
Reads supporting (aligned to +/- strand):  ref base G (21/20);  new base A (2/2);  total (23/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.86e-01

CCAGCGTGGTAACAAACAATGACTGACCTGACGACCCCTGTAGCCGCGCTGCCCAGCCTGCAGCGCAAGCTGGAAGGCCGCGCCC‑TGCGCAGCCTGGTATTGACCACCCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCGCTGATTTCCGTGCTGTACATGCTGATCACTCGCGGCGGGGCACGCCTTAACCTGGAAGTGTTCACCGAGCTGCCGCCGACTGGCTTCGAGATGGGCGGTGGTTTCGGTAACGCTATGGCCGGTACCTTCGTCATGGTCGGCATT  >  NC_002947/3045406‑3045693                                                                                                                                                 |                                                                                                                                                 ccAGCGTGGTAACAAACAATGACTGACCTGACGACCCCTGTAGCGGCTCTGCCCAGCCTGCAGCGCAAGCTGGAAGGCCGCGCCC‑TGCGCAGCCTGGTATTGACCACCCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCGCTGAt                                                                                                                                             <  7:250303/149‑1 (MQ=255)              aaacaaTGACTGACCTGACGACCCCTGTAGCCGCGCTGCCCAGCCTGCAGCGCAAGCTGGAAGGCCGCGCCC‑TGCGCAGCCTGGTATTGACCACCCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCGCTGATTTCCg                                                                                                                                        >  1:256602/1‑141 (MQ=255)              aaacaaTGACTGACCTGACGACCCCTGTAGCCGCGCTGCCCAGCCTGCAGCGCAAGCTGGAAGGCCGCGCCC‑TGCGCAGCCTGGTATTGACCACCCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCGCTGATTTCCg                                                                                                                                        <  2:256602/141‑1 (MQ=255)              aaacaaTGACTGACCTGACGACCCCTGTAGCCGCGCTGCCCAGCCTGCAGCGCAAGCTGGAAGGCCGCGCCC‑TGCGCAGCCTGGTATTGACCACCCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCGCTGATTTCCGTGCTGTa                                                                                                                                 >  8:2666/1‑148 (MQ=255)                acaaTGACTGACCTGACGACCCCTGTAGCCGCGCTGCCCAGCCTGCAGCGCAAGCTGGAAGGCCGCGCCC‑TGCGCAGCCTGGTATTGACCACCCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCGCTGATTTCCGTGCTGTACa                                                                                                                               >  5:108737/1‑148 (MQ=255)                acaaTGACTGACCTGACGACCCCTGTAGCCGCGCTGCCCAGCCTGCAGCGCAAGCTGGAAGGCCGCGCCC‑TGCGCAGCCTGGTATTGACCACCCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCGCTGATTTCCGTGCTGTACa                                                                                                                               <  6:108737/148‑1 (MQ=255)                          acctgacGACCCCTGTAGCCGCGCTGCCCAGCCTGCAGCGCAAGCTGGAAGGCCGCGCCC‑TGCGCAGCCTGGTATTGACCACCCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCGCTGATTTCCGTGCTGTACATGCTGATCa                                                                                                                      <  3:76227/147‑1 (MQ=255)                                 gacCCCTGTAGCCGCGCTGCCCAGCCTGCAGCGCAAGCTGGAAGGCCGCGCCC‑TGCGCAGCCTGGTATTGACCACCCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCGCTGATTTCCGTGCTGTACATGCTGATCACTCgcggcg                                                                                                             >  7:116505/1‑149 (MQ=255)                                   ccccTGTAGCCGCGCTGCCCAGCCTGCAGCGCAAGCTGGAAGGCCGCGCCCGTGCGCAGCCTGGTATTGACCACCCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCGCTGATTTCCGTGCTGTACATGCTGATCACTCGcggcgg                                                                                                            >  1:202699/1‑149 (MQ=255)                                    cccTGTAGCCGCGCTGCCCAGCCTGCAGCGCAAGCTGGAAGGCCGCGCCC‑TGCGCAGCCTGGTATTGACCACCCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCGCTGATTTCCGTGCTGTACATGCTGATCACTCGCGGCgggg                                                                                                          >  3:186105/1‑149 (MQ=255)                                     ccTGTAGCCGCGCTGCCCAGCCTGCAGCGCAAGCTGGAAGGCCGCGCCC‑TGCGCAGCCTGGTATTGACCACCCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCGCTGATTTCCGTGCTGTACATGCTGATCACTCGCGGCgggg                                                                                                          >  6:57656/1‑148 (MQ=255)                                         tAGCCGCGCTGCCCAGCCTGCAGCGCAAGCTGGAAGGCCGCGCCC‑TGCGCAGCCTGGTATTGACCACCCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCGCTGATTTCCGTGCTGTACATGCTGATCACTCGCGGCGGGGCAc                                                                                                       <  6:15950/147‑1 (MQ=255)                                         tAGCCGCGCTGCCCAGCCTGCAGCGCAAGCTGGAAGGCCGCGCCC‑TGCGCAGCCTGGTATTGACCACCCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCGCTGATTTCCGTGCTGTACATGCTGATCACTCGCGGCGGGGCACGc                                                                                                     >  5:64509/1‑149 (MQ=255)                                           gCCGCGCTGCCCAGCCTGCAGCGCAAGCTGGAAGGCCGCGCCC‑TGCGCAGCCTGGTATTGACCACCCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCGCTGATTTCCGTGCTGTACATGCTGATCACTCGCGGCGGGGCACGcc                                                                                                    <  8:192304/148‑1 (MQ=255)                                           gCCGCGCTGCCCAGCCTGCAGCGCAAGCTGGAAGGCCGCGCCC‑TGCGCAGCCTGGTATTGACCACCCTGGCCTGGTTCGCGGCACTGGTGGCCAGCATGCCGCTGATTTCCGTGCTGTACATGCTGATCACTCGCGGCGGGGCACGCCt                                                                                                   <  2:138718/149‑1 (MQ=255)                                            ccGCGCTGCCCAGCCTGCAGCGCAAGCTGGAAGGCCGCGCCC‑TGCGCAGCCTGGTATTGACCACCCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCGCTGATTTCCGTGCTGTACATGCTGATCACTCGCGGCGGGGCACGCCt                                                                                                   <  6:64509/148‑1 (MQ=255)                                                             cAGCGCAAGCTGGAAGGCCGCGCCC‑TGCGCAGCCTGGTATTGACCACCCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCGCTGATTTCCGTGCTGTACATGCTGATCACTCGCGGCGGGGCACGCCTTAACCTGGAAGTGTTCAc                                                                                 >  8:140194/1‑149 (MQ=255)                                                              aGCGCAAGCTGGAAGGCCGCGCCC‑TGCGCAGCCTGGTATTGACCACCCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCGCTGATTTCCGTGCTGTACATGCTGATCACTCGCGGCGGGGCACGCCTTAACCTGGAAGTGTTCAcc                                                                                <  4:186105/149‑1 (MQ=255)                                                               gcgcAAGCTGGAAGGCCGCGCCC‑TGCGCAGCCTGGTATTGACCACCCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCGCTGATTTCCGTGCTGTACATGCTGATCACTCGCGGCGGGGCACGCCTTAACCTgg                                                                                           <  8:218053/137‑1 (MQ=255)                                                               gcgcAAGCTGGAAGGCCGCGCCC‑TGCGCAGCCTGGTATTGACCACCCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCGCTGATTTCCGTGCTGTACATGCTGATCACTCGCGGCGGGGCACGCCTTAACCTGGAAgatcgga                                                                                  >  7:218053/1‑140 (MQ=255)                                                                     gCTGGAAGGCCGCGCCC‑TGCGCAGCCTGGTATTGACCACCCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCGCTGATTTCCGTGCTGTACATGCTGATCACTCGCGGCGGGGCACGCCTTAACCTGGAAGTGTTCACCGAGCt                                                                           >  4:77359/1‑147 (MQ=255)                                                                     gCTGGAAGGCCGCGCCC‑TGCGCAGCCTGGTATTGACCACCCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCGCTGATTTCCGTGCTGTACATGCTGATCACTCGCGGCGGGGCACGCCTTAACCTGGAAGTGTTCACCGAGCt                                                                           <  3:77359/147‑1 (MQ=255)                                                                        ggAAGGCCGCGCCC‑TGCGCAGCCTGGTATTGACCACCCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCGCTGATTTCCGTGCTGTACATGCTGATCACTCGCGGCGGGGCACGCCTTAACCTGGAAGTGTTCACCGAGCTgccgc                                                                      >  2:230615/1‑149 (MQ=255)                                                                        ggAAGGCCGCGCCC‑TGCGCAGCCTGGTATTGACCACCCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCGCTGATTTCCGTGCTGTACATGCTGATCACTCGCGGCGGGGCACGCCTTAACCTGGAAGTGTTCACCGAGCTgccgc                                                                      >  2:234436/1‑149 (MQ=255)                                                                         gAAGGCCGCGCCC‑TGCGCAGCCTGGTATTGACCACCCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCGCTGATTTCCGTGCTGTACATGCTGATCACTCGCGGCGGGGCACGCCTTAACCTGGAAGTGTTCACCGAGCTgccgcc                                                                     <  5:57656/149‑1 (MQ=255)                                                                         gAAGGCCGCGCCC‑TGCGCAGCCTGGTATTGACCACCCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCACTGATTTCCGTGCTGTACATGCTGATCACTCGCGGCGGGGCACGCCTTAACCTGGAAGTGTTCACCGAGCTgccgcc                                                                     >  7:12847/1‑149 (MQ=255)                                                                         gAAGGCCGCGCCC‑TGCGCAGCCTGGTATTGACCACCCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCACTGATTTCCGTGCTGTACATGCTGATCACTCGCGGCGGGGCACGCCTTAACCTGGAAGTGTTCACCGAGCTgccgcc                                                                     >  7:8888/1‑149 (MQ=255)                                                                               cgcgCCC‑TGCGCAGCCTGGTATTGACCACCCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCGCTGATTTCCGTGCTGTACATGCTGATCACTCGCGGCGGGGCACGCCTTAACCTGGAAGTGTTCACCGAGCTGCCGCCGACTgg                                                               >  7:118489/1‑149 (MQ=255)                                                                                   ccc‑TGCGCAGCCTGGTATTGACCACCCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCGCTGATTTCCGTGCTGTACATGCTGATCACTCGCGGCGGGGCACGCCTTAACCTGGAAGTGTTCACCGAGCTGCCGCCGACTGGCTTc                                                           <  2:202699/149‑1 (MQ=255)                                                                                              ccTGGTATTGACCACCCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCGCTGATTTCCGTGCTGTACATGCTGATCACTCGCGGCGGGGCACGCCTTAACCTGGAAGTGTTCACCGAGCTGCCGCCGACTGGCTTCGAGATGGGCg                                                 >  3:220584/1‑149 (MQ=255)                                                                                                     ttGACCACCCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCGCTGATTTCCGTGCTGTACATGCTGATCACTCGCGGCGGGGCACGCCTTAACCTGGAAGTGTTCACCGAGCTGCCGCCGACTGGCTTCGAGATGGGCGGTGGttt                                          >  5:140218/1‑149 (MQ=255)                                                                                                     ttGACCACCCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCGCTGATTTCCGTGCTGTACATGCTGATCACTCGCGGCGGGGCACGCCTTAACCTGGAAGTGTTCACCGAGCTGCCGCCGACTGGCTTCGAGATGGGCGGTGGttt                                          <  4:220584/149‑1 (MQ=255)                                                                                                      tGACCACCCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCGCTGATTTCCGTGCTGTACATGCTGATCACTCGCGGCGGGGCACGCCTTAACCTGGAAGTGTTCACCGAGCTGCCGCCGACTGGCTTCGAGATGGGCGGTGGTTTc                                         >  7:148972/1‑149 (MQ=255)                                                                                                       gACCACCCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCGCTGATTTCCGTGCTGTACATGCTGATCACTCGCGGCGGGGCACGCCTTAACCTGGAAGTGTTCACCGAGCTGCCGCCGACTGGCTTCGAGATgg                                                    >  6:87426/1‑137 (MQ=255)                                                                                                       gACCACCCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCGCTGATTTCCGTGCTGTACATGCTGATCACTCGCGGCGGGGCACGCCTTAACCTGGAAGTGTTCACCGAGCTGCCGCCGACTGGCTTCGAGATgg                                                    <  5:87426/137‑1 (MQ=255)                                                                                                        accaccCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCGCTGATTTCCGTGCTGTACATGCTGATCACTCGCGGCGGGGCACGCCTTAACCTGGAAGTGTTCACCGAGCTGCCGCCGACTGGCTTCGAGATGGGCGGTGGTTTCgg                                       >  4:82289/1‑149 (MQ=255)                                                                                                        accaccCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCGCTGATTTCCGTGCTGTACATGCTGATCACTCGCGGCGGGGCACGCCTTAACCTGGAAGTGTTCACCGAGCTGCCGCCGACTGGCTTCGAGATGGGCGGTGGTTTCg                                        <  8:116505/148‑1 (MQ=255)                                                                                                         ccaccCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCGCTGATTTCCGTGCTGTACATGCTGATCACTCGCGGCGGGGCACGCCTTAACCTGGAAGTGTTCACCGAGCTGCCGCCGACTGGCTTCGAGATGGGCGGTGGTTTCGGt                                      <  7:140194/149‑1 (MQ=255)                                                                                                                 gcctggTTCGCGGCACTGGTGGCCAGCGTGCCGCTGATTTCCGTGCTGTACATGCTGATCACTCGCGGCGGGGCACGCCTTAACCTGGAAGTGTTCACCGAGCTGCCGCCGACTGGCTTCGAGATGGGCGGTGGTTTCGGTAACGCTAt                              <  3:82289/149‑1 (MQ=255)                                                                                                                  cctggTTCGCGGCACTGGTGGCCAGCGTGCCGCTGATTTCCGTGCTGTACATGCTGATCACTCGCGGCGGGGCACGCCTTAACCTGGAAGTGTTCACCGAGCTGCCGCCGACTGGCTTCGAGATGGGCGGTGGTTTCGGTAACGCTATg                             >  7:130154/1‑149 (MQ=255)                                                                                                                                    tggCCAGCGTGCCACTGATTTCCGTGCTGTACATGCTGATCACTCGCGGCGGGGCACGCCTTAACCTGGAAGTGTTCACCGAGCTGCCGCCGACTGGCTTCGAGATGGGCGGTGGTTTCGGTAACGCTATGGCCGGTACCTTCGTCATg           <  8:12847/149‑1 (MQ=255)                                                                                                                                    tggCCAGCGTGCCACTGATTTCCGTGCTGTACATGCTGATCACTCGCGGCGGGGCACGCCTTAACCTGGAAGTGTTCACCGAGCTGCCGCCGACTGGCTTCGAGATGGGCGGTGGTTTCGGTAACGCTATGGCCGGTACCTTCGTCATg           <  8:8888/149‑1 (MQ=255)                                                                                                                                          gCGTGCCGCTGATTTCCGTGCTGTACATGCTGATCACTCGCGGCGGGGCACGCCTTAACCTGGAAGTGTTCACCGAGCTGCCGCCGACTGGCTTCGAGATGGGCGGTGGTTTCGGTAACGCTATGGCCGGTACCTTCGTCATGGTCgg      >  5:80829/1‑148 (MQ=255)                                                                                                                                             tGCCGCTGATTTCCGTGCTGTACATGCTGATCACTCGCGGCGGGGCACGCCTTAACCTGGAAGTGTTCACCGAGCTGCCGCCGACTGGCTTCGAGATGGGCGGTGGTTTCGGTAACGCTATGGCCGGTACCTTCGTCATGGTCGGCAtt  <  1:234436/149‑1 (MQ=255)                                                                                                                                             tGCCGCTGATTTCCGTGCTGTACATGCTGATCACTCGCGGCGGGGCACGCCTTAACCTGGAAGTGTTCACCGAGCTGCCGCCGACTGGCTTCGAGATGGGCGGTGGTTTCGGTAACGCTATGGCCGGTACCTTCGTCATGGTCGGCAtt  <  1:230615/149‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                 CCAGCGTGGTAACAAACAATGACTGACCTGACGACCCCTGTAGCCGCGCTGCCCAGCCTGCAGCGCAAGCTGGAAGGCCGCGCCC‑TGCGCAGCCTGGTATTGACCACCCTGGCCTGGTTCGCGGCACTGGTGGCCAGCGTGCCGCTGATTTCCGTGCTGTACATGCTGATCACTCGCGGCGGGGCACGCCTTAACCTGGAAGTGTTCACCGAGCTGCCGCCGACTGGCTTCGAGATGGGCGGTGGTTTCGGTAACGCTATGGCCGGTACCTTCGTCATGGTCGGCATT  >  NC_002947/3045406‑3045693

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: ‑