Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,189,641	A→C	9.3%	N170H (AAC→CAC)	PP_1937 →	helicase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,189,641	0	A	C	9.3%	115.7 / 2.9	42	N170H (AAC→CAC)	PP_1937	helicase
Reads supporting (aligned to +/- strand):  ref base A (20/18);  new base C (2/2);  total (22/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATCGAGCTGATTCGCGCCGGTCACGTGCGAATTCGTTACCCGACAGGGTACAGACGGCTACATGCAAAAATGTACTGCTCCGCTGGAGCAGTGACGCTTGGGTCCAGCAACTACACTGGACCAGGTTTACATACTCAGCATGAAGCGAACGTGCGCTTCACCTCTGGGGAAAGAGCGCGCTTTGTTGAGACCAATCTCCTAGCTGAGTGCTTTTGGAGCTTGGGGAGAAACGCCGAAGACGCTTTCATTGAGCTGCTAGAGCAGCTTCTCAAGTTCGTCACCTGGCAAGAGGCTTT  >  NC_002947/2189494‑2189789                                                                                                                                                    |                                                                                                                                                     aTCGAGCTGATTCGCGCCGGTCACGTGCGAATTCGTTACCCGACAGGGTACAGACGGCTACATGCAAAAATGTACTGCTCCGCTGGAGCAGTGACGCTTGGGTCCAGCAACTACACTGGACCAGGTTTACATACTCAGCATGAAGCGaa                                                                                                                                                     >  5:57897/1‑149 (MQ=255) aTCGAGCTGATTCGCGCCGGTCACGTGCGAATTCGTTACCCGACAGGGTACAGACGGCTACATGCAAAAATGTACTGCTCCGCTGGAGCAGTGACGCTTGCGTCCAGCAACTACACTGGACCAGGATTACATACTCAGAATGAAGCGaa                                                                                                                                                     >  5:43286/1‑149 (MQ=255)  tCGAGCTGATTCGCGCCGGTCACGTGCGAATTCGTTACCCGACAGGGTACAGACGGCTACATGCAAAAATGTACTGCTCCGCTGGAGCAGTGACGCTTGGGTCCAGCAACTACACTGGACCAGGTTTACATACTCAGCATGAAGCGAAc                                                                                                                                                    <  2:2423/149‑1 (MQ=255)   cGAGCTGATTCGCGCCGGTCACGTGCGAATTCGTTACCCGACAGGGTACAGACGGCTACATGCAAAAATGTACTGCTCCGCTGGAGCAGTGACGCTTGGGTCCAGCAACTACACTGGACCAGGTTTACATACTCAGCATGAAGCGAACg                                                                                                                                                   >  7:96667/1‑149 (MQ=255)        tGATTCGCGCCGGTCACGTGCGAATTCGTTACCCGACAGGGTACAGACGGCTACATGCAAAAATGTACTGCTCCGCTGGAGCAGTGACGCTTGGGTCCAGCAACTACACTGGACCAGGTTTACATACTCAGCATGAAGCGAACGTgcgc                                                                                                                                              >  1:109985/1‑149 (MQ=255)                gcCGGTCACGTGCGAATTCGTTACCCGACAGGGTACAGACGGCTACATGCAAAAATGTACTGCTCCGCTGGAGCAGTGACGCTTGGGTCCAGCAACTACACTGGACCAGGTTTACATACTCAGCATGAAGCGCACGTTCGCTTCatgct                                                                                                                                      <  7:73896/149‑5 (MQ=255)                             gAATTCGTTACCCGACAGGGTACAGACGGCTACATGCAAAAATGTACTGCTCCGCTGGAGCAGTGACGCTTGGGTCCAGCAACTACACTGGACCAGGTTTACATACTCAGCATGAAGCGAACGTGCGCTTCACCTCTGGGGAAAGAgcg                                                                                                                         <  8:96667/149‑1 (MQ=255)                              aaTTCGTTACCCGACAGGGTACAGACGGCTACATGCAAAAATGTACTGCTCCGCTGGAGCAGTGACGCTTGGGTCCAGCAACTACACTGGACCAGGTTTACATACTCAGCATGAAGCGAACGTGCGCTTCACCTCTGGGGAAAGAgcgc                                                                                                                        <  5:49733/149‑1 (MQ=255)                                 tCGTTACCCGACAGGGTACAGACGGCTACATGCAAAAATGTACTGCTCCGCTGGAGCAGTGACGCTTGGGTCCAGCAACTACACTGGACCAGGTTTACATACTCAGCATGAAGCGAACGTGCGCTTCACCTCTgggg                                                                                                                                 >  4:21071/1‑137 (MQ=255)                                 tCGTTACCCGACAGGGTACAGACGGCTACATGCAAAAATGTACTGCTCCGCTGGAGCAGTGACGCTTGGGTCCAGCAACTACACTGGACCAGGTTTACATACTCAGCATGAAGCGAACGTGCGCTTCACCTCTgggg                                                                                                                                 <  3:21071/137‑1 (MQ=255)                                   gTTACCCGACAGGGTACAGACGGCTACATGCAAAAATGTACTGCTCCGCTGGAGCAGTGACGCTTGGGTCCAGCAACTACACTGGACCAGGTTTACATACTCAGCATGAAGCGAACGTGCGCTTCACCTCTGGGGAAAGAGCGCGCttt                                                                                                                   >  3:63979/1‑149 (MQ=255)                                       cccGACAGGGTACAGACGGCTACATGCAAAAATGTACTGCTCCGCTGGAGCAGTGACGCTTGGGTCCAGCAACTACACTGGACCAGGTTTACATACTCAGCATGAAGCGAACGTGCGCTTCACCTCTGGGGAAAGAGCGCGCTttgtt                                                                                                                <  6:57897/148‑1 (MQ=255)                                             aGGGTACAGACGGCTACATGCAAAAATGTACTGCTCCGCTGGAGCAGTGACGCTTGGGTCCAGCAACTACACTGGACCAGGTTTACATACTCAGCATGAAGCGAACGTgcgc                                                                                                                                              >  6:2348/1‑112 (MQ=255)                                             aGGGTACAGACGGCTACATGCAAAAATGTACTGCTCCGCTGGAGCAGTGACGCTTGGGTCCAGCAACTACACTGGACCAGGTTTACATACTCAGCATGAAGCGAACGTgcgc                                                                                                                                              <  5:2348/112‑1 (MQ=255)                                                      aCGGCTACATGCAAAAATGTACTGCTCCGCTGGAGCAGTGACGCTTGGGTCCAGCAACTACACTGGACCAGGTTTACATACTCAGCATGAAGCGAACGTGCGCTTCACCTCTGGGGAAAGAGCGCGCTTTGTTGAGACCAATCTCCTAg                                                                                                <  6:218627/149‑1 (MQ=255)                                                           tACATGCAAAAATGTACTGCTCCGCTGGAGCAGTGACGCTTGGGTCCAGCAACTACACTGGACCAGGTTTACATACTCAGCATGAAGCGAACGTGCGCTTCACCTCTGGGGAAAGAGCGCGCTTTGTTGAGACCAATCTCCTAGCTGAg                                                                                           >  1:98275/1‑149 (MQ=255)                                                                 cAAAAATGTACTGCTCCGCTGGAGCAGTGACGCTTGGGTCCAGCAACTACACTGGACCAGGTTTACATACTCAGCATGAAGCGAACGTGCGCtt                                                                                                                                            >  8:5469/1‑94 (MQ=255)                                                                 cAAAAATGTACTGCTCCGCTGGAGCAGTGACGCTTGGGTCCAGCAACTACACTGGACCAGGTTTACATACTCAGCATGAAGCGAACGTGCGCtt                                                                                                                                            <  7:5469/94‑1 (MQ=255)                                                                 cAAAAATGTACTGCTCCGCTGGAGCAGTGACGCTTGGGTCCAGCAACTACACTGGACCAGGTTTACATACTCAGCATGAAGCGAACGTGCGCTTCACCTCTGGGGAAAGAGCGCGCTTTGTTGAGACCAATCTCCTAGCTGa                                                                                            <  3:42316/142‑1 (MQ=255)                                                                 cAAAAATGTACTGCTCCGCTGGAGCAGTGACGCTTGGGTCCAGCAACTACACTGGACCAGGTTTACATACTCAGCATGAAGCGAACGTGCGCTTCACCTCTGGGGAAAGAGCGCGCTTTGTTGAGACCAATCTCCTAGCTGa                                                                                            >  4:42316/1‑142 (MQ=255)                                                                    aaaTGTACTGCTCCGCTGGAGCAGTGACGCTTGGGTCCAGCAACTACACTGGACCAGGTTTACATACTCAGCATGAAGCGAACGTGCGCTTCACCTCTGGGGAAAGAGCGCGCTTTGTTga                                                                                                              <  2:80383/121‑1 (MQ=255)                                                                    aaaTGTACTGCTCCGCTGGAGCAGTGACGCTTGGGTCCAGCAACTACACTGGACCAGGTTTACATACTCAGCATGAAGCGAACGTGCGCTTCACCTCTGGGGAAAGAGCGCGCTTTGTTga                                                                                                              >  1:80383/1‑121 (MQ=255)                                                                    aaaTGTACTGCTCCGCTGGAGCAGTGACGCTTGGGTCCAGCAACTACACTGGACCAGGTTTACATACTCAGCATGAAGCGAACGTGCGCTTCACCTCTGGGGAAAGAGCGCGCTTTGTTGAGACCAATCTCCTAGCTGAGTGCTTTTgg                                                                                  <  6:196056/149‑1 (MQ=255)                                                                              cTCCGCTGGAGCAGTGACGCTTGGGTCCAGCAACTACACTGGACCAGGTTTACATACTCAGCATGAAGCGAACGTGCGCTTCACCTCTGGGGAAAGAGCGCGCTTTGTTGAGACCAATCTCCTAGCTGAGTGCTTTTGGAGCTTggg                                                                          <  2:109985/147‑1 (MQ=255)                                                                               tCCGCTGGAGCAGTGACGCTTGGGTCCAGCAACTACACTGGACCAGGTTTACATACTCAGCATGAAGCGAACGTGCGCTTCACCTCTGGGGAAAGAGCGCGCTTTGTTGAGACCAATCTCCTAGCTGAGTGCTTTTGGAGCTTggg                                                                          >  2:210871/1‑146 (MQ=255)                                                                               tCCGCTGGAGCAGTGACGCTTGGGTCCAGCAACTACACTGGACCAGGTTTACATACTCAGCATGAAGCGAACGTGCGCTTCACCTCTGGGGAAAGAGCGCGCTTTGTTGAGACCAAACTCCTAGCTGAGTGCTTTTGGCGCTTggc                                                                          >  2:92918/1‑145 (MQ=255)                                                                                           gTGACGCTTGGGTCCAGCAACTACACTGGACCAGGTTTACATACTCAGCATGAAGCGAACGTGCGCTTCACCTCTGGGGAAAGAGCGCGCTTTGTTGAGACCAATCTCCTAGCTGAGTGCTTTTGGAGCTTGGGGAGAAACGCCGAAGa                                                           >  8:107465/1‑149 (MQ=255)                                                                                                     ggTCCATCAACTCGACTGGACCAGGTTTACATACTCAGCATGAAGCGAACGTGCGCTTCACCTCTGGGGAAAGAGCGCGCTTTGTTGAGACCAATCTCCTAGCTGAGTGCTTTTGGAGCTTGGGGAGAAACGCCGAAGACGGTTTCttt                                                 <  6:43286/149‑1 (MQ=255)                                                                                                         cAGCAACTACACTGGACCAGGTTTACATACTCAGCATGAAGCGAACGTGCGCTTCACCTCTGGGGAAAGAGCGCGCTTTGTTGAGACCAATCTCCTAGCTGAGTGCTTTTGGAGCTTGGGGAGAAACGCCGAAGACGCTTTCATTGAg                                              <  4:63979/148‑1 (MQ=255)                                                                                                          aGCAACTACACTGGACCAGGTTTACATACTCAGCATGAAGCGAACGTGCGCTTCACCTCTGGGGAAAGAGCGCGCTTTGTTGAGACCAATCTCCTAGCTGAGTGCTTTTGGAGCTTGGGGAGAAACGCCGAAGACGCTTTCATTGAgct                                            >  3:29421/1‑149 (MQ=255)                                                                                                                  cacTGGACCAGGTTTACATACTCAGCATGAAGCGAACGTGCGCTTCACCTCTGGGGAAAGAGCGCGCTTTGTTGAGACCAATCTCCTAGCTGAGTGCTTTTGGAGCTTGGGGAGAAACGCCGAAGACGCTTTCATTGAGCTGCTAGagc                                    <  7:107465/149‑1 (MQ=255)                                                                                                                   acTGGAACAGGTTTACATACTCAGCATGAAGCGAACGTGCGCTTCACCTATGGGGAAAGAGCGCGCTTTGTTGAGACCAATCTCCTAGCTGAGTGCTTTTGGAGCTTGGGGAGAAACGCCGAAGACGCATTCATTGAGCTGCTagag                                     >  8:32363/1‑147 (MQ=255)                                                                                                                          cAGGTTTACATACTCAGCATGAAGCGAACGTGCGCTTCACCTCTGGGGAAAGAGCGCGCTTTGTTGAGACCAATCTCCTAGCTGAGTGCTTTTGGAGCTTGGGGAGAAACGCCGAAGACGCTTTCATTGAGCTGCTAGAGCAGCTtctc                            <  8:229149/149‑1 (MQ=255)                                                                                                                          cAGGTTTACATACTCAGCATGAAGCGAACGTGCGCTTCACCTCTGGGGAAAGAGCGCGCTTTGTTGAGACCAATCTCCTAGCTGAGTGCTTTTGGAGCTTGGGGAGAAACGCCGAAGACGCTTTCATTGAGCTGCTAGAGCAGCTtct                             >  1:22965/1‑148 (MQ=255)                                                                                                                               ttACATACTCAGCATGAAGCGAACGTGCGCTTCACCTCTGGGGAAAGAGCGCGCTTTGTTGAGACCAATCTCCTAGCTGAGTGCTTTTGGAGCTTGGGGAGAAACGCCGAAGACGCTTTCATTGAGCTGCTAGAGCAGCTTCTCAAGtt                       >  4:89442/1‑149 (MQ=255)                                                                                                                                       tCAGCATGAAGCGAACGTGCGCTTCACCTCTGGGGAAAGAGCGCGCTTTGTTGAGACCAATCTCCTAGCTGAGTGCTTTTGGAGCTTGGGGAGAAACGCCGAAGACGCTTTCATTGAGCTGCTAGAGCAGCTTCTCAAGTTCGTCACCt               >  8:87640/1‑149 (MQ=255)                                                                                                                                       cagaggtGAAGCGCACGTTCGCTTCACCTCTGGGGAAAGAGCGCGCTTTGTTGAGACCAATCTCCTAGCTGAGTGCTTTTGGAGCTTGGGGAGAAACGCCGAAGACGCTTTCATTGAGCTGCTAGAGCAGCTTCTCAAGTTCGTCACCt               >  8:159529/7‑149 (MQ=255)                                                                                                                                        cAGCATCAAGCGAACGTGCGCTACACCACTAGCGAAAGAGCGCGCTTTGATGAGACCAATCACCAAGCAGAGAGGTTTTCCAGCATGGGGAGAAACCCCGAAGACGCTTTCATTGAGCTGCTAGAGGAGCTTCTCAAGTTCgagcccag              >  4:265022/1‑142 (MQ=255)                                                                                                                                         aGCATGAAGCGAACGTGCGCTTCACCTCTGGGGAAAGAGCGCGCTTTGTTGAGACCAATCTCCTAGCTGAGTGCTTTTGGAGCTTGGGGAGAAACGCCGAAGACGCTTTCATTGAGCTGCTAGAGCAGCTTCTCAAGTTCGt                    <  4:250325/142‑1 (MQ=255)                                                                                                                                         aGCATGAAGCGAACGTGCGCTTCACCTCTGGGGAAAGAGCGCGCTTTGTTGAGACCAATCTCCTAGCTGAGTGCTTTTGGAGCTTGGGGAGAAACGCCGAAGACGCTTTCATTGAGCTGCTAGAGCAGCTTCTCAAGTTCGt                    >  3:250325/1‑142 (MQ=255)                                                                                                                                         aGCATGAAGCGAACGTGCGCTTCACCTCTGGGGAAAGAGCGCGCTTTGTTGAGACCAATCTCCTAGCTGAGTGCTTTTGGAGCTTGGGGAGAAACGCCGAAGACGCTTTCATTGAGCTGCTAGAGCAGCTTCTCAAGTTCGTCACCt               <  2:98275/147‑1 (MQ=255)                                                                                                                                            gtGAAGCGCACGTTCGCTTCACCTCTGGGGAAAGAGCGCGCTTTGTTGAGACCAATCTCCTAGCTGAGTGCTTTTGGAGCTTGGGGAGAAACGCCg                                                               >  6:259089/2‑96 (MQ=255)                                                                                                                                            gtGAAGCGCACGTTCGCTTCACCTCTGGGGAAAGAGCGCGCTTTGTTGAGACCAATCTCCTAGCTGAGTGCTTTTGGAGCTTGGGGAGAAACGCCg                                                               <  5:259089/95‑1 (MQ=255)                                                                                                                                            aTGAAGCGAACGTGCGCTTCACCTCTGGGGAAAGAGCGCGCTTTGTTGAGACCAATCTCCTAGCTGAGTGCTTTTGGAGCTTGGGGAGAAACGCCGAAGACGCTTTCGTTGAGCTGCTAGAGCAGCTTCTCAAGTTCGTCACCTGGc            >  3:169821/1‑147 (MQ=255)                                                                                                                                                    aaCGTGCGCTTCACCTCTGGGGAAAGAGCGCGCTTTGTTGAGACCAATCTCCTAGCTGAGTGCTTTTGGAGCTTGGGGAGAAACGCCGAAGACGCTTTCATTGAGCTGCTAGAGCAGCTTCTCAAGTTCGTCACCTGGCAAGAGGCttt  <  4:29421/149‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                     ATCGAGCTGATTCGCGCCGGTCACGTGCGAATTCGTTACCCGACAGGGTACAGACGGCTACATGCAAAAATGTACTGCTCCGCTGGAGCAGTGACGCTTGGGTCCAGCAACTACACTGGACCAGGTTTACATACTCAGCATGAAGCGAACGTGCGCTTCACCTCTGGGGAAAGAGCGCGCTTTGTTGAGACCAATCTCCTAGCTGAGTGCTTTTGGAGCTTGGGGAGAAACGCCGAAGACGCTTTCATTGAGCTGCTAGAGCAGCTTCTCAAGTTCGTCACCTGGCAAGAGGCTTT  >  NC_002947/2189494‑2189789

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑