Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,116,965	A→C	15.1%	L158R (CTC→CGC)	PP_2733 ←	membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,116,965	0	A	C	15.1%	96.3 / 10.3	45	L158R (CTC→CGC)	PP_2733	membrane protein
Reads supporting (aligned to +/- strand):  ref base A (21/17);  new base C (3/4);  total (24/21)
Fisher's exact test for biased strand distribution p-value = 6.89e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGCGTTGTGAAAAAGAGCCTTCTGCCCAGCAAGGTTTGCGTGGTGTGTGGCCGGCCGTTCACCTGGCGCAAGCGCTGGGCACGCTGTTGGGAGCAGGTGCGTTACTGCTCCGAGCGATGTCGCCGGTCAGCGCCGCGCCGCGAGGCGCGCCAGCAGGGGCAGGGCCAAAGCCCATAACGGCATCAGTAGCAGGCCGGTTTCCAGCGCGCCCAATGGCAAGGCAACACCTGCCAGCCTGGCGCCGCCTACATAGGCCAGAGGGCCGCCAATCGCCCCCAGCAGTGCGCCG  >  NC_002947/3116823‑3117111                                                                                                                                               |                                                                                                                                                   ggCGTTGTGAAAAAGAGCCTTCTGCCCAGCAAGGTTTGCGTGGTGTGTGGCCGGCCGTTCACCTGGCGCAAGCGCTGGGCACGCTGTTGGGAGCAGGTGCGTTACTGCTCCGAGCGATGTCGCCGGTCAGCGCCGCGCCTCGCGgcgcgg                                                                                                                                             <  2:1088824/150‑2 (MQ=255) ggCGTTGTGAAAAAGAGCCTTCTGCCCAGCAAGGTTTGCGTGGTGTGTGGCCGGCCGTTCACCTGGCGCAAGCGCTGGGCACGCTGTTGGGAGCAGGTGCGTTACTGCTCCGAGCGATGTCGCCGGTCAGCGCCGCGCCGCGAGgcgcgc                                                                                                                                             >  2:796998/1‑150 (MQ=255)  gCGTTGTGAAAAAGAGCCTTCTGCCCAGCAAGGTTTGCGTGGTGTGTGGCCGGCCGTTCACCTGGCGCAAGCGCTGGGCACGCTGTTGGGAGCAGGTGCGTTACTGCTCCGAGCGATGTCGCCGGTCAGCGCCGCGCCGCGAGGCGCGcc                                                                                                                                            >  1:720565/1‑150 (MQ=255)            aaaGAGCCTTCTGCCCAGCAAGGTTTGCGTGGTGTGTGGCCGGCCGTTCACCTGGCGCAAGCGCTGGGCACGCTGTTGGGAGCAGGTGCGTTACTGCTCCGAGCGATGTCGCCGGTCAGCGCCGCGCCGCGAGGCGCGCCAgcaggggca                                                                                                                                  <  1:1171267/150‑1 (MQ=255)              agagCCTTCTGCCCAGCAAGGTTTGCGTGGTGTGTGGCCGGCCGTTCACCTGGCGCAAGCGCTGGGCACGCTGTTGGGAGCAGGTGCGTTACTGCTCCGAGCGATGTCGCCGGTCAGCGCCGCGCCGCGAGGCGCGCCAgcaggggcagg                                                                                                                                <  2:955920/150‑1 (MQ=255)                    ttCTGCCCAGCAAGGTTTGCGTGGTGTGTGGCCGGCCGTTCACCTGGCGCAAGCGCTGGGCACGCTGTTGGGAGCAGGTGCGTTACTGCTCCGAGCGATGTCGCCGGTCAGCGCCGCGCCGCGAGGCGCGCCAGCAGGGGCAGGGCCaaa                                                                                                                          >  2:1079408/1‑150 (MQ=255)                       tGCCCAGCAAGGTTTGCGTGGTGTGTGGCCGGCCGTTCACCTGGCGCAAGCGCTGACCACGCTGTTGGGAGCAGGTGCGTTACTGCTCCGAGCGATGTCGCCGGTCAGCGCCGCGCCGCGAGGCGCGCCAGCAGGGGCAGGGCCAAAGcc                                                                                                                       <  1:616905/150‑1 (MQ=255)                          ccAGCAAGGTTTGCGTGGTGTGTGGCGGGCCGTTCACCTGGCGCAAGCGCTGGGCACGCTGTTGGGAGCAGGTGCGTTACTGCTCCGAGCGATGTCGCCGGTCAGCGCCGCGCCGCGAGGCGCGCCAGCAGGGGCAGGGCCAAAGCCCAt                                                                                                                    >  2:538698/1‑150 (MQ=255)                               aaGGTTTGCGTGGTGTGTGGCCGGCCGTTCACCTGGCGCAAGCGCTGGGCACGCTGTTGGGAGCAGGTGCGTTACTGCTCCGAGCGATGTCGCCGGTCAGCGCCGCGCCGCGAGGCGCGCCAGCAGGGGCAGGGCCAAAGCCCATAACgg                                                                                                               <  1:796998/150‑1 (MQ=255)                                 ggTTTGCGTGGTGTGTGGCCGGCCGTTCACCTGGCGCAAGCGCTGGGCACGCTGTTGGGAGCAGGTGCGTTACTGCTCCGAGCGATGTCGCCGGTCAGCGCCGCGCCGCGAGGCGCGCCAGCAGGGGCAGGGCCAAAGCCCATAACGGCa                                                                                                             >  2:1055433/1‑150 (MQ=255)                                  gTTTGCGTGGTGTGTGGCCGGCCGTTCACCTGGCGCAAGCGCTGGGCACGCTGTTGGGAGCAGGTGCGTTACTGCTCCGAGCGATGTCGCCGGTCAGCGCCGCGCCGCGAGGCGCGCCAGCAGGGGCAGGGCCAAAGCCCATAACGGCAt                                                                                                            >  1:1075770/1‑150 (MQ=255)                                       cGTGGTGTGTGGCCGGCCGTTCACCTGGCGCAAGCGCTGGGCACGCTGTTGGGAGCAGGTGCGTTACTGCTCCGAGCGATGTCGCCGGTCAGCGCCGCGCCGCGAGGCGCGCCAgcaggggc                                                                                                                                   >  1:104147/1‑122 (MQ=255)                                       cGTGGTGTGTGGCCGGCCGTTCACCTGGCGCAAGCGCTGGGCACGCTGTTGGGAGCAGGTGCGTTACTGCTCCGAGCGATGTCGCCGGTCAGCGCCGCGCCGCGAGGCGCGCCAgcaggggc                                                                                                                                   <  2:104147/122‑1 (MQ=255)                                                  gccggccgTTCACCTGGCGCAAGCGCTGGGCACGCTGTTGGGAGCAGGTGCGTTACTGCTCCGAGCGATGTCGCCGGTCAGCGCCGCGCCGCGAGGCGCGCCAGCAGGGGCAGGGCCAAAGCCCATAACGGCATCAGTAGCAGGCCGGtt                                                                                            <  1:1079408/150‑1 (MQ=255)                                                   ccggccgTTCACCTGGCGCAAGCGCTGGGCACGCTGTTGGGAGCAGGTGCGTTACTGCTCCGAGCGATGTCGCCGGTCAGCGCCGCGCCGCGAGGCGCGCCAGCAGGGGCAGGGCCAAAGCCCATAACGGCATCAGTAGCAGGCCGGttt                                                                                           >  2:685767/1‑150 (MQ=255)                                                    cggccgTTCACCTGGCGCAAGCGCTGGGCACGCTGTTGGGAGCAGGTGCGTTACTGCTCCGAGCGATGTCGCCGGTCAGCGCCGCACCGCGAGGCGCGCCAGCAGGGGCAGGGCCAAAGCCCATAACGGCATCAGTAGCAGGCCGGTTTc                                                                                          <  2:622880/150‑1 (MQ=255)                                                          ttCACCTGGCGCAAGCGCTGGGCACGCTGTTGGGAGCAGGTGCGTTACTGCTCCGAGCGATGTCGCCGGTCAGCGCCGCGCCGCGAGGCGCGCCAGCAGGGGCAGGGCCAAAGc                                                                                                                        >  1:859205/1‑114 (MQ=255)                                                          ttCACCTGGCGCAAGCGCTGGGCACGCTGTTGGGAGCAGGTGCGTTACTGCTCCGAGCGATGTCGCCGGTCAGCGCCGCGCCGCGAGGCGCGCCAGCAGGGGCAGGGCCAAAGc                                                                                                                        <  2:859205/114‑1 (MQ=255)                                                                  gcgcAAGCGCTGGGCACGCTGTTGGGAGCAGGTGCGTTACTGCTCCGAGCGATGTCGCCGGTCAGCGCCGCGCCGCGAGGCGCGCCAGCAGGGGCAGGGCCAAAGCCCATAACGGCATCAGTAGCAGGCCGGTTTCCAGCGCGCCCAATg                                                                            <  2:720565/150‑1 (MQ=255)                                                                          gcTGGGCACGCTGTTGGGAGCAGGTGCGTTACTGCTCCGAGCGATGTCGCCGGTCAGCGCCGCGCCGCGAGGCGCGCCAGCAGGGGCAGGGCCAAAGCCCATAACGGCATCAGTAGCAGGCCGGTTTCCAGCGCGCCCAATggcaaggca                                                                    >  1:76962/1‑150 (MQ=255)                                                                           cTGGGCACGCTGTTGGGAGCAGGTGCGTTACTGCTCCGAGCGATGTCGCCGGTCAGCGCCGCGCCGCGAGGCGCGCCAGCAGGGGCAGGGCCAAAGCCCATAACGGCATCAGTAGCAGGCCGGTTTCCAGCGCGCCCAATggcaaggcaa                                                                   <  2:76962/150‑1 (MQ=255)                                                                             gggCACGCTGTTGGGAGCAGGGGCGTTACTGCTCCGAGCGATGTCGCCGGTCAGCGCCGCGCCGCGAGGCGCGCCAGCAGGGGCAGGGCCAAAGCCCATAACGGCATCAGTAGCAGGCCGGTTTCCAGCGCGCCCAATGGCAAGGCAaca                                                                 <  2:509917/150‑1 (MQ=255)                                                                                 aCGCTGTTGGGAGCAGGTGCGTTACTGCTCCGAGCGATGTCGGCGGTCAGCGCCGCGCCGCGAGGCGCGCCAGCAGGGGCAGGGCCAAAGCCCATAACGGCATCAGTAGCAGGCCGGTTTCCAGCGCGCCCAATGGCAAGGCAACACCTg                                                             >  2:480827/1‑150 (MQ=255)                                                                                       ttGGGAGCAGGTGCGTTACTGCTCCGAGCGATGTCGCCGGTCAGCGCCGCGCCGCGAGGCGCGCCAGCAGGGGCAGGGCCAAAGCCCATAACGGCATCAGTAGCAGGCCGGTTTCCAGCGCGCCCAATGGCAAGGCAACACCTGCCAGcc                                                       >  2:696236/1‑150 (MQ=255)                                                                                        tGGGAGCAGGTGCGTTACTGCTCCGAGCGATGTCGCCGGTCAGCGCCGCGCCGCGAGGCGCGCCAGCAGGGGCAGGGCCAAAGCCCATAACGGCATCAGTAGCAGGCCGGTTTCCAGCGCGCCCAATGGCAAGGCAACACCTGCCAGc                                                        <  2:1077244/148‑1 (MQ=255)                                                                                        tGGGAGCAGGTGCGTTACTGCTCCGAGCGATGTCGCCGGTCAGCGCCGCGCCGCGAGGCGCGCCAGCAGGGGCAGGGCCAAAGCCCATAACGGCATCAGTAGCAGGCCGGTTTCCAGCGCGCCCAATGGCAAGGCAACACCTGCCAGc                                                        >  1:1077244/1‑148 (MQ=255)                                                                                           gAGCAGGTGCGTTACTGCTCCGAGCGATGTCGCCGGTCAGCGCCGCGCCGCGAGGCGCGCCAGCAGGGGCAGGGCCAAAGCCCATAACGGCATCAGTAGCAGGCCGGTTTCCAGCGCGCCCAATGGCAAGGCAACACCTGCCAGCCTGgc                                                   <  1:1055433/150‑1 (MQ=255)                                                                                             gCAGGTGCGTTACTGCTCCGAGCGATGTCGCCGGTCAGCGCCGCGCCGCGAGGCGCGCCAGCAGGGGCAGGGCCAAAGCCCATAACGGCATCAGTAGCAGGCCGGTTTCCAGCGCGCCCAATGGCAAGGCAACACCTGCCAGCCTGgcgc                                                 >  1:219053/1‑150 (MQ=255)                                                                                               aGGTGCGTTACTGCTCCGAGCGATGTCGCCGGTCAGCGCCGCGCCGCGAGGCGCGCCAGCAGGGGCAGGGCCAAAGCCCATAACg                                                                                                                <  2:536952/85‑1 (MQ=255)                                                                                               aGGTGCGTTACTGCTCCGAGCGATGTCGCCGGTCAGCGCCGCGCCGCGAGGCGCGCCAGCAGGGGCAGGGCCAAAGCCCATAACg                                                                                                                >  1:536952/1‑85 (MQ=255)                                                                                                     gTTACTGCTCCGAGCGATGTCGCCGGTCAGCGCCGCGCCGCGAGGCGCGCCAGCAGGGGCAGGGCCAAAGCCCATAACGGCATCAGTAGCAGGCCGGTTTCCAGCGCGCCCAATGGCAAGGCAACACCTGCCAGCCTGGCGCCGCCTACa                                         >  2:7992/1‑150 (MQ=255)                                                                                                                  gCGATGTCGCCGGTCCGCCCCCCTCCGCGAGGCGCGCCAGCAGGGGCAGGGCCAAAGCCCATAACGGCATCAGTAGCAGGCCGGTTTCCAGCGCGCCCAATGGCAAGGCAACACCTGCCAGCCTGGCGCCGCCTACATAGGCCAGAGGgc                            <  2:280024/150‑1 (MQ=255)                                                                                                                        tCGCCGGTCAGCGCCGCGCCGCGAGGCGCGCCAGCAGGGGCAGGGCCAAAGCCCATAACGGCATCAGTAGCAGGCCGGTTTCCAGCGCGCCCAATGGCAAGGCAACACCTGCCAGCCTGGCGCCGCCTACATAGGCCAGAGGGCCGCCaa                      <  1:696236/150‑1 (MQ=255)                                                                                                                          gCCGGTCAGCGCCGCGCCGCGAGGCGCGCCAGCAGGGGCAGGGCCAAAGCCCATAACGGCATCAGTAGCAGGCCGGTTTCCAGCGCGCCCAATGGCAAGGCAACAcc                                                               <  2:1153662/107‑1 (MQ=255)                                                                                                                          gCCGGTCAGCGCCGCGCCGCGAGGCGCGCCAGCAGGGGCAGGGCCAAAGCCCATAACGGCATCAGTAGCAGGCCGGTTTCCAGCGCGCCCAATGGCAAGGCAACAcc                                                               >  1:1153662/1‑107 (MQ=255)                                                                                                                          gCCGGTCAGCGCCGCGCCGCGAGGCGCGCCAGCAGGGGCAGGGCCAAAGCCCATAACGGCATCAGTAGCAGGCCGGTTTCCAGCGCGCCCAATGGCAAGGCAACACCTGCCAGCCTGGCGCCGCCTACATAGGCCAGAGGGCCGCCAATc                    >  2:606407/1‑150 (MQ=255)                                                                                                                          gCCGGTCAGCGCCGCGCCGCGAGGCGCGCCAGCAGGGGCAGGGCCAAAGCCCATAACGGCATCAGTAGCAGGCCGGTTTCCAGCGCGCCCAATGGCAAGGCAACACCTGCCAGCCTGGCGCCGCCTACATAGGCCAGAGGGCCGCCAATc                    >  2:224692/1‑150 (MQ=255)                                                                                                                            cGGTCAGCGCCGCGCCGCGAGGCGCGCCAGCAGGGGCAGGGCCAAAGCCCATAACGGCATCAGTAGCAGGCCGGTTTCCAGCGCGCCCAATGGCAAGGCAACACCTGCCAGCCTGGCGCCGCCTACATAGGCCAGAGGGCCGCCAATCGc                  >  2:515117/1‑150 (MQ=255)                                                                                                                              tggcgcgcctcgcgGCGCGGCGCGCCAGCAGGGGCAGGGCCACAGCCCATAACGGCATCAGTAGCAGGCCGGTTTCCAGCGCGCCCAATGGCAAGGCAACACCTGCCACCCTGGCGCCGCCTACATAGGCCAGAGGGCCGCCAATc                    <  1:979190/142‑1 (MQ=255)                                                                                                                              tggcgcgcctcgcgGCGCGGCGCGCCAGCAGGGGCAGGGCCAAAGCCCATAACGGCATCAGTAGCAGGCCGGTTTCCAGCGCGCCCAATGGCAAGGCAACACCTGCCAGCCTGGCGCCGCCTACATAGGCCAGAGGGCCGCCAATc                    >  2:979190/5‑146 (MQ=255)                                                                                                                                  ctggcgcgcctcgCGGCGCGCCAGCAGGGGCAGGGCCAAAGCCCATAACGGCATCAGTAGCAGGCCGGTTTCCAGCGCGCCCAATGGCAAGGCAACACCTGCCAGCCTGGCGCCGCCTACATAGGCCagag                               >  2:643246/5‑131 (MQ=255)                                                                                                                                  ctggcgcgcctcgCGGCGCGCCAGCAGGGGCAGGGCCAAAGCCCATAACGGCATCAGTAGCAGGCCGGTTTCCAGCGCGCCCAATGGCAAGGCAACACCTGCCAGCCTGGCGCCGCCTACATAGGCCagag                               <  1:643246/127‑1 (MQ=255)                                                                                                                                   tggcgcgcctcgCGGCGCGCCAGCAGGGGCAGGGCCAAAGCCCATAACGGCATCAGTAGCAGGCCGGTTTCCAGCGCGCCCAATGGCAAGGCAACACCTGCCAGCCTGgc                                                   <  2:379173/107‑1 (MQ=255)                                                                                                                                   tggcgcgcctcgCGGCGCGCCAGCAGGGGCAGGGCCAAAGCCCATAACGGCATCAGTAGCAGGCCGGTTTCCAGCGCGCCCAATGGCAAGGCAACAACTGCCAGCCTGgc                                                   >  1:379173/4‑110 (MQ=255)                                                                                                                                            gcgAGGCGCGCCAGCAGGGGCAGGGCCAAAGCCCATAACGGCATCAGTAGCAGGCCGGTTTCCAGCGCGCCCAATGGCAAGGCAACACCTGCCAGCCTGGCGCCGCCTACATAGGCCAGAGGGCCGCCAATCGCCCCCAGCAGTGCGCCg  >  1:1159330/1‑150 (MQ=255)                                                                                                                                               |                                                                                                                                                   GGCGTTGTGAAAAAGAGCCTTCTGCCCAGCAAGGTTTGCGTGGTGTGTGGCCGGCCGTTCACCTGGCGCAAGCGCTGGGCACGCTGTTGGGAGCAGGTGCGTTACTGCTCCGAGCGATGTCGCCGGTCAGCGCCGCGCCGCGAGGCGCGCCAGCAGGGGCAGGGCCAAAGCCCATAACGGCATCAGTAGCAGGCCGGTTTCCAGCGCGCCCAATGGCAAGGCAACACCTGCCAGCCTGGCGCCGCCTACATAGGCCAGAGGGCCGCCAATCGCCCCCAGCAGTGCGCCG  >  NC_002947/3116823‑3117111

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑