Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,052,565	G→A	14.7%	P269S (CCC→TCC)	PP_0910 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,052,565	0	G	A	14.7%	58.9 / 2.0	27	P269S (CCC→TCC)	PP_0910	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (10/13);  new base A (2/2);  total (12/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.87e-01

TTCTTTCTCGCCATCGGCCCCGTCGCCGTTGGGCGCAGTCAGGCAGCCGGTTTGTGCCGGGGTGCAATCGTCGTTGGGCAGCAGGGTGCTGGTCAGGCCCATGTCGCCGGCAAAGGCGTGCACGTTCTGCTGGTTGACGTTGGGCTGCCCGGCTTTCCAGCCGAAGCGGCCGATCACT‑GTTTTGCCCTGGGCGTCGTCCCATACACGGTTGGCCCGCCCGCGGATGCCATCGCGGTTACGGTCGTCCGGGTCTTCGTTGGCCAGCAGGTCGGCTTCGGGGA  >  NC_002947/1052422‑1052702                                                                                                                                                |                                                                                                                                           ttctttctCGCCATCGGCCCCGTCGCCGTTGGGCGCAGTCAGGCAGCCGGTTTGTGCCGGGGTGCAATCGTCGTTGGGCAGCAGGGTGCTGGTCAGGCCCATGTCGCCGGCAAAGGCGTGCACGTTCTGCTGGTTGACGTTGGGCTGccc                                                                                                                                      >  1:283845/1‑150 (MQ=255) ttctttctCGCCATCGGCCCCGTCGCCGTTGGGCGCAGTCAGGCAGCCGGTTTGTGCCGGGGTGCAATCGTCGTTGGGCAGCAGGGTGCTGGTCAGGCCCATGTCGCCGGCAAAGGCGTGCACGTTCTGCTGGTTGACGTTGGGCTGccc                                                                                                                                      >  1:51608/1‑150 (MQ=255)    tttctCGCCATCGGCCCCGTCGCCGTTGGGCGCCGTCAGGCAGCCGGTTTGTGCCGGGGTGCAATCGTCGTTGGGCAGCAGGGTGCTGGTCAGGCCCATGTCGCCGGCAAAGGCGTGCACGTTCTGCTGGTTGCCGCTGGGCtcgggtgt                                                                                                                                   >  1:361682/1‑143 (MQ=255)    tttctCGCCATCGGCCCCGTCGCCGTTGGGCGAAGTCAGGCAGCCGGTTTGTGCCGGGGTGCAATCGTCGTTGGGCAGCAGGGTGCTGGTCAGGCCCATGTCGCCGGCAAAGGCGTGCACGTTCTGCTGGTTGCCGCTGGGCtcgggtgt                                                                                                                                   <  2:361682/150‑8 (MQ=255)                    cggTCGCCGTTGGGCGCAGTCAGGCAGCCGGTTTGTGCCGGGGTGCAATCGTCGTTGGGCAGCAGGGTGCTGGTCAGGCCCATGTCGCCGGCAAAGGCGTGCACGTTCTGCTGGTTGACGTTGGGCTGCCCGGCTTTCCAGCCGAAGCgg                                                                                                                   >  1:96231/3‑150 (MQ=255)                                         aGGCAGCCGGTTTGTGCCGGGGTGCAATCGTCGTTGGGCAGCAGGGTGCTGGTCAGGCCCATGTCGCCGGCAAAGGCGTGCACGTTCTGCTGGTTGACGTTGGGCTGCCCGGCTTTCCAGCCGAAGCGGCCGATCACT‑GTTTTGCCCTgg                                                                                             <  2:359555/150‑1 (MQ=255)                                             aGCCGGTTTGTGCCGGGGTGCAATCGTCGTTGGGCAGCAGGGTGCTGGTCAGGCCCATGTCGCCGGCAAAGGCGTGCACGTTCTGCTGGTTGACGTTGGGCTGCCCGGCTTTCCAGCCGAAGCGGCCGATCACT‑GTTTTGCCCTGGGcgt                                                                                         >  1:475842/1‑150 (MQ=255)                                                  gTTTGTGCCGGGGTGCAATCGTCGTTGGGCAGCAGGGTGCTGGTCAGGCCCATGTCGCCGGCAAAGGCGTGCACGTTCTGCTGGTTGACGTTGGGCTGCCCGGCTTTCCAGCCGAAGCGGCCGATCACT‑GTTTTGCCCTGGGCGTCGTcc                                                                                    <  2:454232/150‑1 (MQ=255)                                                               tGCAATCGTCGTTGGGCAGCAGGGTGCTGGTCAGGCCCATGTCGCCGGCAAAGGCGTGCACGTTCTGCTGGTTGACGTTGGGCTGCCCGGCTTTCCAGCCGAAGCGGCCGATCACT‑GTTTTGCCCTGGGCGTCGTCCCATACACGGTTgg                                                                       <  2:466114/150‑1 (MQ=255)                                                                               cagcagGGTGCTGGTCAGGCCCATGTCGCCGGCAAAGGCGTGCACGTTCTGCTGGTTGACGTTGGGCTGCCCGGCTTTCCAGCCGAAGCGGCCGATCACT‑GTTTTGCCCTGGGCGTCGTCCCATACACGGTTGGCCCGCCCGCGGATGcc                                                       >  1:143300/1‑150 (MQ=255)                                                                                    gggTGCTGGTCAGGCCCATGTCGCCGGCAAAGGCGTGCACGTTCTGCTGGTTGACGTTGGACTGCCCGGCTTTCCAGCCGAAGCGGCCGATCACT‑GTTTTGCCCTGGGCGTCGTCCCATACACGGTTGGCCCGCCCGCGGATGCCATcgc                                                  >  2:95882/1‑150 (MQ=255)                                                                                       tGCTGGTCAGGCCCATGTCGCCGGCAAAGGCGTGCACGTTCTGCTGGTTGACGTTGGGCTGCCCGGCTTTCCAGCCGAAGCGGCCGATCACT‑GTTTTGCCCTGGGCGTCGTACCATACACGGTTGGCCCGCCCGCGGATGCCATCGCGGt                                               <  2:283845/150‑1 (MQ=255)                                                                                           ggTCAGGCCCATGTCGCCGGCAAAGGCGTGCACGTTCTGCTGGTTGACGTTGGGCTGCCCGGCTTTCCAGCCGAAGCGGCCGATCACT‑GTTTTGCCCTGGGCGTCGTCCCATACACGGTTGGCCCGCCCGCGGATGCCATCGCGGTTACg                                           <  1:28024/150‑1 (MQ=255)                                                                                            gTCAGGCCCATGTCGCCGGCAAAGGCGTGCACGTTCTGCTGGTTGACGTTGGGCTGCCCGGCTTTCCAGCCGAAGCGGCCGATCACT‑GTTTTGCCCTGGGCGTCGTCCCATACACGGTTGGCCCGCCCGCGGATGCCATCGCGGTTACgg                                          <  2:24907/150‑1 (MQ=255)                                                                                              cAGGCCCATGTCGCCGGCAAAGGCGTGCACGTTCTGCTGGTTGACGATAAAGTACCCTGCTTTCCAGCCGAAGCGGCCGATCACT‑GTTTTGCCCTGGGCGTCGTCCCATACACGGTTGGCCCGCCCGCGGATGCCATCGCGGTTACGgtc                                        <  2:382105/150‑1 (MQ=255)                                                                                                         cGCCGGCAAAGGCGTGCACGTTCTGCTGGTTGACGTTGGGCTGCCCGGCTTTCCAGCCGAAGCGGCCGATCACT‑GTTTTGCCCTGGGCGTCGTCCCATACACGGTTGGCCCGCCCGCGGATGCCATCGCGGTTACGGTCGTCCGGGTCtt                             >  2:464942/1‑150 (MQ=255)                                                                                                              gCAAAGGCGTGCACGTTCTGCTGGTTGACGTTGGGCTGCCCGGCTTTCCAGCCGAAGCGGCCGATCACT‑GTTTTGCCCTGGGCGTCGTCCCATACACGGTTGGCCCGCCCGCGGATGc                                                        >  2:257642/1‑118 (MQ=255)                                                                                                              gCAAAGGCGTGCACGTTCTGCTGGTTGACGTTGGGCTGCCCGGCTTTCCAGCCGAAGCGGCCGATCACT‑GTTTTGCCCTGGGCGTCGTCCCATACACGGTTGGCCCGCCCGCGGATGc                                                        <  1:257642/118‑1 (MQ=255)                                                                                                                    gCGTGCACGTTCTGCTGGTTGACGTTGGGCTGCCCGGCTTTCCAGCCGAAGCGGCCGATCACT‑GTTTTGCCCTGGGCGTCGTCCTATACACGGTTGGCCCGCCCGCGGATGCCATCGCGGTTACGGTCGTCCGGGTCTTCGTTGGCcagc                  <  1:240485/150‑1 (MQ=255)                                                                                                                          aCGTTCTGCTGGTTGACGTTGGGCTGCCCGGCTTTCCAGCCGAAGCGGCCGATCACT‑GTTTTGCCCTGGGCGTCGTCCCATACACGGTTGGCCCGCCCGCGGATGCCATCGCGGTTACGGTCGTCCGGGTCTTCGTTGGCCAGCAGGTCg            <  2:51608/150‑1 (MQ=255)                                                                                                                           cGTTCTGCTGGTTGACGTTGGACTGCCCGGCTTTCCAGCCGAAGCGGCCGATCACT‑GTTTTGCCCTGGGCGTCGTCCCATACACGGTTGGCCCGCCCGCGGATGCCATCGCGGTTACGGTCGTCCGGGTCTTCGTTGGCCAGCAGGGCgg           >  1:242819/1‑150 (MQ=255)                                                                                                                                 gctgGTTGACGTTGGGCTGCCCGGCTTTCCAGCCGAAGCGGCCGATCAATCGACAAGCATACGTTGTTCT‑GCTCGCACGTATGGCCCGCCCGAAAGTGCCATTGCGGTTACGGTCCTCCGGGTCTTCGTTGGCCAGCAGGTCGGCTTCgg     <  1:479904/150‑1 (MQ=255)                                                                                                                                    ggTTGACGTTGGACTGCCCGGCTTTCCAGCCGAAGCGGCCGATCACT‑GTTTTGCCCTGGGCGTCGTCCCATACACGGTTGGCCCGCCCGCGGATGCCATCGCGGTTACGGTCGTCCGGGGCTTCGTTGGCCAGCAGGTCGGCTTCGGGGa  <  1:95882/150‑1 (MQ=255)                                                                                                                                           gTTGGGCTGCCCGGCTTTCCAGCCGAAGCGGCCGATCACT‑GTTTTGCCCTGGGCGTCGTCCCATACACGGTTGGCCCGCCCGCGGATGCCATCGCGGTTACGGTCGTCCGGGTCTTCGTTGGc                      >  1:84347/1‑123 (MQ=255)                                                                                                                                           gTTGGGCTGCCCGGCTTTCCAGCCGAAGCGGCCGATCACT‑GTTTTGCCCTGGGCGTCGTCCCATACACGGTTGGCCCGCCCGCGGATGCCATCGCGGTTACGGTCGTCCGGGTCTTCGTTGGc                      <  2:84347/123‑1 (MQ=255)                                                                                                                                           gTTGGGCTGCCCGGCTTTCCAGCCGAAGCGGCCGATCACT‑GTTTTGCCCTGGGCGTCGTCCCATACACGGTTGGCCCGCCCGCGGATGCCATCGCGGTTACGGTCGTCCGGGTCTTCGTTGGc                      <  2:84232/123‑1 (MQ=255)                                                                                                                                           gTTGGGCTGCCCGGCTTTCCAGCCGAAGCGGCCGATCACT‑GTTTTGCCCTGGGCGTCGTCCCATACACGGTTGGCCCGCCCGCGGATGCCATCGCGGTTACGGTCGTCCGGGTCTTCGTTGGc                      >  1:84232/1‑123 (MQ=255)                                                                                                                                              gggCTGCCCGGCTTTCCAGCCGAAGCGGCCGATCACT‑GTTTTGCCCTGGGCGTCGTCCCATACACGGTTGGCCCGCCCGCGGATGCCATCGCGGTTACGGTCGTCCGGGTCTTCGTTGGCCAGCAGGTCGGCtt        <  1:278404/134‑1 (MQ=255)                                                                                                                                              gggCTGCCCGGCTTTCCAGCCGAAGCGGCCGATCACT‑GTTTTGCCCTGGGCGTCGTCCCATACACGGTTGGCCCGCCCGCGGATGCCATCGCGGTTACGGTCGTCCGGGTCTTCGTTGGCCAGCAGGTCGGCtt        >  2:278404/1‑134 (MQ=255)                                                                                                                                                |                                                                                                                                           TTCTTTCTCGCCATCGGCCCCGTCGCCGTTGGGCGCAGTCAGGCAGCCGGTTTGTGCCGGGGTGCAATCGTCGTTGGGCAGCAGGGTGCTGGTCAGGCCCATGTCGCCGGCAAAGGCGTGCACGTTCTGCTGGTTGACGTTGGGCTGCCCGGCTTTCCAGCCGAAGCGGCCGATCACT‑GTTTTGCCCTGGGCGTCGTCCCATACACGGTTGGCCCGCCCGCGGATGCCATCGCGGTTACGGTCGTCCGGGTCTTCGTTGGCCAGCAGGTCGGCTTCGGGGA  >  NC_002947/1052422‑1052702

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑