Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,383,546	C→A	7.7%	intergenic (+7/+17)	PP_5547 → / ← PP_2985	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,383,546	0	C	A	7.7%	165.9 / 2.8	52	intergenic (+7/+17)	PP_5547/PP_2985	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (23/25);  new base A (2/2);  total (25/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.82e-01

ACGCCCAAGAGGCAGTCGCCAAGCTGCGCACGTGCCTGTCGAGTAACGATTGGCAGATTTTGATATCGCATAGATCAAACCTTCCTCAATGGATGGCTGAAGCGATTGGGCGCGAAGCAGTCTTTGCTGAGCAGGGCTTCTAATCTACTCGTTTAAATACAATAGCTTAGAGAACGAATGTCCTAATTTTTGCCTTATCTCGGCATGACCCCATACCGGCATGAAGCAGCGCTGCGATAATGAAAGGAGCCTTTTTCTCTAGATACTCAGCCATCCCACCCGTATTGCTCGACTCCAA  >  NC_002947/3383397‑3383694                                                                                                                                                      |                                                                                                                                                     aCGCCCAAGAGGCAGTCGCCAAGCTGCGCACGTGCCTGTCGAGTAACGATTGGCAGATTTTGATATCGCATAGATCAAACCTTCCTCAATGGATGGCTGAAGCGATTGGGCGCGAAGCAGTCTTTGCTGAGCAGGGCTTCTAATCTACTc                                                                                                                                                      >  1:1582017/1‑150 (MQ=255) aCGCCCAAGAGGCAGTCGCCAAGCTGCGCACGTGCCTGTCGAGTAACGATTGGCAGATTTTGATATCGCATAGATCAAACCTTCCTCAATGGATGGCTGAAGCGATTGGGCGCGAAGCAGTCTTTGCTGAGCAGGGCTCCTAATCTACTc                                                                                                                                                      <  1:931598/150‑1 (MQ=255)    cccAAGAGGCAGTCGCCAAGCTGCGCACGTGCCTGTCGAGTAACGATTGGCAGATTTTGATATCGCATAGATCAAACCTTCCTCAATGGATGGCTGAAGCGATTGGGCGCGAAGCAGTCTTTGCTGAGCAGGGCTTCTAATCTACTCGtt                                                                                                                                                   <  1:510466/150‑1 (MQ=255)       aaGAGGCAGTCGCCAAGCTGCGCACGTGCCTGTCGAGTAACGATTGGCAGATTTTGATATCGCATAGATCAAACCTTCCTCAATGGATGGCTGAAGCGATTGGGCGCGAAGCAGTCTTTGCTGAGCAGGGCTTCTAATCTACTCGTTTaa                                                                                                                                                <  1:780947/150‑1 (MQ=255)              aGTCGCCAAGCTGCGCACGTGCCTGTCGAGTAACGATTGGCAGATTTTGATATCGCATAGATCAAACCTTCCTCAATGGATGGCTGAAGCGATTGGGCGCGAAGCAGTCTTTGCTGAGCAGGGCTTCTAATCTACTCGTTTAAATACAAt                                                                                                                                         >  2:9064/1‑150 (MQ=255)               gTCGCCAAGCTGCGCACGTGCCTGTCGAGTAACGATTGGCAGATTTTGATATCGCATAGATCAAACCTTCCTCAATGGATGGCTGAAGCGATTGGGCGCGAAGCAGTCTTTGCTGAGCAGGGCTTCTAATCTACTCGTTTAAATACAATa                                                                                                                                        >  1:726460/1‑150 (MQ=255)                   ccAAGCTGCGCACGTGCCTGTCGAGTAACGATTGGCAGATTTTGATATCGCATAGATCAAACCTTCCTCAATGGATGGCTGAAGCGATTGGGCGCGAAGCAGTCTTTGCTGAGCAGGGCTTCTAATCTACTCGTTTAAATACAATAGCtt                                                                                                                                    >  1:1112679/1‑150 (MQ=255)                   ccAAGCTGCGCACGTGCCTGTCGAGTAACGATTGGCAGATTTTGATATCGCATAGATCAAACCTTCCTCAATGGATGGCTGAAGCGATTGGGCGCGAAGCAGTCTTTGCTGAGCAGGGCTTCTAATCTACTCGTTTAAATACAATAGCtt                                                                                                                                    <  2:678142/150‑1 (MQ=255)                   ccAAGCTGCGCACGTGCCTGTCGAGTAACGATTGGCAGATTTTGATATCGCATAGATCAAACCTTCCTCAATGGATGGCTGAAGCGATTGGGCGCGAAGCAGTCTTTGCTGAGCAGGGCTTCTAATCTACTAGTTTAAATACAATAGCtt                                                                                                                                    >  1:1177575/1‑150 (MQ=255)                   ccAAGCTGCGCACGTGCCTGTCGAGTAACGATTGGCAGATTTTGATATCGCATAGATCAAACCTTCCTCAATGGATGGCTGAAGCGATTGGGCGCGAAGCAGGCTTTGCTGAGCAGGGCTTCTAATCTACTAGTTTAAATACAATAGCtt                                                                                                                                    >  1:1177581/1‑150 (MQ=255)                       gCTGCGCACGTGCCTGTCGAGTAACGATTGGCAGATTTTGATATCGCATAGATCAAACCTTCCTCAATGGATGGCTGAAGCGATTGGGCGCGAAGCAGTCTTTGCTGAGCAGGGCTTCTAATCTACTCGTTTAAATACAATAGCTTagag                                                                                                                                <  1:1369039/150‑1 (MQ=255)                            gcACGTGCCTGTCGAGTAACGATTGGCAGATTTTGATATCGCATAGATCAAACCTTCCTCAATGGATGGCTGAAGCGATTGGGCGCGAAGCAGTCTTTGCTGAGCAGGGCTTCTAATCTACTCGTTTAAATACAATAGCTTAGAGAACGa                                                                                                                           <  2:1582017/150‑1 (MQ=255)                                     tGTCGAGTAACGATTGGCAGATTTTGATATCGCATAGATCAAACCTTCCTCAATGGATGGCTGAAGCGATTGGGCGCGAAGCAGTCTTTGCTGAGCAGGGCTTCTAATCTACTCGTTTAAATACAATAGCTTAGAGAACGAATGTCCTaa                                                                                                                  >  1:1465789/1‑150 (MQ=255)                                      gTCGAGTAACGATTGGCAGATTTTGATATCGCATAGATCAAACCTTCCTCAATGGATGGCTGAAGCGATTGGGCGCGAAGCAGTCTTTGCTGAGCAGGGCTTCTAATCTACTCGTTTAAATACAATAGCTTAGAGAACGAATGTCCTAAt                                                                                                                 >  2:391897/1‑150 (MQ=255)                                          aGTAACGATTGGCAGATTTTGATATCGCATAGATCAAACCTTCCTCAATGGATGGCTGAAGCGATTGGGCGCGAAGCAGTCTTTGCTGAGCAGGGCTTCTAATCTACTCGTTTAAATACAATAGCTTAGAGAACGAATGTCCTAAttttt                                                                                                             >  2:495820/1‑150 (MQ=255)                                          aGTAACGATTGGCAGATTTTGATATCGCATAGATCAAACCTTCCTCAATGGATGGCTGAAGCGATTGGGCGCGAAGCAGTCTTTGCTGAGCAGGGCTTCTAATCTACTCGTTTAAATACAATAGCTTAGAGAACGAATGTCCTAAttttt                                                                                                             <  2:1112679/150‑1 (MQ=255)                                                  ttGGCAGATTTTGATATCGCATAGCTCCACCCTTCATCGCTGGGTGGTCGTGGCCATTGGGCTCTAAGCAGTCTTTGCTGAGCAGGGCTTCTAATCTACTAGTTTAAATACAATAGCTTAGAGAACGAATGTCCTAATTTTTGCCTTAtc                                                                                                     <  2:1177575/150‑1 (MQ=255)                                                  ttGGCAGATTTTGATATCGCATAGATCAAAACTTAATCATTCGCTGGTCGAGGCGAGTGGGCGCGAAGCAGTCTTTGCTGAGCAGGGCTTCTAATCTACTAGTTTCCATCCACTAGCTTAGAGAACGAATGTCCTAATTTTTGCCTTAtc                                                                                                     <  2:1177581/150‑1 (MQ=255)                                                     gCAGATTTTGATATCGCATAGATCAAACCTTCCTCAATGGATGGCTGAAGCGATTGGGCGCGAAGCAGTCTTTGCTGAGCAGGGCTTCTAATCTACTCGTTTAAATACAATAGCTTAGAGAACGAATGTCCTAATTTTTGCCTTATCTCg                                                                                                  <  2:1491383/150‑1 (MQ=255)                                                      cAGATTTTGATATCGCATAGATCAAACCTTCCTCAATGGATGGCTGAAGCGATTGGGCGCGAAGCAGTCTTTGCTGAGCAGGGCTTCTAATCTACTCGTTTAAAt                                                                                                                                              <  2:888109/105‑1 (MQ=255)                                                      cAGATTTTGATATCGCATAGATCAAACCTTCCTCAATGGATGGCTGAAGCGATTGGGCGCGAAGCAGTCTTTGCTGAGCAGGGCTTCTAATCTACTCGTTTAAAt                                                                                                                                              >  1:888109/1‑105 (MQ=255)                                                                tatCGCATAGATCAAACCTTCCTCAATGGATGGCTGAAGCGATTGGGCGCGAAGCAGTCTTTGCTGAGCAGGGCTTCTAATCTACTCGTTTAAATACAATAGCTTAGAGAACGAATGTCCTAATTTTTGCCTTATCTCGGCATGACCCCa                                                                                       >  1:1064472/1‑150 (MQ=255)                                                                        aGATCAAACCTTCCTCAATGGATGGCTGAAGCGATTGGGCGCGAAGCAGTCTTTGCTGAGCAGGGCTTCTAATCTACTCGTTTAAATACAATAGCTTAGAGAACGAATGTCCTAATTTTTGCCTTATCTCGGCATGACCCCATACCGGCa                                                                               <  1:391897/150‑1 (MQ=255)                                                                          aTCAAACCTTCCTCAATGGATGGCTGAAGCGATTGGGCGCGAAGCAGTCTTTGCTGAGCAGGGCTTCTAATCTACTCGTTTAAATACAATAGCTTAGAGAACGAATGTCCTAATTTTTGCCTTAtctc                                                                                                   >  2:1589511/1‑128 (MQ=255)                                                                          aTCAAACCTTCCTCAATGGATGGCTGAAGCGATTGGGCGCGAAGCAGTCTTTGCTGAGCAGGGCTTCTAATCTACTCGTTTAAATACAATAGCTTAGAGAACGAATGTCCTAATTTTTGCCTTAtctc                                                                                                   <  1:1589511/128‑1 (MQ=255)                                                                           tCAAACCTTCCTCAATGGATGGCTGAAGCGATTGGGCGCGAAGCAGTCTTTGCTGAGCAGGGCTTCTAATCTACTCGtt                                                                                                                                                   <  2:838463/79‑1 (MQ=255)                                                                           tCAAACCTTCCTCAATGGATGGCTGAAGCGATTGGGCGCGAAGCAGTCTTTGCTGAGCAGGGCTTCTAATCTACTCGtt                                                                                                                                                   >  1:838463/1‑79 (MQ=255)                                                                                 cTTCCTCAATGGATGGCTGAAGCGATTGGGCGCGAAGCAGTCTTTGCTGAGCAGGGCTTCTAATCTACTCGTTTAAATACAATAGCTTAGAGAACGAATGTCCTAATTTTTGCCTTAtctc                                                                                                   >  2:994274/1‑121 (MQ=255)                                                                                 cTTCCTCAATGGATGGCTGAAGCGATTGGGCGCGAAGCAGTCTTTGCTGAGCAGGGCTTCTAATCTACTCGTTTAAATACAATAGCTTAGAGAACGAATGTCCTAATTTTTGCCTTAtctc                                                                                                   <  1:994274/121‑1 (MQ=255)                                                                                      tCAATGGATGGCTGAAGCGATTGGGCGCGAAGCAGTCTTTGCTGAGCAGGGCTTCTAATCTACTCGTTTAAATACAATAGCTTAGAGAACGAATGTCCTAATTTTTGCCTTATCTCGGCATGACCCCATACCGGCATGAAGCAGCGCTGc                                                                 <  1:9064/150‑1 (MQ=255)                                                                                                     aGCGATTGGGCGCGAAGCAGTCTTTGCTGAGCAGGGCTTCTAATCTACTCGTTTAAATACaa                                                                                                                                          >  2:229592/1‑62 (MQ=255)                                                                                                     aGCGATTGGGCGCGAAGCAGTCTTTGCTGAGCAGGGCTTCTAATCTACTCGTTTAAATACaa                                                                                                                                          <  1:229592/62‑1 (MQ=255)                                                                                                         aTTGGGCGCGAAGCAGTCTTTGCTGAGCAGGGCTTCTAATCTACTCGTTTAAATACAATAGCTTAGAGAACGAAt                                                                                                                         >  2:684881/1‑75 (MQ=255)                                                                                                         aTTGGGCGCGAAGCAGTCTTTGCTGAGCAGGGCTTCTAATCTACTCGTTTAAATACAATAGCTTAGAGAACGAAt                                                                                                                         <  1:684881/75‑1 (MQ=255)                                                                                                               cgcgAAGCAGTCTTTGCTGAGCAGGGCTTCTAATCTACTCGTTTAAATACAATAGCTTAGAGAACGAATGTCCTAATTTTTGCCTTATCTCGGCATGACCCCATACCGGCATGAAGCAGCGCTGCGATAATGAAAGGAGCCTTTTTctct                                        <  1:495820/150‑1 (MQ=255)                                                                                                                gcgAAGCAGTCTTTGCTGAGCAGGGCTTCTAATCTACTCGTTTAAATACAATAGCTTAGAGAACGAATGTCCTAATTTTTGCCTTATCTCGGCATGACCCCATACCGGCATGAAGCAGCGCTGCGATAATGAAAGGAGCCTTTTTCTCTa                                       <  2:726460/150‑1 (MQ=255)                                                                                                                      cAGTCTTTGCTGAGCAGGGCTTCTAATCTACTCGTTTAAATACAATAGCTTAGAGAACGAATGTCCTAATTTTTGCCTTATCTCGGCAt                                                                                              >  1:320851/1‑89 (MQ=255)                                                                                                                      cAGTCTTTGCTGAGCAGGGCTTCTAATCTACTCGTTTAAATACAATAGCTTAGAGAACGAATGTCCTAATTTTTGCCTTATCTCGGCAt                                                                                              <  2:320851/89‑1 (MQ=255)                                                                                                                         tCTTTGCTGAGCAGGGCTTCTAATCTACTCGTTTAAATACAATAGCTTAGAGAACGAATGTCCTAATTTTTGCCTTATCTCGGCATGACCCCATACCGGCATGAAGCAGCGCTGCGATAATGAAAGGAGCCTTTTTCTCTAGATACTCAg                              <  2:1064472/150‑1 (MQ=255)                                                                                                                              gCTGAGCAGGGCTTCTAATCTACTCGTTTAAATACAATAGCTTAGAGAACGAATGTCCTAATTTTTGCCTTATCTCGGCATGAc                                                                                           <  2:1312784/84‑1 (MQ=255)                                                                                                                              gCTGAGCAGGGCTTCTAATCTACTCGTTTAAATACAATAGCTTAGAGAACGAATGTCCTAATTTTTGCCTTATCTCGGCATGAc                                                                                           >  1:1312784/1‑84 (MQ=255)                                                                                                                                 gAGCAGGGCTTCTAATCTACTCGTTTAAATACAATAGCTTAGAGAACGAATGTCCTAATTTTTGCCTTATCTCGGCATGACCCCATACCGGCATGAAGCAGCGCTGCGATAATGaaa                                                       <  1:710484/117‑1 (MQ=255)                                                                                                                                 gAGCAGGGCTTCTAATCTACTCGTTTAAATACAATAGCTTAGAGAACGAATGTCCTAATTTTTGCCTTATCTCGGCATGACCCCATACCGGCATGAAGCAGCGCTGCGATAATGaaa                                                       <  1:710525/117‑1 (MQ=255)                                                                                                                                 gAGCAGGGCTTCTAATCTACTCGTTTAAATACAATAGCTTAGAGAACGAATGTCCTAATTTTTGCCTTATCTCGGCATGACCCCATACCGGCATGAAGCAGCGCTGCGATAATGaaa                                                       >  2:710525/1‑117 (MQ=255)                                                                                                                                 gAGCAGGGCTTCTAATCTACTCGTTTAAATACAATAGCTTAGAGAACGAATGTCCTAATTTTTGCCTTATCTCGGCATGACCCCATACCGGCATGAAGCAGCGCTGCGATAATGaaa                                                       >  2:710484/1‑117 (MQ=255)                                                                                                                                       ggCTTCTAATCTACTCGTTTAAATACAATAGCTTAGAGAACGAATGTCCTAATTTTTGCCTTATCTCGGCACGACCCCATACCGGCATGAAGCAGCGCTGCGATAATGAAAGGAGCCTTTTTCTCTAGATACTCAGCCATCCCACCCGTa                >  1:1107173/1‑150 (MQ=255)                                                                                                                                          ttCTAATCTACTCGTTTAAATACAATAGCTTAGAGAACGAATGTCCTAATTTTTGCCTTATCTCGGCATGACCCCATACCGGCATGAAGCAGCGCTGCGATAATGAAAGGAGCCTTTTTCTCTAGATACTCAGCCATCCCACCCGTAt               <  2:612269/148‑1 (MQ=255)                                                                                                                                          ttCTAATCTACTCGTTTAAATACAATAGCTTAGAGAACGAATGTCCTAATTTTTGCCTTATCTCGGCATGACCCCATACCGGCATGAAGCAGCGCTGCGATAATGAAAGGAGCCTTTTTCTCTAGATACTCAGCCATCCCACCCGTAt               >  1:612269/1‑148 (MQ=255)                                                                                                                                           tCTAATCTACTCGTTTAAATACAATAGCTTAGAGAACGAATGTCCTAATTTTTGCCTTATCTCGGCATGACCCCATACCGGCATGAAGCAGCGCTGCGATAATGAAAGGAGCCTTTTTCTCTAGATACTCAGCCATCCCACCCGTATTGc            >  1:65058/1‑150 (MQ=255)                                                                                                                                           tCTAATCTACTCGTTTAAATACAATAGCTTAGAGAACGAATGTCCTAATTTTTGCCTTATCTCGGCATGACCCCATACCGGCATGAAGCAGCGCTGCGATAATGAAAGGAGCCTTTTTCTCTAGATACTCAGCCATCCCACCCGTATTGc            <  2:1465789/150‑1 (MQ=255)                                                                                                                                             tAATCTACTCGTTTAAATACAATAGCTTAGAGAACGAATGTCCTAATTTTTTTTTTTTTTTTTCATGACCCCATACCGGCATGAAGCAGCGCTGCGATAATGAAAGGAGCCTTTTTCTCTATTTACTCAGTCATCCCACCCGTATTtctc          >  2:114826/1‑150 (MQ=255)                                                                                                                                                    cTCGTTTAAATACAATAGCTTAGAGAACGAATGTCCTAATTTTTGCCTTATCTCGGCATGACCCCATACCg                                                                                  >  2:664795/1‑71 (MQ=255)                                                                                                                                                    cTCGTTTAAATACAATAGCTTAGAGAACGAATGTCCTAATTTTTGCCTTATCTCGGCATGACCCCATACCg                                                                                  <  1:664795/71‑1 (MQ=255)                                                                                                                                                     tCGTTTAAATACAATAGCTTAGAGAACGAATGTCCTAATTTTTGCCTTATCTCGGCATGACCCCATACCGGCATGAAGCAGCGCTGCGATAATGAAAGGAGCCTTTTTCTCTAGATACTCAGCCATCCCACCCGTATTGCTCGACTCCaa  >  1:378843/1‑150 (MQ=255)                                                                                                                                                      |                                                                                                                                                     ACGCCCAAGAGGCAGTCGCCAAGCTGCGCACGTGCCTGTCGAGTAACGATTGGCAGATTTTGATATCGCATAGATCAAACCTTCCTCAATGGATGGCTGAAGCGATTGGGCGCGAAGCAGTCTTTGCTGAGCAGGGCTTCTAATCTACTCGTTTAAATACAATAGCTTAGAGAACGAATGTCCTAATTTTTGCCTTATCTCGGCATGACCCCATACCGGCATGAAGCAGCGCTGCGATAATGAAAGGAGCCTTTTTCTCTAGATACTCAGCCATCCCACCCGTATTGCTCGACTCCAA  >  NC_002947/3383397‑3383694

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: ‑