Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,128,412	C→T	7.2%	N1261N (AAC→AAT)	PP_1887 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,128,412	0	C	T	7.2%	157.9 / 2.3	55	N1261N (AAC→AAT)	PP_1887	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (23/28);  new base T (2/2);  total (25/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.33e-01

GAGACCTATGACGTCGATCACGACCTGGAGGAGTTGTTCAAGATCGTCAAATACGATCCGCAGTTGGCTATCGATTTGCATTACGACGGCAATGGCAACCTGATCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCTGTCGCTACAACTATGACCCAGAGAACATTCTGTCCGGCACGGCCCCTGGCTAAGGGCACCGGGGGGGCGACGAGGCCGGTATAGGGACCGGCCTCGTCGCATTCAGCGGTA  >  NC_002947/2128266‑2128560                                                                                                                                                    |                                                                                                                                                     gagaCCTATGACGTCGATCACGACCTGGAGGAGTTGTTCAAGATCGTCAAATACGATCCGCAGTTGGCTATCGATTTGCATTACGACGGCAATGGCAACCTGATCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CGGGCTGAACCg                                                                                                                                                    >  2:132170/1‑149 (MQ=255) gagaCCTATGACGTCGATCACGACCTGGAGGAGTTGTTCAAGATCGTCAAATACGATCCGCAGTTGGCTATCGATTTGCATTACGACGGCAATGGCAACCTGATCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCg                                                                                                                                                    >  2:261069/1‑149 (MQ=255)      cTATGACGTCGATCACGACCTGGAGGAGTTGTTCAAGATCGTCAAATACGATCCGCAGTTGGCTATCGATTTGCATTACGACGGCAATGGCAACCTGATCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGc                                                                                                                                               >  6:30380/1‑149 (MQ=255)         tGACGTCGATCACGACCTGGAGGAGTTGTTCAAGATCGTCAAATACGATCCGTAGTTGGCTATCGATTTGCATTACGACGGCAATGGCAACCTGATCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCa                                                                                                                                            <  4:35669/149‑1 (MQ=255)             gtagATCACGACCTGGAGGAGTTGTTCAAGATCGTCATATACTATACGCAGTTGGCTATCGATTTGCATTAAGACGGCAATGGCAACATGATAAGTTATTAGCAGGGGCGCGTACTGAGGTATGA‑CTGGATCAACAGATTGCTCAggg                                                                                                                                         >  3:9950/4‑148 (MQ=255)             gTCGATCACGACCTGGAGGAGTTGTTCAAGATCGTCAAATACGATCCGCAGTTGGCTATCGATTTGCATTACGACGGCAATGGCAACCTGATCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCAGGGt                                                                                                                                        <  1:320181/149‑1 (MQ=255)                     cGACCTGGAGGAGTTGTTCAAGATCGTCAAATACGATCCGCAGTTGGCTATCGATTTGCATTACGACGGCAATGGCAACCTGATCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCAGGGTCGAGAccc                                                                                                                                <  2:350116/149‑1 (MQ=255)                         cTGGAGGAGTTGTTCAAGATCGTCAAATACGATCCTCAGTTGGCTATCGATTTGGATTACTACGGCAATGGCAACCTTATCAGTGATGAGCAGGGGCTGGTACTGTCTTATGA‑CGGGCTCAACCGTTTGCTCAGGGTAGAGACCCCTGa                                                                                                                            <  4:9950/149‑1 (MQ=255)                            gaggagTTGTTCAAGATCGTCAAATACGATCCGCAGTTGGCTATCGATTTGCATTACGACGGCAATGGCAACCTGATCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCAGGGTCGAGACCCCTGAc                                                                                                                           <  3:358277/147‑1 (MQ=255)                            gaggagTTGTTCAAGATCGTCAAATACGATCCGCAGTTGGCTATCGATTTGCATTACGACGGCAATGGCAACCTGATCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCAGGGTCGAGACCCCTGACgg                                                                                                                         <  4:22143/149‑1 (MQ=255)                            gaggagTTGTTCAAGATCGTCAAATACGATCCGCAGTTGGCTATCGATTTGCATTACGACGGCAATGGCAACCTGATCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCAGGGTCGAGACCCCTGACg                                                                                                                          <  1:98994/148‑1 (MQ=255)                                  ttgttCAAGATCGTCAAATACGATCCGCAGTTGGCTATCGATTTGCATTACGACGGCAATGGCAACCTGATCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCa                                                                                                                                            >  8:309329/1‑124 (MQ=255)                                  ttgttCAAGATCGTCAAATACGATCCGCAGTTGGCTATCGATTTGCATTACGACGGCAATGGCAACCTGATCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CGGGCCCAACCGTTTGCTCa                                                                                                                                            <  7:309329/124‑1 (MQ=255)                                    gttCAAGATCGTCAAATACGATCCGCAGTTGGCTATCGATTTGCATTACGACGGCAATGGCAACCTGATCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCt                                                                                                                 >  1:100631/1‑149 (MQ=255)                                      tCAAGATCGTCAAATACGATCCGCAGTTGGCTATCGATTTGCATTACGACGGCAATGGCAACCTGATCAGTGATGAGCAGGGGCGGGTACTGACGTATGATCGGGCTCAACCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCt                                                                                                                 <  1:261069/148‑1 (MQ=255)                                        aaGATCGTCAAATACGATCCGCAGTTGGCTATCGATTTGCATTACGACGGCAATGGCAACCTGATCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCTGTCg                                                                                                             >  6:343946/1‑149 (MQ=255)                                        aaGATCGTCAAATACGATCCGCAGTTGGCTATCGATTTGCATTACGACGGCAATGGCAACCTGATCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CCGGCTCAACCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCTGTc                                                                                                              <  1:320701/148‑1 (MQ=255)                                          gATCGTCAAATACGATCCGCAGTTGGCTATCGATTTGCATTACGACGGCAATGGCAACCTGATCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCAGGGt                                                                                                                                        >  7:9527/1‑120 (MQ=255)                                          gATCGTCAAATACGATCCGCAGTTGGCTATCGATTTGCATTACGACGGCAATGGCAACCTGATCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCAGGGt                                                                                                                                        <  8:9527/120‑1 (MQ=255)                                            tCGTCAAATACGATCCGCAGTTGGCTATCGATTTGCATTACGACGGCAATGGCAACCTGATCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCAGGGTCGAGAcccc                                                                                                                               >  6:41826/1‑127 (MQ=255)                                            tCGTCAAATACGATCCGCAGTTGGCTATCGATTTGCATTACGACGGCAATGGCAACCTGATCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCAGGGTCGAGAcccc                                                                                                                               <  5:41826/127‑1 (MQ=255)                                               tCAAATACGATCCGCAGTTGGCTATCGATTTGCATTACGACGGCAATGGCAACCTGATCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCTGTCGCTACAAc                                                                                                      <  2:100631/149‑1 (MQ=255)                                                    tACGATCCGCAGTTGGCTATCGATTTGCATTACGACGGCAATGGCAACCTGATCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCTGTCGCTACAACTATGa                                                                                                 <  7:52671/149‑1 (MQ=255)                                                                     tATCGATTTGCATTACGACGGCAATGGCAACCTGATCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCTGTCGCTACAACTATGACCCAGAGAACATTCTGt                                                                                >  2:88763/1‑149 (MQ=255)                                                                     tATCGATTTGCATTACGACGGCAATGGCAACCTGATCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCTGTCGCTACAACTATGACCCAGAGAACATTCTGt                                                                                >  6:292938/1‑149 (MQ=255)                                                                      aTCGATTTGCATTACGACGGCAATGGCAACCTGATCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCTGTCGCTACAACTATGACCCAGAGAACATTCTGTc                                                                               >  8:27041/1‑149 (MQ=255)                                                                       tCGATTTGCATTACGACGGCAATGGCAACCTGATCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCTGTCGCTACAACTATGACCCAGAGAACATTCTGTc                                                                               <  1:88763/148‑1 (MQ=255)                                                                                 ttACGACGGCAATGGCAACCTGATCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCTGTCGCTACAACTATGACCCAGAGAACATTCTGTCCGGCACGGccc                                                                    >  3:6949/1‑149 (MQ=255)                                                                                     gacgGCAATGGCAACCTGATCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCAGGGTCGAGACGCCTAACGGTGAACGCTGTCGCTACAACTATGACCCAGAGAACATTCTGTCCGGCACGGCCCCTgg                                                                <  6:118009/149‑1 (MQ=255)                                                                                      acgGCAATGGCAACCTGATCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCTGTCGCTACAACTATGACCCAGAGAACATTCTGTCCGGCACGGCCCCTGGc                                                               >  1:214639/1‑149 (MQ=255)                                                                                          cAATGGCAACCTGATCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCTGTCGCTACAACTATGACCCAGAGAACATTCTGTCCGGCACGGCCCCTGGCTAAg                                                           >  2:30241/1‑149 (MQ=255)                                                                                               gCAACCTGATCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCTGTCGCTACAACTATGACCCAGAGAACATTCTGTCCGGCACGGCCCCTGGCTAAGGGCAc                                                      <  5:30380/149‑1 (MQ=255)                                                                                                    cTGATCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCTGTCGCTACAACTATGACCCAGAGAACATTCTGTCCGGCACGGCCCCTGGCTAAGGGCACCgggg                                                 <  2:214639/149‑1 (MQ=255)                                                                                                     tGATCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCTGTCGCTACAACTATGACCCAGAGAACATTCTGTCCGGCACGGCCCCTGGCTAAGGGCACCggggg                                                >  1:291634/1‑149 (MQ=255)                                                                                                      gATCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCTGTCGCTACAACTATGACCCAGAGAACATTCTGTCCGGCACGGCCCCTGGCTaa                                                            >  8:319519/1‑136 (MQ=255)                                                                                                      gATCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCTGTCGCTACAACTATGACCCAGAGAACATTCTGTCCGGCACGGCCCCTGGCTaa                                                            <  7:319519/136‑1 (MQ=255)                                                                                                      gATCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCTGTCGCTACAACTATGACCCAGAGAACATTCTGTCCGGCACGGCCCCTGGCTAAGGGCACCgggggg                                               >  1:3515/1‑149 (MQ=255)                                                                                                      gATCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCTGTCGCTACAACTATGACCCAGAGAACATTCTGTCCGGCACGGCCCCTGGCTAAGGGCACCgggggg                                               >  1:85665/1‑149 (MQ=255)                                                                                                        tCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCTGTCGCTACAACTATGACCCAGAGAACATTCTGTCCGGCACGGCCCCTGGCTAAGGGCACCGGGGGGGc                                             >  4:178696/1‑149 (MQ=255)                                                                                                        tCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCTGTCGCTACAACTATGACCCAGAGAACATTCTGTCCGGCACGGCCCCTGGCTAAGGGCACCGGGGGGGc                                             >  4:332211/1‑149 (MQ=255)                                                                                                            tgatgaGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCTGTCGCTACAACTATGACCCAGAGAACATTCTGTCCGGCACGGc                                                                      <  4:74057/120‑1 (MQ=255)                                                                                                            tgatgaGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCTGTCGCTACAACTATGACCCAGAGAACATTCTGTCCGGCACGGc                                                                      >  3:74057/1‑120 (MQ=255)                                                                                                                 aGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCTGTCGCTACAACTATGACCCAGAGAACATTCTGTCCGGCACGGCCCCTGGCTAAGGGCACCGGGGGGGCGACGAGGcc                                    <  6:261151/149‑1 (MQ=255)                                                                                                                  gCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCTGTCGCTACAACTATGACCCAGAGAACATTCTGTCCGGCACGGCCCCTGGCTAAGGGCACCGGGGGGGCGACGAGGCCg                                   <  3:332211/149‑1 (MQ=255)                                                                                                                       ggCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCTGTCGCTACAACTATGACCCAGAGAACATTCTGTCCGGCACGGCCCCTGGCTAAGGGCACCGGGGGGGCGACGAGGCCGGtata                              <  3:178696/149‑1 (MQ=255)                                                                                                                         cGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCTGTCGCTACAACTATGACCCAGAGAACATTCTGTCCGGCACGGCCCCTGGCTAAGGGCACCGGGGGGGCGACGAGGCCGGTATAgg                            <  1:30241/149‑1 (MQ=255)                                                                                                                                       tGA‑CGGGCTCAACCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCTGTCGCTACAACTATGACCCAGAGAACATTCTGTCCGGCACGGCCCCTGGCTAAGGGCACCGGGGGGGCGACGAGGCCGGTATAGGGACCGGCCtcgtc               <  2:3515/148‑1 (MQ=255)                                                                                                                                         a‑CGGGCTCAATCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCTGTCGCTACAACTATGACCCAGAGAACATTCTGTCCGGCACGGCCCCTGGCTAAGGGCACCGGGGGGGCGACGAGGCCg                                   <  5:79743/126‑1 (MQ=255)                                                                                                                                         a‑CGGGCTCAATCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCTGTCGCTACAACTATGACCCAGAGAACATTCTGTCCGGCACGGCCCCTGGCTAAGGGCACCGGGGGGGCGACGAGGCCg                                   <  3:316226/126‑1 (MQ=255)                                                                                                                                         a‑CGGGCTCAATCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCTGTCGCTACAACTATGACCCAGAGAACATTCTGTCCGGCACGGCCCCTGGCTAAGGGCACCGGGGGGGCGACGAGGCCg                                   >  6:79743/1‑126 (MQ=255)                                                                                                                                         a‑CGGGCTCAATCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCTGTCGCTACAACTATGACCCAGAGAACATTCTGTCCGGCACGGCCCCTGGCTAAGGGCACCGGGGGGGCGACGAGGCCg                                   >  4:316226/1‑126 (MQ=255)                                                                                                                                           cGGGCTCAACCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCTGTCGCTACAACTATGACCCAGAGAACATTCTGTCCGGCACGGCCCCTGGCTAAGGGCACCGGGGGGGCGACGAGGCCGGTATAGGGACCGGCCTCGTCGCAt           <  4:6949/149‑1 (MQ=255)                                                                                                                                            gggCTCAACCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCTGTCGCTACAACTATGACCCAGAGAACATTCTGTCCGGCACGGCCCCTGGCTAAGGGCACCGGGGGGGCGACGAGGCCGGTATAGGGACCGGCCTCGTCGCAtt          <  1:92044/149‑1 (MQ=255)                                                                                                                                                  aaCCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCTGTCGCTACAACTATGACCCAGAGAACATTCTGTCCGGCACGGCCCCTGGCTAAGGGCACCGGGGGGGCGACGAGGc                                     <  4:194928/116‑1 (MQ=255)                                                                                                                                                  aaCCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCTGTCGCTACAACTATGACCCAGAGAACATTCTGTCCGGCACGGCCCCTGGCTAAGGGCACCGGGGGGGCGACGAGGc                                     >  3:194928/1‑116 (MQ=255)                                                                                                                                                    ccGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCTGTCGCTACAACTATGACCCAGAGAACATTCTGTCCGGCACGGCCCCTGGCTAAGGGCACCGGGGGGGCGACGAGGCCGGTATAGGGACCGGCCTCGTCGCATTCAGCGGTa  <  2:291634/149‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                     GAGACCTATGACGTCGATCACGACCTGGAGGAGTTGTTCAAGATCGTCAAATACGATCCGCAGTTGGCTATCGATTTGCATTACGACGGCAATGGCAACCTGATCAGTGATGAGCAGGGGCGGGTACTGACGTATGA‑CGGGCTCAACCGTTTGCTCAGGGTCGAGACCCCTGACGGTGAACGCTGTCGCTACAACTATGACCCAGAGAACATTCTGTCCGGCACGGCCCCTGGCTAAGGGCACCGGGGGGGCGACGAGGCCGGTATAGGGACCGGCCTCGTCGCATTCAGCGGTA  >  NC_002947/2128266‑2128560

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: ‑