Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,816,531	C→G	7.7%	A114G (GCC→GGC)	PP_5092 →	NLP/P60 protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,816,531	0	C	G	7.7%	160.1 / 5.0	52	A114G (GCC→GGC)	PP_5092	NLP/P60 protein
Reads supporting (aligned to +/- strand):  ref base C (23/25);  new base G (2/2);  total (25/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.72e-01

CCGCCATGTCGCCTAAGCAAAGCAGCGATGTGCTGAGCCGTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACG‑GGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTGGCGACCTGATCTTCTTCAACATCAAGAGCCGTCGGGTCAATCACGTAGCCATCTACCTG  >  NC_002947/5816390‑5816670                                                                                                                                               |                                                                                                                                             ccgccATGTCGCCTAAGCAAAGCAGCGATGTGCTGAGCCGTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTc                                                                                                                                       >  7:227726/1‑149 (MQ=255)  cgccATGTCGCCTAAGCAAAGCAGCGATGTGCTGAGCCGTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTCg                                                                                                                                      <  1:121857/149‑1 (MQ=255)         tCGCCTAAGCAAAGCAGCGATGTGCTGAGCCGTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGGCGACGTCgtt                                                                                                                                    <  4:140660/144‑3 (MQ=255)         tCGCCTAAGCAAAGCAGCGATGTGCTGAGCCGTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGGCGACGTCgtt                                                                                                                                    >  3:140660/1‑142 (MQ=255)           gCCTAAGCAAAGCAGCGATGTGCTGAGCCGTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCcgc                                                                                                                             >  6:131568/1‑149 (MQ=255)            ccTAAGCAAAGCAGCGATGTGCTGAGCCGTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCcgcg                                                                                                                            >  7:170882/1‑149 (MQ=255)               aagcaaagcaCCGATTGGCTGAGCCGTCCGGTAAATGGGCCCGGAACTCCTTATGTTTGGGGCGGCAGAAGCCCGAAAAACGGCTTTGTCTGCAGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCAc                                                                                                                         <  1:213245/149‑1 (MQ=255)                  caaagcaGCGATGTGCTGAGCCGTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTc                                                                                                                      <  8:170882/149‑1 (MQ=255)                   aaagcaGCGATGTGCTGAGCCGTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTcc                                                                                                                     <  3:260347/149‑1 (MQ=255)                      gcagcGATGTGCTGAGCCGTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGGCGACGTCg                                                                                                                                      >  8:192001/1‑129 (MQ=255)                      gcagcGATGTGCTGAGCCGTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGGCGACGTCg                                                                                                                                      <  7:192001/129‑1 (MQ=255)                        agcGATGTGCTGAGCCGTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGc                                                                                                                >  2:159716/1‑149 (MQ=255)                                   gAGCCGTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCggg                                                                                                     <  2:139934/149‑1 (MQ=255)                                    aGCCGTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCggg                                                                                                     <  5:166134/148‑1 (MQ=255)                                      ccGTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTCCACCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGc                                                                                                   >  6:58792/1‑148 (MQ=255)                                         tGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACg                                                                                               >  5:24650/1‑149 (MQ=255)                                              tAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCa                                                                                                              >  4:182762/1‑129 (MQ=255)                                              tAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCa                                                                                                              <  3:182762/129‑1 (MQ=255)                                                     gCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACG‑GGGTGAAGGTgg                                                                                  >  3:157973/1‑149 (MQ=255)                                                           tACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACG‑GGGTGAAGGTGGCCAAgg                                                                            <  2:251473/149‑1 (MQ=255)                                                               ccTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACG‑GGGTGAAGGTGGCCAAGGGTGa                                                                        >  6:103591/1‑149 (MQ=255)                                                               ccTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACG‑GGGTGAAGGTGGCCAAGGGTGa                                                                        >  5:124388/1‑149 (MQ=255)                                                                cTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACG‑GGGTGAAGGTGGCCAAGGGTGAt                                                                       >  5:183386/1‑149 (MQ=255)                                                                   aTGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACG‑GGGTGAAGGTGGCCAAGGGTGATCt                                                                     <  3:86160/148‑1 (MQ=255)                                                                      tttGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGATCAAATACGCCTTAAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACG‑GGGTGAAGGTGGCCAAGGGTGATCTg                                                                    >  1:63942/1‑147 (MQ=255)                                                                      tttGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACG‑GGGTGAAGGTGGCCAAGGGTGATCTGaa                                                                  <  1:159716/148‑1 (MQ=255)                                                                      tttGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACG‑GGGTGAAGGTGGCCAAGGGTGATCTGaa                                                                  <  6:124388/148‑1 (MQ=255)                                                                          gggCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCGGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACG‑GGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTg                                                             <  1:122885/149‑1 (MQ=255)                                                                                   cagcCCGAAAAAAGGCTTTGACTGCAGCGGGCTGG‑TCAAATACGCCTTCAACGCCGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACG‑GGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTGGCGACCTg                                                     >  7:238791/1‑148 (MQ=255)                                                                                        cGAAAAAAGGCTTTGACTGCAGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACG‑GGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTg                                                             <  6:29724/135‑1 (MQ=255)                                                                                        cGAAAAAAGGCTTTGACTGCAGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACG‑GGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTg                                                             >  5:29724/1‑135 (MQ=255)                                                                                        cGAAAAAAGGCTTTGACTGCAGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACG‑GGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTGGCGACCTGAtcttc                                               <  4:157973/149‑1 (MQ=255)                                                                                          aaaaaaGGCTTTGACTGCAGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACG‑GGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTGGCGACCTGATcttctt                                             <  5:131568/149‑1 (MQ=255)                                                                                                   tttGACTGCAGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACG‑GGGTGAAGGTGGccccgg                                                                            >  1:119715/1‑105 (MQ=255)                                                                                                   tttGACTGCAGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACG‑GGGTGAAGGTGGccccgg                                                                            <  2:119715/109‑5 (MQ=255)                                                                                                     tGACTGCAGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACG‑GGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTGGCGACCTGATCTTCTTCAACATCaa                                    <  8:87940/147‑1 (MQ=255)                                                                                                      gACTGCAGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACG‑GGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTGGCGACCTGATCTTCTTCAACATCAagag                                 >  3:232173/1‑149 (MQ=255)                                                                                                         tGCAGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACG‑GGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTGGCGACCTGATCTTCTTCAACATCAAGAGCCg                              >  5:262544/1‑149 (MQ=255)                                                                                                           cAGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACG‑GGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTGGCGACCTGATCTTCTTCAACATCAAGAGCCGTc                            <  6:24650/149‑1 (MQ=255)                                                                                                            aGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACG‑GGGTGAAGGGGGCCAAGGGTGATCTGAAGCCTGGCGACCTGATCTTCTTCAACATCAAGAGCCGTCg                           <  8:227726/149‑1 (MQ=255)                                                                                                              cGGGCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACG‑GGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTGGCGACCTGATCTTCTTCAACATCAAGAGCCGTCggg                         <  6:183386/149‑1 (MQ=255)                                                                                                                 gCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACGCGGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTg                                                             <  1:36848/111‑1 (MQ=255)                                                                                                                 gCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACG‑GGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTg                                                             >  2:36848/1‑110 (MQ=255)                                                                                                                     g‑TCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACG‑GGGTGAAGGTGGCCAAGGGTGATCAGAAGCCTGGCGACCTGATCTTCTTCAACATCAAGAGCCGTCGGGTCAATc                   <  5:58792/148‑1 (MQ=255)                                                                                                                         aaaTACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACG‑GGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTGGCGACCTGATCTTCTTCAACATCAAGAGCCGTCGGGTCAATCACGt               >  1:108582/1‑149 (MQ=255)                                                                                                                          aaTACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACG‑GGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTGGCGACCTGATCTTCTTCAACATCAAGAGCCGTCGGGTCAATCACGTa              <  4:232173/149‑1 (MQ=255)                                                                                                                              cGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAAAGCCATGGCCCGGGGCCCCG‑GGGAGAAGGTGGCCAAGGGGGATCAGAAGCCTGGCGACCTGATCTTCTTCAACATCAAGAGGCGTCGGGGCAAACACGAAGc            >  8:78435/1‑147 (MQ=255)                                                                                                                                  ttCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACG‑GGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTGGCGACCTGATcttctt                                             <  4:31220/110‑1 (MQ=255)                                                                                                                                  ttCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACG‑GGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTGGCGACCTGATcttctt                                             >  3:31220/1‑110 (MQ=255)                                                                                                                                    cAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACG‑GGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTGGCGACCTGATCTTCTTCAACATCAAGAGCCGTCGGGTCAATCACGTAGCCATCTa      <  5:103591/147‑1 (MQ=255)                                                                                                                                    cAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACG‑GGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTGGCGACCTGATCTTCTTCAACATCAAGAGCCGTCGGGTCAATCACGTAGCCATCTAcc    >  7:163415/1‑149 (MQ=255)                                                                                                                                      acgacgTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACG‑GGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTGGCGACCTGATCTTCTTCAACATCAAGAGCCGTCGGGTCAATCACGTAGCCATCTCCCTg  >  8:168996/1‑149 (MQ=255)                                                                                                                                               |                                                                                                                                             CCGCCATGTCGCCTAAGCAAAGCAGCGATGTGCTGAGCCGTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGG‑TCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACG‑GGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTGGCGACCTGATCTTCTTCAACATCAAGAGCCGTCGGGTCAATCACGTAGCCATCTACCTG  >  NC_002947/5816390‑5816670

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: ‑