Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,489,097	G→A	9.1%	intergenic (+450/+121)	PP_3981 → / ← PP_3982	transposase/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,489,097	0	G	A	9.1%	122.3 / 2.8	44	intergenic (+450/+121)	PP_3981/PP_3982	transposase/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (20/20);  new base A (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 = 8.49e-01

AGGGCTTATCTGAGGCCTTGCTTGCACACGGGCGGGAACCTCCCGCCCATATGCGCGTACTTCATAGCGCGACAATCCACTCCAAGACCTCACATCTCACTTGGCTGAACTGGGCCTAAAACTCTCCATAGGTGATGTCTGACGCCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTTGGCGACCGGCCTGTTCTCATACCCCGCGAAATGGTCGATTGAATCAACTGTGGCATGGTGCGATCAGGGAACTCGTAAACGCAAAGCATTC  >  NC_002947/4488954‑4489245                                                                                                                                                |                                                                                                                                                     aGGGCTTATCTGAGGCCTTGCTTGCACACGGGCGGGAACCTCCCGCCCATATGCGCGTACTTCATAGCGCGACAATCCACTCCAAGACCTCACATCTCACTTGGCTGAACTGGGCCTAAAACTCTCAATAGGTGATGTCTGACGCCTGc                                                                                                                                                 >  7:70293/1‑149 (MQ=255)           tGAGGCCTTGCTTGCACACGGGCGGGAACCTCCCGCCCATATGCGCGTACTTCATAGCGCGACAATCCACTCCAAGACCTCACATCTCACTTGGCTGAACTGGGCCTAAAACTCTCCATAGGTGATGTCTGACGCCTGCCACATCaa                                                                                                                                         >  1:268007/1‑147 (MQ=255)           tGAGGCCTTGCTTGCACACGGGCGGGAACCTCCCGCCCATATGCGCGTACTTCATAGCGCGACAATCCACTCCAAGACCTCACATCTCACTTGGCTGAACTGGGCCTAAAACTCTCCATAGGTGATGTCTGACGCCTGCCACATCaa                                                                                                                                         <  2:268007/147‑1 (MQ=255)                        gcACACGGGCGGGAACCTCCCGCCCATATGCGCGTACTTCATAGCGCGACAATCCACTCCAAGACCTCACATCTCACTTGGCTGAACTGGGCCTAAAACTCTCCATAGGTGATGTCTGACGCCTGCCACATCAATACCGAGGTAACGa                                                                                                                           <  6:6975/148‑1 (MQ=255)                          acacGGGCGGGAACCTCCCGCCCATATGCGCGTACTTCATAGCGCGACAATCCACTCCAAGACCTCCCATCTCACTTGGCTGAACTGGGCCTAAAACTCTCCATAGGTGATGTCTGACGCCTGCCACATCAATACCGAGGTAACGAGtt                                                                                                                        >  5:231147/1‑149 (MQ=255)                                                   atGCGCGTACTTCATAGCGCGACAATCCACTCCAAGACCTCACATCTCACTTGGCTGAACTGGGCCTAAAACTCTCCATAGGTGATGTCTGACGCCTGCCACATCAATACCGAGGTAACGa                                                                                                                           <  1:258563/121‑1 (MQ=255)                                                   atGCGCGTACTTCATAGCGCGACAATCCACTCCAAGACCTCACATCTCACTTGGCTGAACTGGGCCTAAAACTCTCCATAGGTGATGTCTGACGCCTGCCACATCAATACCGAGGTAACGa                                                                                                                           >  2:258563/1‑121 (MQ=255)                                                       gcgTACTTCATAGCGCGACAATCCACTCCAAGACCTCACATCTCACTTGGCTGAACTGGGCCTAAAACTCTCCATAGGTGATGTCTGACGCCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTTgg                                                                                           >  6:274430/1‑149 (MQ=255)                                                                   gcgcGACAATCCACTCCAAGACCTCACATCTCACTTGGCTGAACTGGGCCTAAAACTCTCCATAGGTGATGTCTGACGCCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTTGGCGACCGGCCTGt                                                                               >  1:213809/1‑149 (MQ=255)                                                                       gACAATCCACTCCAAGACCTCACATCTCACTTGGCTGAACTGGGCCTAAAACTCTCCATAGGTGATGTCTGACGCCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTTGGCGACCGGCCTGTtctc                                                                           <  8:70293/149‑1 (MQ=255)                                                                       gACAATCCACTCCAAGACCTCACATCTCACTTGGCTGAACTGGGCCTAAAACTCTCCATAGGTGATGTCTGACGCCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTTGGCGACCGGCCTGTtct                                                                            >  7:18301/1‑148 (MQ=255)                                                                            tCCACTCCAAGACCTCACATCTCACTTGGCTGAACTGGGCCTAAAACTCTCCATAGGTGATGTCTGACGCCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTTGGCGACCGGCCTGTTCTCATAcc                                                                      >  7:87915/1‑149 (MQ=255)                                                                               aCTCCAAGACCTCACATCTCACTTGGCTGAACTGGGCCTAAAACTCTCCATAGGTGATGTCTGACGCCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTTGGCGACCGGCCTGTTCTCATACCCcg                                                                   <  8:18301/149‑1 (MQ=255)                                                                                 tCCAAGACCTCACATCTCACTTGGCTGAACTGGGCCTAAAACTCTCCATAGGTGATGTCTGACGCCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTAGGCGACCGGCCTGTTCTCATACCCcgcg                                                                 <  1:150503/149‑1 (MQ=255)                                                                                   cAAGACCTCACATCTCACTTGGCTGAACTGGGCCTAAAACTCTCCATAGGTGATGTCTGACGCCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTTGGCGACCGGc                                                                                   <  5:218579/129‑1 (MQ=255)                                                                                   cAAGACCTCACATCTCACTTGGCTGAACTGGGCCTAAAACTCTCCATAGGTGATGTCTGACGCCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTTGGCGACCGGc                                                                                   >  6:218579/1‑129 (MQ=255)                                                                                   cAAGACCTCACATCTCACTTGGCTGAACTGGGCCTAAAACTCTCCATAGGTGATGTCTGACACCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTTGGCGACCGGCCTGTTCTCATACCCCGCGa                                                                >  3:8662/1‑148 (MQ=255)                                                                                   cAAGACCTCACATCTCACTTGGCTGAACTGGGCCTAAAACTCTCCATAGGTGATGTCTGACACCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTTGGCGACCGGCCTGTTCTCATACCCCGCGa                                                                >  3:12374/1‑148 (MQ=255)                                                                                      gACCTCACATCTCACTTGGCTGAACTGGGCCTAAAACTCTCCATAGGTGATGTCTGACGCCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTTGGCGACCGGCCTGTTCTCATACCCCGCGAAATg                                                            <  5:274430/149‑1 (MQ=255)                                                                                      gACCTCACATCTCACTTGGCTGAACTGGGCCTAAAACTCTCCATAGGTGATGTCTGACGCCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTTGGCGACCGGCCTGTTCTCATACCCCGCGAAATg                                                            <  6:147606/149‑1 (MQ=255)                                                                                        ccTCACATCTCACTTGGCTGAACTGGGCCTAAAACTCTCCATAGGTGATGTCTGACGCCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTTGGCGACCGGCCTGTTCTCATACCCCGCGAAATGGt                                                          <  6:114168/149‑1 (MQ=255)                                                                                         cTCACATCTCACTTGGCTGAACTGGGCCTAAAACTCTCCATAGGTGATGTCTGACGCCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTTGGCGACCGGCCTGTTCTCATACCCCGCGAAATGGTc                                                         >  5:128710/1‑149 (MQ=255)                                                                                         cTCACATCTCACTTGGCTGAACTGGGCCTAAAACTCTCCATAGGTGATGTCTGACACCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTTGGCGACCGGCCTGTTCTCATACCCCGCGAAATGGTc                                                         <  4:8662/149‑1 (MQ=255)                                                                                         cTCACATCTCACTTGGCTGAACTGGGCCTAAAACTCTCCATAGGTGATGTCTGACACCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTTGGCGACCGGCCTGTTCTCATACCCCGCGAAATGGTc                                                         <  4:12374/149‑1 (MQ=255)                                                                                          tCACATCTCACTTGGCTGAACTGGGCCTAAAACTCTCCATAGGTGATGTCTGACGCCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTTGGCGACCGGCCTGTTCTCATACCCCGCGAAATGGt                                                          <  4:152989/147‑1 (MQ=255)                                                                                          tCACATCTCACTTGGCTGAACTGGGCCTAAAACTCTCCATAGGTGATGTCTGACGCCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTTGGCGACCGGCCTGTTCTCATACCCCGCGAAATGGt                                                          >  3:152989/1‑147 (MQ=255)                                                                                                ctcACTTGGCTGAACTGGGCCTAAAACTCTCCATAGGTGATGTCTGACGCCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTTg                                                                                            <  2:233960/107‑1 (MQ=255)                                                                                                ctcACTTGGCTGAACTGGGCCTAAAACTCTCCATAGGTGATGTCTGACGCCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTTg                                                                                            >  1:233960/1‑107 (MQ=255)                                                                                                       ggCTGAACTGGGCCTAAAACTCTCCATAGGTGATGTCTGACGCCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTTGGCGACCGGCCTGTTCTCATa                                                                        >  5:274042/1‑120 (MQ=255)                                                                                                       ggCTGAACTGGGCCTAAAACTCTCCATAGGTGATGTCTGACGCCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTTGGCGACCGGCCTGTTCTCATa                                                                        <  6:274042/120‑1 (MQ=255)                                                                                                                   ccTAAAACTCTCCATAGGTGATGTCTGACGCCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTTGGCGACCGGCCTGTTCTCATACCCCGCGAAATGGTCGATTGAATCAACTGTGGCATGGTGc                                >  1:198548/1‑148 (MQ=255)                                                                                                                       aaaCTCTCCATAGGTGATGTCTGACGCCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTTGGCGACCGGCCTGTTCTCATACCCCGCGAAATGGTCGATTGAATCAACTGTGGCATGGTGCGATc                            <  8:87915/148‑1 (MQ=255)                                                                                                                         aCTCTCCATAGGTGATGTCTGACGCCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTTGGCGACCGGCCTGTTCTCATACCCCGCGAAATGGTCGATTGAATCAACTGTGGCATGGTGCGATCAgg                         <  2:213809/149‑1 (MQ=255)                                                                                                                           tctcCATAGGTGATGTCTGACGCCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTTGGCGACCGGCCTGTTCTCATACCCCGCGAAATGGTCGATTGAATCAACtgtg                                         <  7:73659/131‑1 (MQ=255)                                                                                                                           tctcCATAGGTGATGTCTGACGCCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTTGGCGACCGGCCTGTTCTCATACCCCGCGAAATGGTCGATTGAATCAACtgtg                                         >  8:73659/1‑131 (MQ=255)                                                                                                                           tctcCATAGGTGATGTCTGACGCCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTTGGCGACCGGCCTGTTCTCATACCCCGCGAAATGGTCGATTGAATCAACTGTGGCATGGTGCGATc                            >  6:170853/1‑144 (MQ=255)                                                                                                                           tctcCATAGGTGATGTCTGACGCCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTTGGCGACCGGCCTGTTCTCATACCCCGCGAAATGGTCGATTGAATCAACTGTGGCATGGTGCGATc                            <  5:170853/144‑1 (MQ=255)                                                                                                                             tcCATAGGTGATGTCTGACGCCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTTGGCGACCGGCCTGTTCTCATACCCCGCGAAATGGTCGAtt                                                     <  7:110928/117‑1 (MQ=255)                                                                                                                             tcCATAGGTGATGTCTGACGCCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTTGGCGACCGGCCTGTTCTCATACCCCGCGAAATGGTCGAtt                                                     >  8:110928/1‑117 (MQ=255)                                                                                                                                         gTCTGACGCCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTTGGCGACCGGCCTGTTCTCATACCCCGCGAAATGGTCGATTGAATCAACTGTGGCATGGTGCGATCAGGGAACTCGTAAACGCa          >  4:21812/1‑148 (MQ=255)                                                                                                                                          tCTGACGCCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTTGGCGACCGGCCTGTTCTCATACCCCGCGAAATGGTCGATTGAATCAACtgt                                          <  7:196372/115‑1 (MQ=255)                                                                                                                                          tCTGACGCCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTTGGCGACCGGCCTGTTCTCATACCCCGCGAAATGGTCGATTGAATCAACtgt                                          >  8:196372/1‑115 (MQ=255)                                                                                                                                           cTGACGCCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTTGGCGACCGGCCTGTTCTCATACCCCGCGAAATGGTCGATTGAATCAACTGTGGCATGGTGCGATCAGGGAACTCGt                 <  5:99123/139‑1 (MQ=255)                                                                                                                                           cTGACGCCTGCCACATCAATACCGAGGTAACGAGTTTCACAACCGCTAACTACGCCTCCGGTTGGCGACCGGCCTGTTCTCATACCCCGCGAAATGGTCGATTGAATCAACTGTGGCATGGTGCGATCAGGGAACTCGt                 >  6:99123/1‑139 (MQ=255)                                                                                                                                                gCCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTTGGCGACCGGCCTGTTCTCATACCCCGCGAAATGGTCGATTGAATCAACTGTGGCATGGTGCGATCAGGGAACTCGTAAACGCAAAGCATTc  <  3:21812/149‑1 (MQ=255)                                                                                                                                                |                                                                                                                                                     AGGGCTTATCTGAGGCCTTGCTTGCACACGGGCGGGAACCTCCCGCCCATATGCGCGTACTTCATAGCGCGACAATCCACTCCAAGACCTCACATCTCACTTGGCTGAACTGGGCCTAAAACTCTCCATAGGTGATGTCTGACGCCTGCCACATCAATACCGAGGTAACGAGTTTCACCACCGCTAACTACGCCTCCGGTTGGCGACCGGCCTGTTCTCATACCCCGCGAAATGGTCGATTGAATCAACTGTGGCATGGTGCGATCAGGGAACTCGTAAACGCAAAGCATTC  >  NC_002947/4488954‑4489245

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: ‑