Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,564,973	A→T	8.7%	L133Q (CTG→CAG)	pitB ←	phosphate transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,564,973	0	A	T	8.7%	132.2 / 5.2	46	L133Q (CTG→CAG)	pitB	phosphate transporter
Reads supporting (aligned to +/- strand):  ref base A (22/20);  new base T (2/2);  total (24/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.06e-01

GCGCCACCATTTCAGGCCGATCAGCACCAGGGCAGCAACGGCGAAGCCGGCCATTGGCGAGACCACCAGCGACATGGCGATATCGATCGCTTTCTGCCAGTTGACGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCAACACCGAGGATGGAACCGATCAGCGTGTGCGAACTGGAGGCGGGGATGCCAAAGTACCAGGTGCCCAGGTTCCAGGTGATGGCCGCAGCCAGCAACGAGAAGACCATGGCCAGGCCGTGGCCGGTGTTCACATTGATCAGC  >  NC_002947/1564828‑1565119                                                                                                                                                    |                                                                                                                                                   gcgcCACCATTTCAGGCCGATCAGCACCAGGGCAGCAACGGCGAAGCCGGCCATTGGCGAGACCACCAGCGACATGGCGATATCGATCGCTTTCTGCCAGTTGACGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTggccaggcc                                                                                                                                                >  2:1142965/1‑150 (MQ=255)   gcgaccaTTTCAGGCCGATCAGCACCAGGGCAGCAACGGCGAAGCCGGCCATTGGCGAGACCACCAGCGACATGGCGATATCGATCGCTTTCTGCCAGTTGACGCCGTCGGCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCaa                                                                                                                                              >  2:477105/4‑150 (MQ=255)   gcCACCATTTCAGGCCGATCAGCACCAGGGCAGCAACGGCGAAGCCGGCCATTGGCGAGACCACCAGCGACATGGCGATATCGATCGCTTTCTGCCAGTTGACGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCaa                                                                                                                                              <  2:1075737/150‑1 (MQ=255)     caccaTTTCAGGCCGATCAGCACCAGGGCAGCAACGGCGACGATCAGGATTAGTCACTCCACCAGCGACATTGCGATATCGATCGCTTTCTGCCAGTTGACGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCTGGCCAacg                                                                                                                                            >  1:328211/1‑149 (MQ=255)     caccaTTTCAGGCCGATCAGCACCAGGGCAGCAACGGCGAAGCCGGCCATTGGCGAGACCACCAGCGACATGGCGATATCGATCGCTTTCTGCCAGTTGACGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCAaca                                                                                                                                            >  1:158966/1‑150 (MQ=255)     caccaTTTCAGGCCGATCAGCACCAGGGCAGCAACGGCGAAGCCGGCCATTGGCGAGACCACCAGCGACATGGCGATATCGATCGCTTTCTGCCAGTTGACGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCAaca                                                                                                                                            >  2:1202812/1‑150 (MQ=255)        caTTTCAGGCCGATCAGCACCAGGGCAGCAACGGCGAAGCCGGCCATTGGCGAGACCACCAGCGACATGGCGATATCGATCGCTTTCTGCCAGTTGACGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCTGGCCAACGccc                                                                                                                                         <  2:328211/150‑2 (MQ=255)        caTTTCAGGCCGATCAGCACCAGGGCAGCAACGGCGAAGCCGGCCATTGGCGAGACCACCAGCGACATGGCGATATCGATCGCTTTCTGCCAGTTGACGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCTGGCCAACGccc                                                                                                                                         <  2:1193152/150‑2 (MQ=255)         aTTTCAGGCCGATCAGCACCAGGGCAGCAACGGCGAAGCCGGCCATTGGCGAGACCACCAGCGACATGGCGATATCGATCGCTTTCTGCCAGTTGACGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGCGCGTTGGCCAGGCCAACACCGa                                                                                                                                        >  2:613036/1‑150 (MQ=255)             cAGGCCGATCAGCACCAGGGCAGCAACGGCGAAGCCGGCCATTGGCGAGACCACCAGCGACATGGCGATATCGATCGCTTTCTGCCAGTTGACGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCAACACCGAGGAt                                                                                                                                    <  1:987641/150‑1 (MQ=255)              aGGCCGATCAGCACCAGGACAGCAACGGCGAAGCCGGCCATTGGCGAGACCACCAGCGACATGGCGATATCGATCGCTTTCTGCCAGTTGACGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCAACACCGAGGATg                                                                                                                                   >  1:371622/1‑150 (MQ=255)                gCCGATCAGCACCAGGGCAGCAACGGCGAAGCCGGCCATTGGCGAGACCACCAGCGACATGGCGATATCGATCGCTTTCTGCCAGTTGACGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCAACACCGAGGATGGa                                                                                                                                 >  2:793199/1‑150 (MQ=255)                     tCAGCACCAGGGCAGCAACGGCGAAGCCGGCCATTGGCGAGACCACCAGCGACATGGCGATATCGATCGCTTTCTGCCAGTTGACGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCAACACCGAGGATGGAACCGa                                                                                                                            >  2:1028115/1‑150 (MQ=255)                             aGGGCAGCAACGGCGAAGCCGGCCATTGGCGAGACCACCAGCGACATGGCGATATCGATCGCTTTCTGCCAGTTGACGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCAACACCGAGGATGGAACCGATCAGCgtg                                                                                                                    <  2:158966/150‑1 (MQ=255)                              gggCAGCAACGGCGAAGCCGGCCATTGGCGAGACCACCAGCGACATGGCGATATCGATCGCTTTCTGCCAGTTGACGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCAACACCGAGGATGGAACCGATCAGCgtgt                                                                                                                   <  1:1202812/150‑1 (MQ=255)                                                 ggCCATTGGCGAGACCACCAGCGACATGGCGATATCGATCGCTTTCTGCCAGTTGACGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCAACACCGAGGATGGAACCGAt                                                                                                                           <  1:568256/123‑1 (MQ=255)                                                 ggCCATTGGCGAGACCACCAGCGACATGGCGATATCGATCGCTTTCTGCCAGTTGACGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCAACACCGAGGATGGAACCGAt                                                                                                                           >  2:568256/1‑123 (MQ=255)                                                 ggCCATTGGCGAGACCACCAGCGACATGGCGATATCGATCGCTTTCTGCCAGTTGACGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCAACACCGAGGATGGAACCGATCAGCgt                                                                                                                     <  2:1102181/129‑1 (MQ=255)                                                 ggCCATTGGCGAGACCACCAGCGACATGGCGATATCGATCGCTTTCTGCCAGTTGACGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCAACACCGAGGATGGAACCGATCAGCgt                                                                                                                     >  1:1102181/1‑129 (MQ=255)                                                 ggCCATTGGCGAGACCACCAGCGACATGGCGATATCGATCGCTTTCTGCCAGTTGACGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCAACACCGAGGATGGAACCGATCAGCGTGTGCGAACTGGAGGCGGGGAt                                                                                                <  2:747988/150‑1 (MQ=255)                                                   ccATTGGCGAGACCACCAGCGACATGGCGATATCGATCGCTTTCTGCCAGTTGACGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCAACACCGAGGATGGAACCGATCAGCGTGTGCGAACTGGAGGCGGGGATGc                                                                                              <  2:205426/150‑1 (MQ=255)                                                    cATTGGCGAGACCACCAGCGACATGGCGATATCGATCGCTTTCTGCCAGTTGACGCCGTCGCCCAGAGCGGAAGAGCGT‑‑AGCGTGGCGTTGGCCAGGCCAACACCGAGGATGGAACCGATCAGCGTGTGCGAACTGGAGGCGGGGATGcc                                                                                             >  2:644593/1‑150 (MQ=255)                                                        ggCGAGACCACCAGCGACATGGCGATATCGATCGCTTTCTGCCAGTTGACGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCAACACCGAGGATGGAACCGATCAGCGTGTGCGAACTGGAGGCGGGGATGCCAAAg                                                                                         <  1:340739/150‑1 (MQ=255)                                                           gagaCCACCAGCGACATGGCGATATCGATCGCTTTCTGCCAGTTGACGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCAACACCGAGGATGGAACCGATCAGCGTGTGCGAACTGGAGGCgg                                                                                                    >  1:683659/1‑136 (MQ=255)                                                           gagaCCACCAGCGACATGGCGATATCGATCGCTTTCTGCCAGTTGACGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCAACACCGAGGATGGAACCGATCAGCGTGTGCGAACTGGAGGCgg                                                                                                    <  2:683659/136‑1 (MQ=255)                                                           gagaCCACCAGCGACATGGCGATATCGATCGCTTTCTGCCAGTTGACGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCAACACCGAGGATGGAACCGATCAGCGTGTGCGAACTGGAGGCGGGGATGCCAAAGTAc                                                                                      <  1:1142965/150‑1 (MQ=255)                                                             gacgacCAGAGACATGGCGATATCGATCGCTTTCTGCCAGTTGACGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCAACAGCGAGGATGGAACCGATCAGCGGGTGCGAACTGGAGGCGGGGATGCCAAAGTACCa                                                                                    <  2:510213/150‑1 (MQ=255)                                                              accaccAGCGACATGGCGATATCGATCGCTTTCTGCCAGTTGACGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCAACACCGAGGATGGAACCGATCAGCGTGTGCGAACTGGCGGCGGGGGTGCCAAGGTACCAg                                                                                   >  1:33445/1‑150 (MQ=255)                                                                    aGCGACATGGCGATATCGATCGCTTTCTGCCAGTTGACGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCAACACCGAGGATGGAACCGATCAGCGTGTGCGAACTGGAGGCGGGGATGCCAAAGTACCAGGTGccc                                                                             <  1:388150/150‑1 (MQ=255)                                                                                 tatCGATCGCTTTCTGCCAGTTGACGCCGGCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCAACACCGAGGATGGAACCGATCAGCGTGTGCGAACTGGAGGCGGGGATGCCAAAGTACCAGGTGCCCAGGTTCCAGGTGa                                                                <  1:1028115/150‑1 (MQ=255)                                                                                     gatcgCTTTCTGCCAGTTGACGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCAACACCGAGGATGGAACCGATCAGCGTGTGCGAACTGGAGGCGGGGATGCCAAAGTACCAGGTGCCCAGGTTACAGGTGATGGc                                                            >  2:305886/1‑150 (MQ=255)                                                                                           tttCTGCCAGTTGACGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCAACACCGAGGATGGAACCGATCAGCGTGTGCGAACTGGAGGCGGGGATGCCAAAGTACCAGGTGCCCAGGTTCCAGGTGATGGCCGcagc                                                      >  1:1154974/1‑150 (MQ=255)                                                                                                gCCAGTTGACGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCAACACCGAGGATGGAACCGATCAGCGTGTGCGAACTGGAGGCGGGGATGCCAAAGTACCATGTGCCCAGGTTCCAgg                                                                   <  2:710380/132‑1 (MQ=255)                                                                                                gCCAGTTGACGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCAACACCGAGGATGGAACCGATCAGCGTGTGCGAACTGGAGGCGGGGATGCCAAAGTACCAGGTGCCCAGGTTCCAgg                                                                   >  1:710380/1‑132 (MQ=255)                                                                                                gCCAGTTGACGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCAACACCGAGGATGGAACCGATCAGCGTGTGCGAACTGGAGGCGGGGATGCCAAAGTACCAGGTGCCCAGGTTCCAGGTGATGGCCGCAGCCAGCa                                                 >  2:1025573/1‑150 (MQ=255)                                                                                                 ccAGTTGACGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCAACACCGAGGATGGAACCGATCAGCGTGTGCGAACTGGAGGCGGGGATGCCAAAGTACCAGGTGCCCAGGTTCCAGGTGATGGCCGCAGCCAGCaa                                                <  2:371622/150‑1 (MQ=255)                                                                                                    gTTGACGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCAACACCGAGGATGGAACCGATCAGCGTGTGCGAACTGGAGGCGGGGATGCCAAAGTACCAGGTGCCCAGGTTCCAGGTGATGGCCGCAGCCAGCAACga                                             >  1:895373/1‑150 (MQ=255)                                                                                                        aCGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCAACACCGAGGATGGAACCGATCAGCGTGTGCGAACTGGAGGCGGGGATGCCAAAGTACCAg                                                                                   >  1:962655/1‑108 (MQ=255)                                                                                                        aCGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCAACACCGAGGATGGAACCGATCAGCGTGTGCGAACTGGAGGCGGGGATGCCAAAGTACCAg                                                                                   <  2:962655/108‑1 (MQ=255)                                                                                                         cGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCAACACCGAGGATGGAACCGATCAGCGTGTGCGAACTGGAGGCGGGGATGCCAAAGTACCAGGTGCCCAGGTTCCAGGTGATGGCCGCAGCCAGCAACGagaaga                                        <  1:613036/150‑1 (MQ=255)                                                                                                          gCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCAACACCGAGGATGGAACCGATCAGCGTGTGCGAACTGGAGGCGGGGATGCCAAAGTACCAGGTGCCCAGGTTCCAGGTGATGGCCGCAGCCAGCAACGAGAAGAc                                       >  2:895631/1‑150 (MQ=255)                                                                                                             gTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCAACACCGAGGATGGAACCGATCAGCGTGTGCGAACTGGAGGCGGGGATGCCAAAGTACCAGGTGCCCAGGTTCCAGGTGATGGCCGCAGCCAGCAACGAGAAGACCAt                                    <  1:1164552/150‑1 (MQ=255)                                                                                                                  cc‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCAACACCGAGGATGGAACCGATCAGCGTGTGCGAACTGGAGGCGGGGATGCCAAAGTACCAGGTGCCCAGGTTCCAGGTGATGGCCGCAGCCAGCAACGAGAAGACCATGGCCa                               >  2:770599/1‑150 (MQ=255)                                                                                                                        cGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCAACACCGAGGATGGAACCGATCAGCGTGTGCGAACTGGAGGCGGGGATGCCAAAGTACCAGGTGCCCAGGTTCCAGGTGATGGCCGCAGCCAGCAACGAGAAGACCATGGCCAGGcc                           >  2:1106063/1‑150 (MQ=255)                                                                                                                                  ttGATCAGGGCGTTGGCCAGGCCAACACCGAGGATGGAACCGATCAGCGTGTGCGAACTGGAGGCGGGGATGCCAAAGTACCAGGTGCCCAGGTTCCAGGTGATGGCCGCAGCCAGCAACGAGAAGACCATGGCCAGGCCGTGGCCGgtg                 <  2:277515/150‑1 (MQ=255)                                                                                                                                        tcggtgTTGGCCTGGCCAACACCGAGGATGGAACCGATCAGCGTGTGCGAACTGGAGGCGGGGATGCCAAAGTAACAGGTGCAAAGGCTCCCGGTAATGGCTCAAGACAGCACCGAAAAGACTAGTGTCAGGCCGTGGACGGTATTcaca           >  2:918806/6‑150 (MQ=255)                                                                                                                                              ttGGCCAGGCCAACACCGAGGATGGAACCGATCAGCGTGTGCGAACTGGAGGCGGGGATGCCAAAGTACCAGGTGCCCAGGTTCCAGGTGATGGCCGCAGCCAGCAACGAGAAGACCATGGCCAGGCCGTGGCCGGTGTTCACATTGATc     >  1:1142116/1‑150 (MQ=255)                                                                                                                                                 gccaggccaACACCGAGGATGGAACCGATCAGCGTGTGCGAACTGGAGGCGGGGATGCCAAAGTACCAGGTGCCCAGGTTCCAGGTGATGGCCGCAGCCAGCAACGAGAAGACCATg                                   <  2:976802/117‑1 (MQ=255)                                                                                                                                                 gccaggccaACACCGAGGATGGAACCGATCAGCGTGTGCGAACTGGAGGCGGGGATGCCAAAGTACCAGGTGCCCAGGTTCCAGGTGATGGCCGCAGCCAGCAACGAGAAGACCATg                                   >  1:976802/1‑117 (MQ=255)                                                                                                                                                 gccaggccaACACCGAGGATGGAACCGATCAGCGTGTGCGAACTGGAGGCGGGGATGCCAAAGTACCAGGTGCCCAGGTTCCAGGTGATGGCCGCAGCCAGCAACGAGAAGACCATGGCCAGGCCGTGGCCGGTGTTCACATTGATcagc  <  1:793199/150‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                   GCGCCACCATTTCAGGCCGATCAGCACCAGGGCAGCAACGGCGAAGCCGGCCATTGGCGAGACCACCAGCGACATGGCGATATCGATCGCTTTCTGCCAGTTGACGCCGTCGCCC‑‑AGCGGAATGTCGTTGATCAGGGCGTTGGCCAGGCCAACACCGAGGATGGAACCGATCAGCGTGTGCGAACTGGAGGCGGGGATGCCAAAGTACCAGGTGCCCAGGTTCCAGGTGATGGCCGCAGCCAGCAACGAGAAGACCATGGCCAGGCCGTGGCCGGTGTTCACATTGATCAGC  >  NC_002947/1564828‑1565119

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑