Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,350,502	T→A	9.4%	K11I (AAA→ATA) ‡	PP_1176 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,350,502	0	T	A	9.4%	140.6 / 3.8	50	K11I (AAA→ATA) ‡	PP_1176	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (23/22);  new base A (3/2);  total (26/24)
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

AGCCGTTTCTGACGAGAACGGGATTCCGCTATGTGAGCGTTCTTAAGCGCCGGAAAACG‑TTATCGCGATGTCCAAAAACAGGCAAGGTCGGCAGCCGTAGGAAACGTCCTGTTCTGCTTCTGCCAGGCAAT‑AAAAAGGCTGCCATTTGGCAGCCTTGTTGATGCTCAGCCCGGTCAATCAATCCCAGCTCAACGCCCCACCCGTCTGATACTCGATCACACGCGTCTCAAAGAAGTTCTTCTCCTTCTTCAAGTCCATGATCTCGCTCATCCATGGGAACGGGTTGG  >  NC_002947/1350357‑1350643                                                                                                                                                    |                                                                                                                                              agCCGTTTCTGACGAGAACGGGATTCCGCTATGTGAGCGTTCTTAAGCGCCGGAAAACG‑TTATCGCGATGTCCAAAAACAGGCAAGGTCGGCAGCCGTAGGAAACGTCCTGTTCTGCTTCTGCCAGGCAAT‑AAAAAGGCTGCCATTTgg                                                                                                                                            >  1:265563/1‑149 (MQ=255)  gCCGTTTCTGACGAGAACGGGATTCCGCTATGTGAGCGTTCTTAAGCGCCGGAAAACT‑TTATCGCGATGTCCAAAAACAGGCAAGGTCGGCAGCCGTAGGAAACGTCCTGTTCTGCTTCTGCCAGGCAAT‑AAAAAGGCTGCCATTTGGc                                                                                                                                           <  3:85027/149‑1 (MQ=255)  gCCGTTTCTGACGAGAACGGGATTCCGCTATGTGAGCGTTCTTAAGCGCCGGAAAACG‑TTATCGCGATGTCCAAAAACAGGCAAGGTCGGCAGCCGTAGGAAACGTCCTGTTCTGCTTCTGCCAGGCAAT‑AAAAAGGCTGCCATTTgg                                                                                                                                            >  8:197006/1‑148 (MQ=255)   ccGTTTCTGACGAGAACGGGATTCCGCTATGTGAGCGTTCTTAAGCGCCGGAAAACGATTATCCCGATGTCCAAAAAAAGCCAAGGACGCCAGCCGTAGGAAACGACATGTTATCATACTCCCAGGAAAT‑AAAAAGCATCCAATTTgg                                                                                                                                            >  1:277921/1‑148 (MQ=255)            aCGAGAACGGGATTCCGCTATGTGAGCGTTCTTAAGCGCCGGAAAACG‑TTATCGCGATGTCCAAAAACAGGCAAGGTCGGCAGCCGTAGGAAACGTCCTGTTCTGCTTCTGCCAGGCAAT‑AAAAAGGCTGCCATTTGGCAGCCttgttg                                                                                                                                 <  7:151568/149‑1 (MQ=255)            aCGAGAACGGGATTCCGCTATGTGAGCGTTCTTAAGCGCCGGAAAACG‑TTATCGCGATGTCCAAAAACAGGCAAGGTCGGCAGCCGTAGGAAACGTCCTGTTCTGCTTCTGCCAGGCAAT‑AAAAAGGCTGCCATTTGGCAGCCttg                                                                                                                                    <  2:231527/146‑1 (MQ=255)            aCGAGAACGGGATTCCGCTATGTGAGCGTTCTTAAGCGCCGGAAAACG‑TTATCGCGATGTCCAAAAACAGGCAAGGTCGGCAGCCGTAGGAAACGTCCTGTTCTGCTTCTGCCAGGCAAT‑AAAAAGGCTGCCAAATGGCAGCCtttt                                                                                                                                   <  7:148430/147‑3 (MQ=255)                   cGGGATTCCGCTATGTGAGCGTTCTTAAGCGCCGGAAAACG‑TTATCGCGATGTCCAAAAACAGGCAAGGTCGGCAGCCGTAGGAAACGTCCTGTTCTGCTTCTGCCAGGCAAT‑AAAAAGGCTGCCATTTGGCAGCCTTGTTGATGCt                                                                                                                            >  1:135998/1‑147 (MQ=255)                   cGGGATTCCGCTATGTGAGCGTTCTTAAGCGCCGGAAAACG‑TTATCGCGATGTCCAAAAACAGGCAAGGTCGGCAGCCGTAGGAAACGTCCTGTTCTGCTTCTGCCAGGCAAT‑AAAAAGGCTGCCATTTGGCAGCCTTGTTGATGCt                                                                                                                            >  3:104853/1‑147 (MQ=255)                   cGGGATTCCGCTATGTGAGCGTTCTTAAGCGCCGGAAAACG‑TTATCGCGATGTCCAAAAACAGGCAAGGTCGGCAGCCGTAGGAAACGTCCTGTTCTGCTTCTGCCAGGCAAT‑AAAAAGGCTGCCATTTGGCAGCCTTGTTGATGCt                                                                                                                            <  2:135998/147‑1 (MQ=255)                           cGCTATGTGAGCGTTCTTAAGCGCCGGAAAACG‑TTATCGCGATGTCCAAAAACAGGCAAGGTCGGCAGCCGTAGGAAACGTCCTGTTCTGCTTCTGCCAGGCAAT‑AAAAAGGCTGCCATTTGGCAGCCTTGTTGATGCTCAGCCCGGt                                                                                                                   >  8:195220/1‑148 (MQ=255)                                tgtgAGCGTTCTTAAGCGCCGGAAAACG‑TTATCGCGATGTCCAAAAACAGGCAAGGGCGGCAGCCGTAGGAAACGTCCTGTTCTGCTTCTGCCAGGCAAT‑AAAAAGGCTGCCATTTGGCAGCCTTGTTGATGCTCAGCCCGGtcaat                                                                                                               <  2:277921/147‑1 (MQ=255)                                  tgAGCGTTCTTAAGCGCCGGAAAACG‑TTATCGCGATGTCCAAAAACAGGCAAGGTCGGCAGCCGTAGGAAACGTCCTGTTCTGCTTCTGCCAGGCAAT‑AAAAAGGCTGCCATTTGGCAGCCTTGTTGATGCTCAGCCCGGTcaatcaat                                                                                                           >  7:263900/1‑149 (MQ=255)                                    aGCGTTCTTAAGCGCCGGAAAACG‑TTATCGCGATGTCCAAAAACAGGCAAGGTCGGCAGCCGTAGGAAACGTCCTGTTCTGCTTCTGCCAGGCAAT‑AAAAAGGCTGCCATTTGGCAGcc                                                                                                                                       >  8:132249/1‑119 (MQ=255)                                    aGCGTTCTTAAGCGCCGGAAAACG‑TTATCGCGATGTCCAAAAACAGGCAAGGTCGGCAGCCGTAGGAAACGTCCTGTTCTGCTTCTGCCAGGCAAT‑AAAAAGGCTGCCATTTGGCAGcc                                                                                                                                       <  7:132249/119‑1 (MQ=255)                                    aGCGTTCTTAAGCGCCGGAAAACG‑TTATCGCGATGTCCAAAAACAGGCAAGGTCGGCAGCCGTAGGAAACGTCCTGTTCTGCTTCTGCCAGGCAAT‑AAAAAGGCTGCCATTTGGCAGCCTTGTTGATGCTCAGCCCGGTCaatcaatc                                                                                                          <  8:263900/148‑1 (MQ=255)                                    aGCGTTCTTAAGCGCCGGAAAACG‑TTATCGCGATGTCCAAAAACAGGCAAGGTCGGCAGCCGTAGGAAACGTCCTGTTCTGCTTCTGCCAGGCAAT‑AAAAAGGCTGCCATTTGGCAGCCTTGTTGATGCTCAGCCCGGTCAATCAATcc                                                                                                         >  6:32596/1‑149 (MQ=255)                                     gggttgttAATCGCAGGAAAACG‑TTATCGCGATGTCCAAAAACAGGCAAGGTCGGCAGCAGTAGGAAACGTCGTGTTCTGCTTCTGCCAGGCTAT‑AAAAAGGCTGCCATTTGGAAGCCTTGTTGATGCTCAGCCCGGTCAATCAATcc                                                                                                         >  6:98455/3‑148 (MQ=255)                                           ttAAGCGCCGGAAAACG‑TTATCGCGATGTCCAAAAACAGGCAAGGTCGGCAGCCGTAGGAAACGTCCTGTTCTGCTTCTGCCAGGCAAT‑AAAAAGGCTGCCATTTGGCAGCCTTGTTGATGCTCAGCCCGGTCAATCAATCCCAGCTc                                                                                                   >  8:155455/1‑148 (MQ=255)                                                  ccGGAAAACG‑TTATCGCGATGTCCAAAAACAGGCAAGGTCGGCAGCCGTAGGAAACGTCCTGTTCTGCTTCTGCCAGGCAAT‑AAAAAGGCTGCCATTTGGCAGCCTTGTTGATGCTCAGCCCGGTCAATCAATCCCAGCTCAACGccc                                                                                            >  1:100520/1‑148 (MQ=255)                                                                         ccAAAAACAGGCAAGGTCGGCAGCCGTAGGAAACGTCCTGTTCTGCTTCTGCCAGGCAAT‑AAAAAGGCTGCCATTTGGCAGCCTTGTTGATGCTCAGCCCGGTCAATCAATCCCAGCTCAACGCCCCACCCGTCTGATACTCGATcaca                                                                     >  1:38821/1‑149 (MQ=255)                                                                          cAAAAACAGGCAAGGTCGGCAGCCGTAGGAAACGTCCTGTTCTGCTTCTGCCAGGCAAT‑AAAAAGGCTGCCATTTGGCAGCCTTGTTGATGCTCAGCCCGGTCAATCAATCCCAGCTCAACGCCCCACCCGTCTGATACTCGATcaca                                                                     <  2:100520/148‑1 (MQ=255)                                                                          cAAAAACAGGCAAGGTCGGCAGCCGTAGGAAACGTCCTGTTCTGCTTCTGCCAGGCAAT‑AAAAAGGCTGCCATTTGGCAGCCTTGTTGATGCTCAGCCCGGTCAATCAATCCCAGCTCAACGCCCCACCCGTCTGATACTCGATCacac                                                                    >  2:2159/1‑149 (MQ=255)                                                                          cAAAAACAGGCAAGGTCGGCAGCCGTAGGAAACGTCCTGTTCTGCTTCTGCCAGGCAAT‑AAAAAGGCTGCCATTTGGCAGCCTTGTTGATGCTCAGCCCGGTCAATCAATCCCAGCTCAACGCCCCACCCGTCTGATACTCGATCacac                                                                    >  3:206795/1‑149 (MQ=255)                                                                          cAAAAACAGGCAAGGTCGGCAGCCGTAGGAAACGTCCTGTTCTGCTTCTGCCAGGCAAT‑AAAAAGGCTGCCATTTGGCAGCCTTGTTGATGCTCAGCCCGGTCAATCAATCCCAGCTCAACGCCCCACCCATCTGATACTCGATCacac                                                                    >  1:100621/1‑149 (MQ=255)                                                                          cAAAAACAGGCAAGGTCGGCAGCCGTAGGAAACGTCCTGTGCTGCTTCTGCCAGGCAAT‑AAAAAGGCTGCCATTTGGCAGCCTTGTTGATGCTCAGCCCGGTCAATCAATCCCAGCTCAACGCCCCACCCGTCTGATACTCGATCacac                                                                    <  4:104853/149‑1 (MQ=255)                                                                           aaaaaCAGGCAAGGTCGGCAGCCGTAGGAAACGTCCTGTTCTGCTTCTGCCAGGCAAT‑AAAAAGGCTGCCATTTGGCAGCCTTGTTGATGCTCAGCCCGGTCAATCAATCCCAGCTCAACGCCCCACCCGTCTGATACTCGATCACAcg                                                                   >  1:141496/1‑149 (MQ=255)                                                                                 aGGCAAGGTCGGCAGCCGTAGGAAACGTCCTGTTCTGCTTCTGCCAGGCAAT‑AAAAAGGCTGCCATTTGGCAGCCTTGTTGATGCTCAGCCCGGTCAATCAATCCCAGCTCAACGCCCCACCCGTCTGATACTCGATCACACGCGtctc                                                             <  5:32596/149‑1 (MQ=255)                                                                                      aGGTCGGCAGCCGTAGGAAACGTCCTGTTCTGCTTCTGCCAGGCAAT‑AAAAAGGCTGCCATTTGGCAGCCTTGTTGATGCTCAGCCCGGTCAATCAATCCCAGCTCAACGCCCCACCCGTCTGATACTCGATCACACGCGTCTCAaag                                                         >  5:162033/1‑148 (MQ=255)                                                                                       ggTCGGCAGCCGTAGGAAACGTCCTGTTCTGCTTCTGCCAGGCAAT‑AAAAAGGCTGCCAAATGGCAGCCttttta                                                                                                                                 <  4:84194/75‑2 (MQ=38)                                                                                       ggTCGGCAGCCGTAGGAAACGTCCTGTTCTGCTTCTGCCAGGCAAT‑AAAAAGGCTGCCAAATGGCAGCCttttta                                                                                                                                 >  3:84194/1‑74 (MQ=38)                                                                                           ggCAGCCGTAGGAAACGTCCTGTTCTGCTTCTGCCAGGCAAT‑AAAAAGGCTGCCATTTGGCAGCCTTGTTGATGCTCAGCCCGGTCAATCAATCCCAGCTCAACGCCCCACCCGTCTGATACTCGATCACACGCGTCTCAAAGAAGttc                                                   <  7:197006/149‑1 (MQ=255)                                                                                             cAGCCGTAGGAAACGTCCTGTTCTGCTTCTGCCAGGCAAT‑AAAAAGGCTGCCATTTGGCAGCCTTGTTGATGCTCAGCCCGGTCAATCAATCCCAGCTCAACGCCCCACCCGTCTGATACTCGATCACACGCGTCTCAAAGAAGttctt                                                 <  2:38821/149‑1 (MQ=255)                                                                                                      gAAACGTCCTGTTCTGCTTCTGCCAGGCAATAAAAAAGGCTGCCATTTGGCAGCCTTGTTGATGCTCAGCCCGGTCAATCAATCCCAGCTCAACGCCCCACCCGTCTGATACTCGATCACACGCGTCTCAAAGAAGttcttc                                                >  4:324072/1‑142 (MQ=255)                                                                                                      gAAACGTCCTGTTCTGCTTCTGCCAGGCAATAAAAAAGGCTGCCATTTGGCAGCCTTGTTGATGCTCAGCCCGGTCAATCAATCCCAGCTCAACGCCCCACCCGTCTGATACTCGATCACACGCGTCTCAAAGAAGttcttc                                                <  3:324072/142‑1 (MQ=255)                                                                                                       aaaCGTCCTGTTCTGCTTCTGCCAGGCAAT‑AAAAAGGCTGCCATTTGGCAGCCTTGTTGATGCTCAGCCCGGTCAATCAATCCCAGCTCAACGCCCCACCCGTCTGATACTCGATCACACGCGTCTCAAAGAAGTTCTTCTCCttcttc                                       <  6:162033/149‑1 (MQ=255)                                                                                                            tCCTGTTCTGCTTCTGCCAGGCAAT‑AAAAAGGCTGCCATTTGGCAGCCTTGTTGATGCTCAGCCCGGTCAATCAATCCCAGCTCAACGCCCCACCCGTCTGATACTCGATCACACGCGTCTCAAAGAAGTTCTTCTCCttcttc                                       >  1:100935/1‑144 (MQ=255)                                                                                                            tCCTGTTCTGCTTCTGCCAGGCAAT‑AAAAAGGCTGCCATTTGGCAGCCTTGTTGATGCTCAGCCCGGTCAATCAATCCCAGCTCAACGCCCCACCCGTCTGATACTCGATCACACGCGTCTCAAAGAAGTTCTTCTCCttcttc                                       <  2:100935/144‑1 (MQ=255)                                                                                                                 ttctgcttctgcCAGGCAAT‑AAAAAGGCTGCCATTTGGCAGCCTTGTTGATGCTCAGCCCGGTCAATCAATCCCAGCTCAACGCCCCACCCGTCTGATACTCGATCACACGCGTCTCAAAGAAGTTCTTCTCCTTCTTCAAGTCCATg                              <  7:155455/148‑1 (MQ=255)                                                                                                                 ttctgcttctgcCAGGCAAT‑AAAAAGGCTGCCATTTGGCAGCCTTGTTGATGCTCAGCCCGGTCAATCAATCCCAGCTCAACGCCCCACCCGTCTGATACTCGATCACACGCGTCTCAAAGAAGTTCTTCTCCTTCTTCAAGTCCATGa                             <  1:2159/149‑1 (MQ=255)                                                                                                                   ctgcttctgcCAGGCAAT‑AAAAAGGCTGCCATTTGGCAGCCTTGTTGATGCTCAGCCCGGTCAATCAATCCCAGCTCAACGCCCCACCCGTCTGATACTCGATCACACGCGTCTCAAAGAAGTTCTTCTCCTTCTTCAAGTCCATGAtc                           >  4:73537/1‑149 (MQ=255)                                                                                                                      cttctgcCAGGCAAT‑AAAAAGGCTGCCATTTGGCAGCCTTGTTGATGCTCAGCCCGGTCAATCAATCCCAGCTCAACGCCCCACCCGTCTGATACTCGATCACACGCGTCTCAAAGAAGTTCTTCTCCTTCTTCAAGTCCATGAtctc                         <  7:195220/148‑1 (MQ=255)                                                                                                                              aGGCAAT‑AAAAAGGCTGCCATTTGGCAGCCTTGTTGATGCTCAGCCCGGTCAATCAATCCCAGCTCAACGCCCCACCCGTCTGATACTCGATCACACGCGTCTCAAAGAAGTTCTTCTCCTTCTTCAAGTCCATGATCTCGCTCATCCa                <  4:206795/149‑1 (MQ=255)                                                                                                                                 cAAT‑AAAAAGGCTGCCATTTGGCAGCCTTGTTGATGCTCAGCCCGGTCAATCAATCCCAGCTCAACGCCCCACCCGTCTGATACTCGATCACACGCGTCTCAAAGAAGTTCTTCTCCTTCTTCAAGTCCATGATCTCGCTCATCCATgg             >  1:184744/1‑149 (MQ=255)                                                                                                                                    tcaacaaGGCTGCCAAATGGCAGCCTTTTTGATGCTCAGCCCGGTCAATCAATCCCAGCTCAACGCCCCACCCGTCTGATACTCGATCACACGCGTCTCAAAGAAGTTCTTCTCCTTCTTCAAGTCCATGATCTCGCTCATCCATggg            >  1:66687/6‑148 (MQ=255)                                                                                                                                    t‑AAAAAGGCTGCCATTTGGCAGCCTTGTTGATGCTCAGCCCGGTCAATCAATCCCAGCTCAACGCCCCACCCGTCTGATACTCGATCACACGCGTCTCAAAGAAGTTCTTCTCCTTCTTCAAGTCCATGATCTCGCTCATCCATGGGaa          >  1:174371/1‑149 (MQ=255)                                                                                                                                        aaaGGCTGCCATTTGGCAGCCTTGTTGATGCTCAGCCCGGTCAATCAATCCCAGCTCAACGCCCCACCCGTCTGATACTCGATCACACGCGTCTCAAAGAAGTTCTTCTCCTTCTTCAAGTCCATGATCTCGCTCATCCATGGGAACgg       <  2:184744/149‑1 (MQ=255)                                                                                                                                           ggCTGCCATTTGGCAGCCTTGTTGATGCTCAGCCCGGTCAATCAATCCCAGCTCAACGCCCCACCCGTCTGATACTCGATCACACGCGTCTCAAAGAAGTTCTTCTCCTTCTTCAAGTCCATGATCTCGCTCATCCATGGGAACGGGtt    <  2:265563/149‑1 (MQ=255)                                                                                                                                           ggCTGCCAAATGGCAGCCTTGTTGATGCTCAGCCCGGTCAATCAATCCCAGCTCAACGCCCCACCCGTCTGATACTCGATCACACGCGTCTCAAAGAACTTATTCTCCTTCTTCTATTCCATGATCTCGCTCATCCATGGGAACGGGtt    >  8:243945/1‑149 (MQ=255)                                                                                                                                             cTGCCATTTGGCAGCCTTGTTGATGCTCAGCCCGTTAAATCAATCACATCTCAACGCCCCACCCGTCTGATACTCGATCACACGCGTATCAAAGAAGTTCTTCTCCTTCTTCAAGTCCATGATCTCGCTCATCCATGGGAACGGGTTgg  <  5:98455/149‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                              AGCCGTTTCTGACGAGAACGGGATTCCGCTATGTGAGCGTTCTTAAGCGCCGGAAAACG‑TTATCGCGATGTCCAAAAACAGGCAAGGTCGGCAGCCGTAGGAAACGTCCTGTTCTGCTTCTGCCAGGCAAT‑AAAAAGGCTGCCATTTGGCAGCCTTGTTGATGCTCAGCCCGGTCAATCAATCCCAGCTCAACGCCCCACCCGTCTGATACTCGATCACACGCGTCTCAAAGAAGTTCTTCTCCTTCTTCAAGTCCATGATCTCGCTCATCCATGGGAACGGGTTGG  >  NC_002947/1350357‑1350643

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: ‑