Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,777,000	C→G	9.1%	A169P (GCA→CCA)	PP_2429 ←	membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,777,000	0	C	G	9.1%	147.9 / 7.2	55	A169P (GCA→CCA)	PP_2429	membrane protein
Reads supporting (aligned to +/- strand):  ref base C (23/27);  new base G (3/2);  total (26/29)
Fisher's exact test for biased strand distribution p-value = 6.59e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.95e-01

TTTCGCGAGGCGTTGACACGTTGAGCCGAGGCCGCTCAGGCCCCTTGTCGGTCAAGTAGAGGCTCAGGCCAATACTGCAGCCCATGCCGATATCAACAAAACCCCCGCCAACACTTGGTTGAACACCCGCAACCGCCCCGGTGCCTGCAGCCACC‑GGGCGCTCCCCACCCCCAACACCGCCCAGGCGGCCATGCTCGGCAGAGCGATCAGCAAGAA‑CACCAGCGCCAGCTGCCACACTGGCAACGACGGCGCGGCAAATACCCCGACCACCGCCACGGCCATCAAC  >  NC_002947/2776857‑2777142                                                                                                                                                |                                                                                                                                                 tttCGCGAGGCGTTGACACGTTGAGCCGAGGCCGCTCAGGCCCCTTGTCGGTCAAGTAGAGGCTCAGGCCAATACTGCAGCCCATGCCGATATCAACAAAACCCCCGCCAACACTTGGTTGAACACCCGCAACCGCCCCGGTGGCTg                                                                                                                                               >  6:317356/1‑147 (MQ=255) tttCGCGAGGCGTTGACACGTTGAGCCGAGGCCGCTCAGGCCCCTTGTCGGTCAAGTAGAGGCTCAGGCCAATACTGCAGCCCATGCCGATATCAACAAAACCCCCGCCAACACTTGGTTGAACACCCGCAACCGCCCCGGTGCCTGCa                                                                                                                                             >  8:311875/1‑149 (MQ=255)   tCGCGAGGCGTTGACACGTTGAGCCGAGGCCGCTCAGGCCCCTTGTCGGTCAAGTAGAGGCTCAGGCCAATACTGCAGCCCATGCCGATATCAACAAAACCCCCGCCAACACTTGGTTGAACACCCGCAACCGCCCCGGTGCCTGCa                                                                                                                                             <  6:345496/147‑1 (MQ=255)    cgcgAGGCGTTGACACGTTGAGCCGAGGCCGCTCAGGCCCCTTGTCGGTCAAGTAGAGGCTCAGGCCAATACTGCAGCCCATGCCGATATCAACAAAACCCCCGCCAACACTTGGTTGAACACCCGCAACCGCCCCGGTGCCTGCAGc                                                                                                                                           <  4:57115/148‑1 (MQ=255)            gTTGACACGTTGAGCCGAGGCCGCTCAGGCCCCTTGTCGGTCAAGTAGAGGCTCAGGCCAATACTGCAGCCCATGCCGATATCAACAAAACCCCCGCCAACACTTGGTTGAACACCCGCAACCGCCCCGGTGGCTGCAGGCACC‑ggggc                                                                                                                                 <  5:317356/149‑3 (MQ=255)                acacGTTGAGCCGAGGCCGCTCAGGCCCCTTGTCGGTCAAGTAGAGGCTCAGGCCAATACTGCAGCCCATGCCGATATCAACAAAACCCCCGCCAACACTTGGTTGAACACCCGCAACCGCCCCGGTGCCTGCAGCCACC‑GGGCGCTcc                                                                                                                             >  4:190258/1‑149 (MQ=255)                acacGTTGAGCCGAGGCCGCTCAGGCCCCTTGTCGGTCAAGTAGAGGCTCAGGCCAATACTGCAGCCCATGCCGATATCAACAAAACCCCCGCCAACACTTGGTTGAACACCCGCAACCGCCCCGGTGCCTGCAGCCACC‑GGGCGCTc                                                                                                                              <  7:311875/148‑1 (MQ=255)                  acGTTGAGCCGAGGCCGCTCAGGCCCCTTGTCGGTCAAGTAGAGGCTCAGGCCAATATTGCAGCCCATGCCGATATCAACAAAACCCCCGCCAACACTTGGTTGAACACCCGCAACCGCCCCGGTGCCTGCAGCCACC‑GGGCGCTcccc                                                                                                                           <  6:281881/149‑1 (MQ=255)                        aGCCGAGGCCGCTCAGGCCCCTTGTCGGTCAAGTAGAGGCTCAGGCCAATACTGCAGCCCATGCCGATATCAACAAAACCCCCGCCAACACTTGGTTGAACACCCGCAACCGCCCCGGTGCCTGCAGCCACC‑GGGCGCTCCCCAccccc                                                                                                                     >  6:266323/1‑149 (MQ=255)                         gCCGAGGCCGCTCAGGCCCCTTGTCGGTCAAGTAGAGGCTCAGGCCAATACTGCAGCCCATGCCGATATCAACAAAACCCCCGCCAACACTTGGTTGAACACCCGCAACCGCCCCGGTGCCTGc                                                                                                                                              >  3:137776/1‑124 (MQ=255)                         gCCGAGGCCGCTCAGGCCCCTTGTCGGTCAAGTAGAGGCTCAGGCCAATACTGCAGCCCATGCCGATATCAACAAAACCCCCGCCAACACTTGGTTGAACACCCGCAACCGCCCCGGTGCCTGc                                                                                                                                              <  4:137776/124‑1 (MQ=255)                         gCCGAGGCCGCTCAGGCCCCTTGTCGGTCAAGTAGAGGCTCAGGCCAATACTGCAGCCCATGCCGATATCAACAAAACACCCGCCAACACTTGGTTGAAAACCCGCAACCGCCCCCGTGCCTGCAGCCACC‑GGGCGCTCACCAccccc                                                                                                                     >  4:149756/1‑148 (MQ=255)                                    tCAGGCCCCTTGTCGGTCAAGTAGAGGCTCAGGCCAATACTGCAGCCCATGCCGATATCAACAAAACCCCCGCCAACACTTGGTTGAACACCCGCAACCGCCCCGGTGCCTGCAGCCACC‑GGGCGCTCCCCACCCCCACCACCGCCCAg                                                                                                         >  8:162802/1‑149 (MQ=255)                                        gCCCCTTGTCGGTCAAGTAGAGGCTCAGGCCAATACTGCAGCCCATGCCGATATCAACAAAACCCCCGCCAACACTTGGTTGAACACCCGCAACCGCCCCGGTGCCTGCAGCCACC‑GGGCGCTCCCCACCCCCAACACCGCCCAggcgg                                                                                                     <  1:185344/149‑1 (MQ=255)                                                 cGGTCAAGTAGAGGCTCAGGCCAATACTGCAGCCCATGCCGATATCAACAAAACCCCCGCCAACACTTGGTTGAACACCCGCAACCGCCCCGGTGCCTGCAGCCACC‑GGGCGCTCCCCACCCCCAACAcc                                                                                                               <  3:165470/130‑1 (MQ=255)                                                 cGGTCAAGTAGAGGCTCAGGCCAATACTGCAGCCCATGCCGATATCAACAAAACCCCCGCCAACACATGGTTGAACACCCGCAACCGCCCCGGTGCCTGCAGCCACC‑GGGCGCTCCCCACCCCCAACAcc                                                                                                               >  4:165470/1‑130 (MQ=255)                                                  ggTCAAGTAGAGGCTCAGGCCAATACTGCAGCCCATGCCGATATCAACAAAACCCCCGCCAACACTTGGTTGAACACCCGCAACCGCCCCGGTGCCTGCAGCCACC‑GGGCGCTCCCCACCCCCAACACCGCCCAGGCGGCCATGCTCgg                                                                                           <  3:149756/149‑1 (MQ=255)                                                    tCAAGTAGAGGCTCAGGCCAATACTGCAGCCCATGCCGATATCAACAAAACCCCCGCCAACACTTGGTTGAACCCCCGCAACCGCCCCGGTGCCTGCAGCCACC‑GGGCGCGCCCCACCCCCAACACCGCCCCGGCGGCCCTGCTCgg                                                                                           >  6:332349/1‑147 (MQ=255)                                                        gTAGAGGCTCAGGCCAATACTGCAGCCCATGCCGATATCAACAAAACCCCCGCCAACACTTGGTTGAACACCCGCAACCGCCCCGGTGCCGGCAGCCCCC‑GGGGGCGGCCCCCCCCCAACACCGCCCAGGCGGCCCAGCGCGGCCGAGc                                                                                     >  8:52741/1‑149 (MQ=255)                                                             ggCTCAGGCCAATACTGCAGCCCATGCCGATATCAACAAAACCCCCGCCAACACTTGGTTGAACACCCGCAACCGCCCCGGTGCCTGCAGCCACC‑GGGCGCTCCCCACCCCCAACACCGCCCAGGCGGCCATGCTCGGCAGAGCGATCa                                                                                <  5:266323/149‑1 (MQ=255)                                                                tCAGGCCAATACTGCAGCCCATGCCGATATCAACAAAACCCCCGCCAACACTTGGTTGAACACCCGCAACCGCCCCGGTGCCt                                                                                                                                                <  1:150374/83‑1 (MQ=255)                                                                tCAGGCCAATACTGCAGCCCATGCCGATATCAACAAAACACCCGCCAACACTTGGTTGAACACCCGCAACCGCCCCGGTGCCt                                                                                                                                                >  2:150374/1‑83 (MQ=255)                                                                 cAGGCCAATACTGCAGCCCATGCCGATATCAACAAAACCCCCGCCAACACTTGGTTGAACACCCGCAACCG‑CCCGGTGCCTGCAGCCACC‑GGGCGCTCCCCACCCCCAACACCGCCCAGGCGGCCATGCTCGGCAGAGCGATCAGCAAg                                                                           <  7:101150/149‑1 (MQ=255)                                                                    gCCAATACTGCAGCCCATGCCGATATCAACAAAACCCCCGCCAACACTTGGTTGAACACCCGCAACCGCCCCGGTGCCTGCAGCCACC‑GGGCGCTCCCCACCCCCAACCCCGCCCAGGCGGCCATGCTCGGCAGAGCGATCAGCAAGaa                                                                         >  4:288299/1‑149 (MQ=255)                                                                      cAATACTGCAGCCCATGCCGATATCAACAAAACCCCCGCCAACACTTGGTTGAACACCCGCAACCGCCCCCGTGCCTGCAGCCACC‑CGGCGCTCCCCCCCCCCAACACCCCCCAGGCGGCCAAGCACGGCAGAGCGAACAGCAAGAa‑cc                                                                      >  2:4408/1‑148 (MQ=255)                                                                      cAATACTGCAGCCCATGACCATATCAACAAAACCCCCGCCAACACTTGGTTGAACACCCGCAACCGCCCCGCAGCCACCACCCACC‑CGGCGCTCCCCACCCCCAACACCCCCCAGGCCGCCATGCTCGGCAGAGCGATCAGCAacaa‑ca                                                                      >  4:206109/1‑149 (MQ=255)                                                                           cTGCAGCCCATGCCGATATCAACAAAACCCCCGCCAACACTTGGTTGAACACCCGCAACCGCCCCGGTGCCTGCAGCCACC‑GGGCGCTCCCCAc                                                                                                                         <  4:279726/94‑1 (MQ=255)                                                                           cTGCAGCCCATGCCGATATCAACAAAACCCCCGCCAACACTTGGTTGAACACCCGCAACCGCCCCGGTGCCTGCAGCCACC‑GGGCGCTCCCCAc                                                                                                                         >  3:279726/1‑94 (MQ=255)                                                                           cTGCAGCCCATGCCGATATCAACAAAACCCCCGCCAACACTTGGTTGAACACCCGCAACCGCCCCGGTGCCTGCAGCCACC‑GGGCGCTCCCCACCCCCAACACCGCCCAGGCGGCCATGCTCGGCAGAGCGATCAGCAAGAA‑CACCAgc                                                                 <  5:332349/149‑1 (MQ=255)                                                                                 cccATGCCGATATCAACAAACCCCCCGCCAACACTTGGTTGAACACCCGCAACCGCCCCGGTGCCAGCAGCCACC‑GGGCGCGCCCCACCCCCAACCCCGCCCAGGCCGCCATGCTCGGCAGAGCGATCCGCCAGAA‑CCCCCCCGCCAGc                                                           >  8:249465/1‑149 (MQ=255)                                                                                    aTGCCGATATCAACAAAACCCCCGCCAACACTTGGTTGAACACCCGCAACCGCCCCGGTGCCTGCAGCCACC‑GGGCGCTCCCCACCCCCAACACCGCCCAGGCGGCCATGCTCGGCAGAGCGATCAGCaa                                                                            <  5:309608/130‑1 (MQ=255)                                                                                        cGATATCAACAAAACCCCCTCCAACACTTGGTTTAACACCCGCAACCGCCCCGGTGCCTGCAGCCACC‑GGGCGCTCCCCACCCCCAACACCGCCCAGGCGGCCATGCt                                                                                              <  1:340510/108‑1 (MQ=255)                                                                                            atCAACTATACCCCCGCCAACTCTTGGTTGAACACCCGCAACCGCCCCGGTGCCTGCAGCCACC‑GGGCGCTCCCCACCCCCAACACCGCCCAGGCGGCCATGCTCGGCAGAGCGATCAGCAAGAA‑CACCAGCGCCAGCTGCCACACt                                                  <  7:166960/147‑1 (MQ=255)                                                                                               aacaaAACCCCCGCCAACACTTGGTTGAACACCCGCAACCGCCCCGGTGCCTGCAGCCACC‑GGGCGCTCCCCACCCCCAACACCGCCCAGGCGGCCATGCTCGGCAGAGCGATCAGCAAGAA‑CACCAGCGCCAGCTGCCACACTGGCa                                              <  1:122110/148‑1 (MQ=255)                                                                                                acaaAACCCCCGCCAACACTTGGTTGAACACCCGCAACCGCCCCGGTGCCTGCAGCCACC‑GGGCGCTCCCCACCCCCAACACCGCCCAGGCGGCCATGCTCGGCagag                                                                                      <  7:92296/108‑1 (MQ=255)                                                                                                acaaAACCCCCGCCAACACTTGGTTGAACACCCGCAACCGCCCCGGTGCCTGCAGCCACC‑GGGCGCTCCCCACCCCCAACACCGCCCAGGCGGCCATGCTCGGCAGAGCGATCAGCAAGAACCACCAGCGCCAGCTGCCACACTGGCaa                                             <  1:4408/149‑1 (MQ=255)                                                                                                acaaAACCCCCGCCAACACATGGGTGAACACACCCAACCGCACCGCTGCCTGCCGCCCCC‑GGGCGCTCCCCACCCCCCACACCCCCCAGGCGCGCATGCTCGGAAGACCGAAAAGCAAGAA‑AACCAGCGCCAGCTGCCACACAGGCa                                              >  2:105916/1‑147 (MQ=255)                                                                                                 caaAACCCCCGCCAACACTTGGTTGAACACCCGCAACCGCCCCAGTGCCTGCAGCCACC‑CGGCGCTCCCCCCCCCCAACACCCCCCAGGCGGCCATGCTCGGCAGAGCGATCAGCAAGAA‑CACCAGCCCCCGCTGCCACACAGGCAacg                                           >  4:150395/1‑149 (MQ=255)                                                                                                    aaCCCCCGCCAACACTTGGATGAACACCCGCAACCGCCCCGGTGCCTGCAGCCACC‑GGGCGCTCCCCACCCCCAACACCGCCCAGGCGGCCATGCTCGGCAGAGCGATCAGCAAGAA‑CACCAGCGCCAGCTGCCACACTGGCAacgacg                                        <  3:206109/149‑1 (MQ=255)                                                                                                        cccGCCAACACTTGGTTGAACACCCGCAACCGCCCCGGTGCCTGCAGCCACC‑GGGCGCTCCCCACCCCCAACACCGCCCAGGCGGCCATGCTCGGCAGAGCGATCAGCAAGAA‑CACCAgc                                                                 <  3:346755/120‑1 (MQ=255)                                                                                                        cccGCCAACACTTGGTTGAACACCCGCAACCGCCCCGGTGCCTGCAGCCACC‑GGGCGCTCCCCACCCCCAACACCGCCCAGGCGGCCATGCTCGGCAGAGCGATCAGCAAGAA‑CACCAgc                                                                 >  4:346755/1‑120 (MQ=255)                                                                                                         ccGCCAACACTTGGTTGAACACCCGCAACCGCCCCGGTGCCTGCAGCCACC‑GGGCGCTCCCCACCCCCAACACCGCCCAGGCGGCCATGCTCGGCAGAGCGATCAGCAAGAA‑CACCAGCGCCAGCTGCCACACTGGCAACGACGGcgcg                                   <  7:162802/149‑1 (MQ=255)                                                                                                             cAACACTTGGTTGAACACCCGCAACCGCCCCGGTGCCTGCAGCCACC‑GGGCGCTCCCCACCCCCAACACCGCCCAGGCGGCCATGCTCGGCAGAGCGATCAGCAAGAA‑CACCAGCGCCAGCTGCCACACTGGCAACGACGGCGCGGCaa                               <  3:190258/149‑1 (MQ=255)                                                                                                                 acTTGGTTGAACACCCGCAACCGCCCCGGTGCCTGCAGCCACC‑GGGCGCTCCCCACCCCCAACACCGCCCAGGCGGCCATGCTCGGCAGAGCGATCAGCAAGAA‑CACCAGCGCCAGCTGCCACACTGGCAACGACCGCGCGGCAAATAc                           >  2:294876/1‑149 (MQ=255)                                                                                                                   ttGGTTGAACACCCGCAACCGCCCCGGTGCCTGCAGCCACC‑GGGCGCTCCCCACCCCCAACACCGCCCAGGCGGCCATGCTCGGCAGAGCGATCAGCAAGAA‑CACCAGCGCCAGCTGCCACACTGGCAACGACGGCGCGGCAAATAccc                         >  5:83454/1‑149 (MQ=255)                                                                                                                              cccGCAACCGCCCCGGTGCCTGCAGCCACC‑GGGCGCTCCCCACCCCCAACACCGCCCAGGCGGCCATGCTCGGCAGAGCGATCAGCAAGAA‑CACCAGCGCCAGCTGCCACACTGGCAACGACGGCGCGGCAAATACCCCGACCACCGcc              <  7:52741/149‑1 (MQ=255)                                                                                                                               ccGCAACCGCCCCGGTGCCTGCAGCCACC‑GGGCGCTCCCCACCCCCAACACCGCCCAGGCGGcc                                                                                                   >  6:62966/1‑64 (MQ=255)                                                                                                                               ccGCAACCGCCCCGGTGCCTGCAGCCACC‑GGGCGCTCCCCACCCCCAACACCGCCCAGGCGGcc                                                                                                   <  5:62966/64‑1 (MQ=255)                                                                                                                               ccGCAACCGCCCCGGTGCCTGCAGCCACC‑GGGCGCTCCCCACCCCCAACACCGCCCAGGCGGCCATGCTCGGCAGAGCGATCAGCAAGAA‑CACCAGCGCCAGCTGCCACACTGGCAACGACGGCGCGGCAAATACCCCGACCACCGCCa             >  3:177424/1‑149 (MQ=255)                                                                                                                                  cAACCGCCCCGGTGCCTGCAGCCACC‑GGGCGCTCCCCACCCCCAACACCGCCCAGGCGGCCATGCTCGGCAGAGCGATCAGCAAGAA‑CACCAGCGCCAGCTGCCACACTGGCAACGACGGCGCGGCAAATACCCCGACCACCGCCACgg          <  4:177424/149‑1 (MQ=255)                                                                                                                                    gagcgcccGGTGGCTGCAGGCACCGGGGCGCTCCCCACCCCCAACACCGCCCAGGCGGCCATGCTCGGCAGAGCGATCAGCAAGAA‑CACCAGCGCCAGCTGCCACACTGGCAACGACGGCGCGGCAAATACCCCGa                      >  3:74350/6‑136 (MQ=255)                                                                                                                                    gagcgcccGGTGGCTGCAGGCACCGGGGCGCTCCCCACCCCCAACACCGCCCAGGCGGCCATGCTCGGCAGAGCGATCAGCAAGAA‑CACCAGCGCCAGCTGCCACACTGGCAACGACGGCGCGGCAAATACCCCGa                      <  4:74350/131‑1 (MQ=255)                                                                                                                                       gCCCCGGTGCCTGCAGCCACC‑GGGCGCTCCCCACCCCCAACACCGCCCAGGCGGCCATGCTCGGCAGAGCGATCAGCAAGAA‑CACCAGCGCCAGCTGCCACACTGGCAACGACGGCGCGGCAAATACCCCGACCACCGCCACGGCCATc     <  3:288299/149‑1 (MQ=255)                                                                                                                                         cccGGTGGCTGCAGGCACCGGGGCGCTCCCCACCCCCAACACCGCCCAGGCGGCCATGCTCGGCAGAGCGATCAGCAAGAA‑CACCAGCGCCAGCTGCCACACTGGCAACGACGGCGCGGCAAATACCCCGACCACCGCCACGGCCATc     >  3:47502/1‑148 (MQ=255)                                                                                                                                          ccGGTGCCTGCAGCCACC‑GGGCGCTCCCCACCCCCAACACCGCCCAGGCGGCCATGCTCGGCAGAGCGATCAGCAAGAA‑CACCAGCGCCAGCTGCCACACTGGCAACGACGGCGCGGCAAATACCCCGACCACCGCCACGGCCATCAAc  >  1:132276/1‑149 (MQ=255)                                                                                                                                                |                                                                                                                                                 TTTCGCGAGGCGTTGACACGTTGAGCCGAGGCCGCTCAGGCCCCTTGTCGGTCAAGTAGAGGCTCAGGCCAATACTGCAGCCCATGCCGATATCAACAAAACCCCCGCCAACACTTGGTTGAACACCCGCAACCGCCCCGGTGCCTGCAGCCACC‑GGGCGCTCCCCACCCCCAACACCGCCCAGGCGGCCATGCTCGGCAGAGCGATCAGCAAGAA‑CACCAGCGCCAGCTGCCACACTGGCAACGACGGCGCGGCAAATACCCCGACCACCGCCACGGCCATCAAC  >  NC_002947/2776857‑2777142

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑