Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,275,084	G→C	9.1%	intergenic (‑281/+31)	PP_5462 ← / ← PP_5463	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,275,084	0	G	C	9.1%	114.5 / 4.7	44	intergenic (‑281/+31)	PP_5462/PP_5463	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (20/20);  new base C (2/2);  total (22/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.94e-01

GAATGGGCATTTTGGTCTATCCGGCGGAGAGTGAATGTCGAAGCCTGCTTCCCGGTTACGTCGGCTCCAATAAGGTGCGGGAGAGCGGTAATGATGGGGGTGATGGTGGTAAAGGTGAAAGGAGAATGAGCAAAGCCCGCCGATGGGCGGGCTTCA‑GGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACTCCTCATCAGGAATCGCACTTTCAGGTGACTGCCTTTGGATAAGTTGTATCCAGCCT  >  NC_002947/1274943‑1275227                                                                                                                                              |                                                                                                                                                 gAATGGGCATTTTGGTCTATCCGGCGGAGAGTGAATGTCGAAGCCTGCTTCCCGGTTACGTCGGCTCCAATAAGGTGCGGGAGAGCGGTAATGATGGGGGTGATGGTGGTAAAGGTGAAAGGAGAATGAGCAAAGCCCGCCGATgggcg                                                                                                                                           >  3:355230/1‑149 (MQ=255)        cATTTTGGTCTATCCGGCGGAGAGTGAATGTCGAAGCCTGCTTCCCGGTTACGTCGGCTCCAATAAGGTGCGGGAGAGCGGTAATGATGGGGGTGATGGTGGTAAAGGTGAAAGGAGAATGAGCAAAGCCCGCCCATCGGCGGGCtttg                                                                                                                                    <  6:338591/149‑3 (MQ=255)         aTTTTGGTCTATCCGGCGGAGAGTGAATGTCGAAGCCTGCTTCCCGGTTACGTCGGCTCCAATAAGGTGCGGGAGAGCGGTAATGATGGGGGTGATGGTGGTAAAGGTGAAAGGAGAATGAGCAAAGCCCGCCGATGGGCGGGCTTCA‑g                                                                                                                                  >  5:253258/1‑149 (MQ=255)          ttttGGTCTATCCGGCGGAGAGTGAATGTCGAAGCCTGCTTCCCGGTTACGTCGGCTCCAATAAGGTGCGGGAGAGCGGTAATGATGGGGGTGATGGTGGTAAAGGTGAAAGGAGAATGAGCAAAGCCCGCCGATGGGCGGGCTTCA‑gg                                                                                                                                 <  4:181808/149‑1 (MQ=255)          ttttGGTCTATCCGGCGGAGAGTGAATGTCGAAGCCTGCTTCCCGGTTACGTCGGCTCCAATAAGGTGCGGGAGAGCGGTAATGATGGGGGTGATGGTGGTAAAGGTGAAAGGAGAATGAGCAAAGCCCGCCCATCGGCGGGCtttgct                                                                                                                                  <  3:193776/149‑5 (MQ=255)              ggTCTATCCGGCGGAGAGTGAATGTCGAAGCCTGCTTCCCGGTTACGTCGGCTCCAATAAGGTGCGGGAGAGCGGTAATGATGGGGGTGATGGTGGTAAAGGTGAAAGGAGAATGAGCAAAGCCCGCCGATGGGCGGGCTTCA‑ggggg                                                                                                                              <  3:356290/148‑1 (MQ=255)               gTCTATCCGGCGGAGAGTGAATGTCGAAGCCTGCTTCCCGGTTACGTCGGCTCCAATAAGGTGCGGGAGAGCGGTAATGATGGGGGTGATGGTGGTAAAGGTGAAAGGAGAATGAGCAAAGCCCGCCGATGGGCGGGCTTCA‑gggggg                                                                                                                             <  4:355230/148‑1 (MQ=255)                    tCCGGCGGAGAGTGAATGTCGAAGCCTGCTTCCCGGTTACGTCGGCTCCAATAAGGTGCGGGAGAGCGGTAATGATGGGGGTGATGGTGGTAAAGGTGAAAGGAGAATGAGCAAAGCCCGCCGATGGGCGGGCTTCA‑GGGGGGGGCAg                                                                                                                        >  5:310371/1‑148 (MQ=255)                    tCCGGCGGAGAGTGAATGTCGAAGCCTGCTTCCCGGTTACGTCGGCTCCAATAACGTGCGGGAGAGCGGTAATGATGGGGGTGATGGTGGTAAAGGTGAAATGAGAATGAGCAAAGCCCGCCGATGGGCGGGCTTCA‑GGGGGGGGCAg                                                                                                                        >  7:55382/1‑148 (MQ=255)                        gcggAGTGTGAATGTCGAAGCCTGCTTCCCGGATACGGCGGCTCCAATTAGGTGCGGGAGAGCGGTAATGAGGGGGGTGATGGTGGTAAAGGTGAAAGGAGAATGAGCAAAGCCCGCCGATGGGCGGGCTTCA‑GGGGGGGGCAGAAggg                                                                                                                   <  6:86973/149‑1 (MQ=255)                                   ctggccaaGCCTGCTTCCCGGGTACGTCGGCTCCAATAAGGTGCGGGCGAGCGGTAATGAGGGGGGTGATGGGGGTAAAGGTGAACGGAGAATGACCAAAGCCCGCCGATGGGCGGGCTTCA‑GGGGGGGGCAGAAGGGCTATCGtacta                                                                                                        <  6:310371/143‑1 (MQ=255)                                              tGCTTCCCGGTTACGTCGGCTCCAATAAGGTGCGGGAGAGCGGTAATGATGGGGGTGATGGTGGTAAAGGTGAAAGGAGAATTAGCAAAGCCCGCCGATGGGCGGGCTTCA‑GGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTtct                                                                                             >  3:368464/1‑149 (MQ=255)                                                      gggtccctCGGCCCCACTAAGGGGCCGGAGAGCGGTAAGGATGGGGGTGCGGGGGGTCAAGCTGACAGCCGAATGCGCAAAGCCCGCCGAGGGGCGGGCTTCA‑GGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCAcc                                                                                     <  6:96813/142‑1 (MQ=255)                                                       gTTACGTCGGCTCCAATAAGGTGCGGGAGAGCGGTAATGATGGGGGTGATGGTGGTAAAGGTGAAAGGAGAATGAGCAAAGCCCGCCGATGGGCGGGCTTCA‑GGGGGGGGCAGAAggg                                                                                                                   <  7:84899/118‑1 (MQ=255)                                                          cccgccgCTCCAAATAGGTCCGGGCTTGCTGTAATGATGGGGGTGATGGTGGTAAAGGTGAATGTACATTCAGCAAAGCCCGCCGATGGGCGGGCTTCA‑CGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGaa                                                                                  <  8:55382/142‑1 (MQ=255)                                                                gCTCCAATAAGGTGCGGGAGAGCGGTAATGATGGGGGTGATGGTGGTAAAGGTGAAAGGAGAATGAGCAAAGCCCGCCGATGGGCGGGCtt                                                                                                                                      >  2:34364/1‑91 (MQ=255)                                                                gCTCCAATAAGGTGCGGGAGAGCGGTAATGATGGGGGTGATGGTGGTAAAGGTGAAAGGAGAATGAGCAAAGCCCGCCGATGGGCGGGCtt                                                                                                                                      <  1:34364/91‑1 (MQ=255)                                                                  tCCAATAAGGTGCGGGAGAGCGGTAATGATGGGGGTGATGGTGGTAAAGGTGAAAGGAGAATGAGCAAAGCCCGCCGATGGGCGGGCTTCA‑GGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAgg                                                                           >  3:160011/1‑147 (MQ=255)                                                                    cAATAAGGGCCGGGAGCGCGGTAATCATGGGGGTGAGGGTGGTACAGGTGAACGGACCATCCGCAAAGCCCCCCGATGGGCGGGCGTCA‑GGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGaa                                                                         <  6:253258/147‑1 (MQ=255)                                                                            cgCGGGCGAGCGGTAAGGCTGGGGGTGAGGGGGGTAACGGTGAACGCAGCAGGCGCAAAGCCCGCCGCTGGGCGGGCTTCA‑GGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCAcccgccc                                                               <  4:368464/148‑1 (MQ=255)                                                                                                    gTGATGGTGGTAAAGGTGAAAGGAGAATGAGCAAAGCCCGCCGATGGGCGGGCTTCAGGGGGGGGGCAGAAGGGCTATCGTACTACGGTCGATTATCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACGCCTAATCAGGAAACgaaa                                        >  7:458/1‑146 (MQ=255)                                                                                                    gTGATGGTGGTAAAGGTGAAAGGAGAATGAGCAAAGCCCGCCGATGGGCGGGCTTCA‑GGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACTCCTCATCAGGAATCGCACt                                       >  2:213942/1‑149 (MQ=255)                                                                                                        tggtggTAAAGGTGAAAGGAGAATGAGCAAAGCCCGCCGATGGGCGGGCTTCA‑GGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACTCCTCATCAGGAAt                                             >  3:96926/1‑139 (MQ=255)                                                                                                        tggtggTAAAGGTGAAAGGAGAATGAGCAAAGCCCGCCGATGGGCGGGCTTCA‑GGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACTCCTCATCAGGAAt                                             <  4:96926/139‑1 (MQ=255)                                                                                                         ggtggtAAAGGTGAAAGGAGAATGAGCAAAGCCCGCCGATGGGCGGGCTTCA‑GGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACTCCTCATCAGGAATCGCACTTTCAg                                  >  3:194287/1‑149 (MQ=255)                                                                                                          gtggtAAAGGTGAAAGGAGAATGAGCAAAGCCCGCCGATGGGCGGGCTTCA‑GGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACTCCTCATCAGGAATCGCACTTTCAg                                  <  4:194287/148‑1 (MQ=255)                                                                                                                   gTGAAAGGAGAATGAGCAAAGCCCGCCGATGGGCGGGCTTCA‑GGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACTCCTCATCAGGAATCGCACTTTCAGGTGACTGCCt                        >  2:200924/1‑149 (MQ=255)                                                                                                                    tGAAAGGAGAATGAGCAAAGCCCGCCGATGGGCGGGCTTCA‑GGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACTCCTCATCAGGAATCGCACTTTCAGGTGACTGCCtt                       <  1:200924/149‑1 (MQ=255)                                                                                                                     gAAAGGAGAATGAGCAAAGCCCGCCGATGGGCGGGCTTCA‑GGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCAc                                                           >  3:73275/1‑112 (MQ=255)                                                                                                                     gAAAGGAGAATGAGCAAAGCCCGCCGATGGGCGGGCTTCA‑GGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCAc                                                           <  4:73275/112‑1 (MQ=255)                                                                                                                     gAAAGGAGAATGAGCAAAGCCCGCCGATGGGCCGGCTTCA‑GGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTGCACCCAAAGGTAGGAAGCACCCGCCCGCACTCGTCATGAGGAATCGCACTTTCAGGTGACTGCCttt                      >  4:124927/1‑149 (MQ=255)                                                                                                                      aaaGGAGAATGAGCAAAGCCCGCCGATGGGCGGGCTTCA‑GGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACTCCTCATCAGGAATCGCACTTTCAGGTGACTGCCTTTg                     >  4:41470/1‑149 (MQ=255)                                                                                                                      aaaGGAGAATGAGCAAAGCACGCCGATGGGCGGGCTTCA‑GGGGGGGGCAGAAGGGCAATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCCCCCGCCCGCACTCCTCATCAGGAATCGCACTTTCAGGTGCATGCCTTTg                     >  5:178283/1‑149 (MQ=255)                                                                                                                              aTGAGCAAAGCCCGCCGATGGGCGGGCTTCA‑GGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACTCCTCATCAGGAATCGCACTTTCAGGTGACTGCCTTTGGAt                  <  5:318204/144‑1 (MQ=255)                                                                                                                              aTGAGCAAAGCCCGCCGATGGGCGGGCTTCA‑GGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACTCCTCATCAGGAATCGCACTTTCAGGTGACTGCCTTTGGAt                  >  6:318204/1‑144 (MQ=255)                                                                                                                              aTGAGCAAAGCCCGCCGATGGGCGGGCTTCA‑GGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACTCCTCATCAGGAATCGCACTTTCAGGTGACTGCCTTTGGATAAGtt             <  4:160011/149‑1 (MQ=255)                                                                                                                                gAGCAAAGCCCGCCGATGGGCGGGCTTCA‑GGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACTCCTCATCAGGAATCGCACTTTCAGGTGACTGCCTTTGGATAAGTTg            >  3:8766/1‑148 (MQ=255)                                                                                                                                 aGCATAGCCCGCCGATGTGCGGGCTTCA‑GGGGGGGGCAGAAGGGCTATGGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACTCCTCATCAGGAATCGCACTTTCAGGTGACTGCCTTTTGATAAGTTGt           <  6:178283/148‑1 (MQ=255)                                                                                                                                 aGCAAAGCCCGCCGATGGGCGTGCTTCA‑GGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACTCCTCATCAGGAATCGCACTTTCAGGTGACTGCCTTTGGATAAGTTGt           <  1:213942/148‑1 (MQ=255)                                                                                                                                 aGCAAAGCCCGCCGATGGGCGGGCTTCA‑GGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACTCCTCATCAGCAATCGCACTTTCAGGTGACTGCCTTTGGATAAGTTGTa          >  4:107152/1‑149 (MQ=255)                                                                                                                                  ctgaaGCCCGCCCATCGGCGGGCTTCA‑GGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACTCCTCATCAGGAATCGCACTTTCAGGTGACTGCCTTTGGATAAGTTGTAt         >  2:317445/4‑149 (MQ=255)                                                                                                                                    gaaGCCCGCCCATCGGCGGGCTTCA‑GGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACTCCTCATCAGGAATCGCACTTTCAGGTGACTGCCTTTGGATAAGTTGTATc        >  2:157346/2‑148 (MQ=255)                                                                                                                                      aGCCCGCCGATGGGCGGGCTTCA‑GGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACTCCTCATCAGGAATCGCACTTTCAGGTGACTGCCTTTGGATAAGTTGTATCCAg     >  3:241388/1‑149 (MQ=255)                                                                                                                                       tccccccGAGGGGCGCTCTTCA‑GGGCGCGTCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAATGTAGGAAGCACCCGCCCGCACTCCTCATCAGGAATCGCACTTTCAGGTGACTGCCTTTGGATAAGTTGTATCCAGc    <  3:136854/148‑1 (MQ=255)                                                                                                                                       gcccgcccATCGGCGGGCTTCA‑GGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCCCCCGCCCGCACTCCTCATCAGGAATCGCACTTTCAGGTGACTGCCtt                       >  2:211904/1‑130 (MQ=255)                                                                                                                                         ccgcccATCGGCGGGCTTCA‑GGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACTCCTCATCAGGAATCGCACTTTCAGGTGACTGCCTTTGGATAAGTTGTATCCAGCCt  <  1:317445/149‑1 (MQ=255)                                                                                                                                          cgccgATGGGCGGGCTTCA‑GGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACTCCTCATCAGGAATCGCACTTTCAGGTGACTGc                          <  2:216867/124‑1 (MQ=255)                                                                                                                                          cgccgATGGGCGGGCTTCA‑GGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACTCCTCATCAGGAATCGCACTTTCAGGTGACTGc                          >  1:216867/1‑124 (MQ=255)                                                                                                                                              |                                                                                                                                                 GAATGGGCATTTTGGTCTATCCGGCGGAGAGTGAATGTCGAAGCCTGCTTCCCGGTTACGTCGGCTCCAATAAGGTGCGGGAGAGCGGTAATGATGGGGGTGATGGTGGTAAAGGTGAAAGGAGAATGAGCAAAGCCCGCCGATGGGCGGGCTTCA‑GGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACTCCTCATCAGGAATCGCACTTTCAGGTGACTGCCTTTGGATAAGTTGTATCCAGCCT  >  NC_002947/1274943‑1275227

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑