Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,988,366	G→A	12.8%	S11S (TCC→TCT)	PP_2612 ←	membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,988,366	0	G	A	12.8%	70.6 / 2.8	31	S11S (TCC→TCT)	PP_2612	membrane protein
Reads supporting (aligned to +/- strand):  ref base G (14/13);  new base A (2/2);  total (16/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

GTGTAGGCCGAGTGCTGCAGCGTGGGGAAGCCTTGTTCCAGGTTGAAGCCTGCATCGGCATAGCGGCAGGCGGGGGCGTCGGCGGTGCGGGGCACGATGGCGTAGCGCACTGGCAGGATGGGCACGCGAGCGCTGCAGGCAGGGCCGGAGGTGGCGCTGCTTACGGAGGCGTTAGTCATGGGCAGGCTCCTTGCTTTCGACCAGTGCCTGGAGCTCGCGAAGGCGGGCCTGGGGCGACTCTTCGAGGTTGGTGTAGATTTTTCCCGCCTTGTCATTGCTCATCAGCCA  >  NC_002947/2988220‑2988507                                                                                                                                                   |                                                                                                                                              gtgtAGGCCGAGTGCTGCAGCGTGGGGAAGCCTTGTTCCAGGTTGAAGCCTGCATCGGCATAGCGGCAGGCGGGGGCGTCGGCGGTGCGGGGCACGATGGCGTAGCGCACTGGCAGGATGGGCACGCGAGCGCTGCAGGCAGGGCCGGa                                                                                                                                             <  1:188088/149‑1 (MQ=32)   gtAGGCCGAGTGCTGCAGCGTGGGGAAGCCTTGTTCCAGGTTGAAGCCTGCATCGGCATAGCGGCAGGCGGGGGCGTCGGCGGTGCGGGGCACGATGGCGTAGCGCACTGGCAGGATGGGCACGCGAGCGCTGCAGGCAGGGCCGGAgg                                                                                                                                           <  5:63883/149‑1 (MQ=32)                      gTGGGGAAGCCTTGTTCCAGGTTGAAGCCTGCATCGGCATAGCGGCAGGCGGGGGCGTCGGCGGTGCGGGGCACGATGGCGTAGCGCACTGGCAGGATGGGCACGCGAGCGCTGCAGGCAGGGCCGGAGGTGGCGCTGCTTACGGAGGc                                                                                                                        <  6:150714/149‑1 (MQ=37)                          ggAAGCCTTGTTCCAGGTTGAAGCCTGCATCGGCATAGCGGCAGGCGGGGGCGTCGGCGGTGCGGGGCACGATGGCGTAGCGCACTGGCAGGATGGGCACGCGAGCGCTGCAGGCAGGGCCGGAGGTGGCGCTGCTTACg                                                                                                                             <  6:100259/140‑1 (MQ=37)                          ggAAGCCTTGTTCCAGGTTGAAGCCTGCATCGGCATAGCGGCAGGCGGGGGCGTCGGCGGTGCGGGGCACGATGGCGTAGCGCACTGGCAGGATGGGCACGCGAGCGCTGCAGGCAGGGCCGGAGGTGGCGCTGCTTACg                                                                                                                             >  5:100259/1‑140 (MQ=37)                          ggAAGCCTTGGTCCAGGTTGAAGCCTGCATCGGCATAGCGGCAGGCGGGGGCGTCGGCGGTGCGGGGCACGATGGCGTAGCGCACTGGCAGGATGGGCACGCGAGCGCTGCAGGCAGGGCCGGAGGTGGCGCTGCTTACGGAGGCGTTa                                                                                                                    <  4:3704/149‑1 (MQ=255)                                cTTGTTCCAGGTTGAAGCCTGCATCGGCATAGCGGCAGGCGGGGGCGTCGGCGGTGCGGGGCACGATGGCGTAGCGCACTGGCAGGATGGGCACGCGAGCGCTGCAGGCAGGGCCGGAGGTGGCGCTGCTTACGGAGGCGTTAGTCATg                                                                                                              >  1:51206/1‑149 (MQ=255)                                 ttGTTCCAGGTTGAAGCCTGCATCGGCATAGCGGCAGGCGGGGGCGTCGGCGGTGCGGGGCACGATGGCGTAGCGCACTGGCAGGATGGGCACGCGAGCGCTGCAGGCAGGGCCGGAGGTGGCGCTGCTTACGGAGGCGTTAGTCAt                                                                                                               >  7:43711/1‑147 (MQ=255)                                 ttGTTCCAGGTTGAAGCCTGCATCGGCATAGCGGCAGGCGGGGGCGTCGGCGGTGCGGGGCACGATGGCGTAGCGCACTGGCAGGATGGGCACGCGAGCGCTGCAGGCAGGGCCGGAGGTGGCGCTGCTTACGGAGGCGTTAGTCAt                                                                                                               <  8:43711/147‑1 (MQ=255)                                 ttGTTCCAGGTTGAAGCCTGCATCGGCATAGCGGCAGGCGGGGGCGTCGGCGGTGCGGGGCACGATGGCGTAGCGCACTGGCAGGATGGGCACGCGAGCGCTGCAGGCAGGGCCGGAGGTGGCGCTGCTTACGGAGGCGTTAGTCATgg                                                                                                             >  8:246004/1‑149 (MQ=255)                                   gTTCCAGGTTGAAGCCTGCATCGGCATAGCGGCAGGCGGGGGCGTCGGCGGTGCGGGGCACGATGGCGTAGCGCACTGGCAGGATGGGCACGCGAGCGCTGCAGGCAGGGCCGGAGGTGGCGCTGCTTACGGAGGCGTTAGTCATggg                                                                                                            <  7:246004/148‑1 (MQ=255)                                   gTTCCAGGTTGAAGCCTGCATCGGCATAGCGGCAGGCGGGGGCGTCGGCGGTGCGGGGCACGATGGCGTAGCGCACTGGCAGGATGGGCACGCGAGCGCTGCAGGCAGGGCCGGAGGTGGCGCTGCTTACGGAGGCGTTAGTCATggg                                                                                                            >  7:230487/1‑148 (MQ=255)                                    ttCCAGGTTGAAGCCTGCATCGGCATAGCGGCAGGCGGGGGCGTCGGCGGTGCGGGGCACGATGGCGTAGCGCACTGGCAGGATGGGCACGCGAGCGCTGCAGGCAGGGCCAGAGGTGGCGCTGCTTACGGAGGCGTTAGTCATggg                                                                                                            >  6:110992/1‑147 (MQ=255)                                    ttCCAGGTTGAAGCCTGCATCGGCATAGCGGCAGGCGGGGGCGTCGGCGGTGCGGGGCACGATGGCGTAGCGCACTGGCAGGATGGGCACGCGAGCGCTGCAGGCAGGGCCAGAGGTGGCGCTGCTTACGGAGGCGTTAGTCATggg                                                                                                            >  6:106767/1‑147 (MQ=255)                                                  cTGCATCGGCATAGCGGCAGGCGGGGGCGTCGGCGGTGCGGGGCACGATGGCGTAGCGCACTGGCAGGATGGGCACGCGAGCGCTGCAGGCAGGGCCGGAGGTGGCGCTGCTTACGGAGGCGTTAGTCATGGGCAGGCTCCTTGCTTTc                                                                                            >  2:50029/1‑149 (MQ=255)                                                    gCATCGGCATAGCGGCAGGCGGGGGCGTCGGCGGTGCGGGGCACGATGGCGTAGCGCACTGGCAGGATGGGCACGCGAGCGCTGCAGGCAGGGCCGGAGGTGGCGCTGCTTACGGAGGCGTTAGTCATGGGCAgg                                                                                                        <  8:246752/135‑1 (MQ=255)                                                    gCATCGGCATAGCGGCAGGCGGGGGCGTCGGCGGTGCGGGGCACGATGGCGTAGCGCACTGGCAGGATGGGCACGCGAGCGCTGCAGGCAGGGCCGGAGGTGGCGCTGCTTACGGAGGCGTTAGTCATGGGCAgg                                                                                                        >  7:246752/1‑135 (MQ=255)                                                               gCGGCAGGCGGGGGCGTCGGCGGTGCGGGGCACGATGGCGTAGCGCACTGGCAGGATGGGCACGCGAGCGCTGCAGGCAGGGCCGGAGGTGGCGCTGCTTACGGAGGCGTTAGTCATGGGCAGGCTCCTTGCTTTCGACCAGTGCCTg                                                                                >  2:141565/1‑148 (MQ=255)                                                                cGGCAGGCGGGGGCGTCGGCGGTGCGGGGCACGATGGCGTAGCGCACTGGCAGGATGGGCACGCGAGCGCTGCAGGCAGGGCCGGAGGTGGCGCTGCTTACGGAGGCGTTAGTCATGGGCAGGCTCCTTGCTTTCGACCAGTGCCTgg                                                                               <  8:230487/148‑1 (MQ=255)                                                                cGGCAGGCGGGGGCGTCGGCGGTGCGGGGCACGATGGCGTAGCGCACTGGCAGGATGGGCACGCGAGCGCTGCAGGCAGGGCCAGAGGTGGCGCTGCTTACGGAGGCGTTAGTCATGGGCAGGCTCCTTGCTTTCGACCAGTGCCTGGa                                                                              <  5:110992/149‑1 (MQ=255)                                                                cGGCAGGCGGGGGCGTCGGCGGTGCGGGGCACGATGGCGTAGCGCACTGGCAGGATGGGCACGCGAGCGCTGCAGGCAGGGCCAGAGGTGGCGCTGCTTACGGAGGCGTTAGTCATGGGCAGGCTCCTTGCTTTCGACCAGTGCCTGGa                                                                              <  5:106767/149‑1 (MQ=255)                                                                 ggCAGGCGGGGGCGTCGGCGGTGCGGGGCACGATGGCGTAGCGCACTGGCAGGATGGGCACGCGAGCGCTGCAGGCAGGGCCGGAGGTGGCGCTGCTTACGGAGGCGTTAGTCATGGGCAGGCTCCTTGCTTTCGa                                                                                          >  1:72170/1‑136 (MQ=255)                                                                 ggCAGGCGGGGGCGTCGGCGGTGCGGGGCACGATGGCGTAGCGCACTGGCAGGATGGGCACGCGAGCGCTGCAGGCAGGGCCGGAGGTGGCGCTGCTTACGGAGGCGTTAGTCATGGGCAGGCTCCTTGCTTTCGa                                                                                          <  2:72170/136‑1 (MQ=255)                                                                                                         gcgcACTGGCAGGATGGGCACGCGAGCGCTGCAGGCAGGGCCGGAGGTGGCGCTGCTTACGGAGGCGTTAGTCATGGGCAGGCTCCTTGCTTTCGACCAGTGCCTGGAGCTCGCGAAGGCGGGCCTGGGGCGACTCTTCGAGGTTGgtg                                     >  8:172958/1‑149 (MQ=255)                                                                                                                    ggATGGGCACGCGAGCGCTGCAGGCAGGGCCGGAGGTGGCGCTGCTTACGGAGGCGTTAGTCATGGGCAGGCTCCTTGCTTTCGACCAGTGCCTGGAGCTCGCGAAGGCGGGCCTGGGGCGACTCTTCGAGGTTGGTGTAGATTTTTcc                          <  1:141565/149‑1 (MQ=255)                                                                                                                     gATGGGCACGCGAGCGCTGCAGGCAGGGCCGGAGGTGGCGCTGCTTACGGAGGCGTTAGTCATGGGCAGGCTCCTTGCTTTCGACCAGTGCCTGGAGCTCGCGAAGGCGGGCCTGGGGCGACTCTTCGAGGTTGGTGTAGATTTTTccc                         <  2:51206/149‑1 (MQ=255)                                                                                                                     gATGGGCACGCGAGCGCTGCAGGCAGGGCCGGAGGTGGCGCTGCTTACGGAGGCGTTAGTCATGGGCAGGCTCCTTGCTTTCGACCAGTGCCTGGAGCTCGCGAAGGCGGGCCTGGGGCGACTCTTCGAGGTTGGTGTAGATTTTTccc                         >  7:114101/1‑149 (MQ=255)                                                                                                                               cgAGCGCTGCAGGCAGGGCCGGAGGTGGCGCTGCTTACGGAGGCGTTAGTCATGGGCAGGCTCCTTGCTTTCGACCAGTGCCTGGAGCTCGCGAAGGCGGGCCTGGGGCGACTCTTCGAGGTTGGTGTAGATTTTTCCCGCCTTGTCAt               <  7:172958/149‑1 (MQ=255)                                                                                                                                     cTGCAGGCAGGGCCGGAGGTGGCGCTGCTTACGGAGGCGTTAGTCATGGGCAGGCTCCTTGCTTTCGACCAGTGCCTGGAGCTCGCGAAGGCGGGCCTGGGGCGACTCTTCGAGGTTGGTGTAGATTTTTACCGCCTTGTCATTGCtc          >  3:155509/1‑148 (MQ=255)                                                                                                                                          ggcaggGCCGGAGGTGGCGCTGCTTACGGAGGCGTTAGTCATGGGCAGGCTCCTTGCTTTCGACCAGTGCCTGGAGCTCGCGAAGGCGGGCCTGGGGCGACTCTTCGAGGTTGGTGTAGATTTTTCCCGCCTTGTCATTGCTCATCAGc    >  6:142681/1‑149 (MQ=255)                                                                                                                                             aggGCCGGAGGTGGCGCTGCTTACGGAGGCGTTAGTCATGGGCAGGCTCCTTGCTTTCGACCAGTGCCTGGAGCTCGCGAAGGCGGGCCTGGGGCGACTCTTCGAGGTTGGTGTAGATTTTTCCCGCCTTGTCATTGCTCATCAGCca  >  5:241160/1‑148 (MQ=255)                                                                                                                                                   |                                                                                                                                              GTGTAGGCCGAGTGCTGCAGCGTGGGGAAGCCTTGTTCCAGGTTGAAGCCTGCATCGGCATAGCGGCAGGCGGGGGCGTCGGCGGTGCGGGGCACGATGGCGTAGCGCACTGGCAGGATGGGCACGCGAGCGCTGCAGGCAGGGCCGGAGGTGGCGCTGCTTACGGAGGCGTTAGTCATGGGCAGGCTCCTTGCTTTCGACCAGTGCCTGGAGCTCGCGAAGGCGGGCCTGGGGCGACTCTTCGAGGTTGGTGTAGATTTTTCCCGCCTTGTCATTGCTCATCAGCCA  >  NC_002947/2988220‑2988507

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: ‑