Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,076,094	T→G	9.8%	intergenic (‑42/+32)	PP_2685 ← / ← PP_2686	hypothetical protein/transglutaminase domain‑containing protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,076,094	0	T	G	9.8%	129.3 / 6.0	51	intergenic (‑42/+32)	PP_2685/PP_2686	hypothetical protein/transglutaminase domain‑containing protein
Reads supporting (aligned to +/- strand):  ref base T (22/23);  new base G (3/2);  total (26/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.52e-01

GAACAACTTGGTGAACGTGGAGATCTGGTCGATGCCGGCATTAGTGCGTGAGTCGCTGATGAAGACAAGCCCGTCCTCCAGGTGCATGGCGACACAGTAAGTCATGCGGTTTCCCTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGTGA‑ACGCTGGCCTGCATCGATTCGGCGCCGCCGCCGCGGCGTACGCCCCTGACCGGGCAGGCATCAAGGTAGTCCAGGCCCACCGCCAGCTTCA  >  NC_002947/3075948‑3076235                                                                                                                                                    |                                                                                                                                               gAACAACTTGGTGAACGTGGAGATCTGGTCGATGCCGGCATTAGTTCGTGAGTCGCTGATGAAGACAAGCCCGTCCTCCAGGTGCATGGCGACACAGTAAGTCATGCGGTTTCCCTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCACTcg                                                                                                                                              >  6:209201/1‑149 (MQ=255)              aaCGTGGAGATCTGGTCGATGCCGGCATTAGTGCGTGAGTCGCTGATCAAGACAAGCCCGTCCTCCAGGTGCATGGCGACACAGTAAGTCATGCGGTTTCCCTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCg                                                                                                                                 <  5:222440/149‑1 (MQ=255)                cGTGGAGATCTGGTCGATGCCGGCATTAGTGCGTGAGTCGCTGATGAAGACAAGCCCGTCCTCCAGGTGCATGGCGACACAGTAAGTCATGCGGTTTCCCTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGt                                                                                                                               <  3:74735/149‑1 (MQ=255)                         cTGGTCGATGCCGGCATTAGTGCGTGAGTCGCTGATGAAGCCAAGCCCGTCCTCCAGGTGCATGGCGACACAGTAAGTCATGCGGGTTCCCTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGCCa                                                                                                                      <  1:82730/149‑1 (MQ=255)                          ggggggATGGCGGCATTAGTGCGTGAGGCGTTTATTAACACATGCCCGTCCTCTTGTTGCCTGCCCACACTTTAAGGATTGCGTTTGCCGTTGTTTTGCGTGTGGACGGGCC‑TTCCCTCACTCGGGGGCAAAGACCGGTCTGAAGCCa                                                                                                                      <  2:189806/143‑1 (MQ=255)                            gTCGATGCCGGCATTAGTGCGTGAGTCGCTGATGAAGACAAGCCCGTCCTCCAGGTGCATGGCGACACAGTAAGTCATGCGGTTTCCCTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGcc                                                                                                                       <  5:209201/145‑1 (MQ=255)                                   ccGGCATTAGTGCGTGAGTCGCTTAGGAAGACAAGCCCGTCCTCCAGGTGCATGCCGACACAGTAAGTCATGCGGTTTCCCTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCAc                                                                                                             <  5:392915/148‑1 (MQ=255)                                    cGGCATTAGTGCGTGAGTCGCTGATGAAGACAAGCCCGTCCTCCAGGTGCATGGCGACACAGTAAGTCATGCGGTTTCCCTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCACTcgcgc                                                                                                                                           >  3:380975/1‑117 (MQ=255)                                    cGGCATTAGTGCGTGAGTCGCTGATGAAGACAAGCCCGTCCTCCAGGTGCATGGCGACACAGTAAGTCATGCGGTTTCCCTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCACTcgcgc                                                                                                                                           <  4:380975/117‑1 (MQ=255)                                    cGGCATTAGTGCGTGAGTCGCTGATGAAGACAAGCCCGTCCTCCAGGTGCATAGCGACACAGTAAGTCATGCGGTTTCCCTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGaa                                                                                                                          <  5:115160/134‑1 (MQ=255)                                    cGGCATTAGTGCGTGAGTCGCTGATGAAGACAAGCCCGTCCTCCAGGTGCATAGCGACACAGTAAGTCATGCGGTTTCCCTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGaa                                                                                                                          >  6:115160/1‑134 (MQ=255)                                                       gCTGATGAAGACAAGCCCGTCCTCCAGGTGCATGGCGACACAGTAAGTCATGCGGTTTCCCTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGTGA‑ACGCTg                                                                                       >  3:81716/1‑149 (MQ=255)                                                          gatgaAGACAAGCCCGTCCTCCAGGTGCATGGCGACACAGTAAGTCATGCGGTTTCCCTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGTGATGCACGTGA‑ACGCTGGcc                                                                                    >  5:195486/1‑149 (MQ=255)                                                          gatgaAGACAAGCCCGTCCTCCAGGTGCATGGCGACACAGTAAGTCATGCGGTTTCCCTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGt                                                                                                <  5:133414/138‑1 (MQ=255)                                                          gatgaAGACAAGCCCGTCCTCCAGGTGCATGGCGACACAGTAAGTCATGCGGTTTCCCTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGt                                                                                                >  6:133414/1‑138 (MQ=255)                                                             gaAGACAAGCCCGTCCTCCAGGTGCATGGCGACACAGTAAGTCATGCGGTTTCCCTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCAc                                                                                                  >  2:276195/1‑133 (MQ=255)                                                             gaAGACAAGCCCGTCCTCCAGGTGCATGGCGACACAGTAAGTCATGCGGTTTCCCTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCAc                                                                                                  <  1:276195/133‑1 (MQ=255)                                                                gACAAGCCCGTCCTCCAGGTGCATGGCGACACAGTAAGTCATGCGGTTTCCCTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCGCGAGTGCGGCAAg                                                                                                                                     <  4:110879/95‑1 (MQ=39)                                                                gACAAGCCCGTCCTCCAGGTGCATGGCGACACAGTAAGTCATGCGGTTTCCCTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCGCGAGTGCGGCAAg                                                                                                                                     >  3:110879/1‑95 (MQ=39)                                                                 aCAAGCCCGTCCTCCAGGTGCATGGCGACACAGTAAGTCATGCGGTTTCCCTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGTGA‑ACGCTGGCCTGCATc                                                                              >  8:243582/1‑148 (MQ=255)                                                                   aaGCCCGTCCTCCAGGTGCATGGCGACACAGTAAGTCATGCGGTTTCCCTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGTGA‑ACGCTGGCCTGCATCGAt                                                                           >  4:99174/1‑149 (MQ=255)                                                                     gCCCGTCCTCCAGGTGCATGGCGACACAGTAAGTCATGCGGTTTCCCTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTgg                                                                                                          <  7:128024/117‑1 (MQ=255)                                                                     gCCCGTCCTCCAGGTGCATGGCGACACAGTAAGTCATGCGGTTTCCCTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTgg                                                                                                          >  8:128024/1‑117 (MQ=255)                                                                        cGTCCTCCAGGTGGATGGCGACACAGTAAGTCATGCGGTTTCCCTTGTGTTGCGTGTGGATGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCTCGTGA‑ACGCTGGCCTGCATCGATTCGgc                                                                      <  2:90201/149‑1 (MQ=255)                                                                                        ggCGACACAGTAAGTCATGCGGTTTCCCTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGTGA‑ACGCTGGCCTGCATCGATTCGGCGCCgcggcggcggcgc                                                      <  7:243582/149‑2 (MQ=255)                                                                                                   aaGTCATGCGGTTTCCCTTGTGTTGCGTGTGGAAGGGTCATTCCCGCAGACGCCCGGAAAGACCGGGATAAAGCAAGGATGACACTGCCGATGCACTTGA‑ACGATGGCGTGAAAGGATACGCCGCC‑CCGCCCCCGCCTAccccccatca                                           >  2:121499/1‑145 (MQ=255)                                                                                                         tGCGGTTTCCCTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGTGATGCACGTGA‑ACGCTGGCCTGCATCGATTCGGCGCCGCCGCCGCGGCGTACGCCCCTGACCGggca                                     <  6:195486/149‑1 (MQ=255)                                                                                                         tGCGGTTTCCCTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGTGA‑ACGCTGGCCTGCATCGAATTGGCGCCGCCGCCGCGGCGTACGCCCCTGACCggg                                       >  3:353319/1‑147 (MQ=255)                                                                                                          gCGGTTTCCCTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGTGA‑ACGCTGGCCTGCATCGATTCGGCGCCGCCGCCGCGGCGTACGCCCCTGACCGggcag                                    >  8:226435/1‑149 (MQ=255)                                                                                                           cGGTTTCCCTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGTGA‑ACGCTGGCCTGCATCGATTCGGCGCCGCCGCCGCGGCGTACGCCCCTGACCGggcagg                                   >  2:125120/1‑149 (MQ=255)                                                                                                            ggTTTCCCTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGTGA‑ACGCTGGCCTGCATCGATTCGGCGCCGCCGCCGCGGCGTACGCCCCTGACCGggcaggc                                  <  3:99174/149‑1 (MQ=255)                                                                                                            ggTTTCCCTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGTGA‑ACGCTGGCCTGCATCGATTCGGCGCCGCCGCCGCGGCGTACGCCCCTGACCGggcaggc                                  <  4:81716/149‑1 (MQ=255)                                                                                                                  ccTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGTGA‑ACGCTGGCCTGCATCGATTCGGCGCCGCCGCCGCGCCGTACGCCCCTGACCGGGCAGGCATCAAg                            >  1:56206/1‑149 (MQ=255)                                                                                                                  ccTTGTGTTGCGGGTGGAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGTTACACGCTGGCCTGCATCGATTCGGCGCCGCCGCCGCGGCGTACGCCCCTGACCGGGCAGGCATCa                              <  1:121499/148‑1 (MQ=255)                                                                                                                   cTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGTGA‑ACGCTGGCCTGCATCGATTCGGCGCCGCCGCCGCGGCGTACGCCCCTGACCGGGCAGGCATCAAgg                           >  1:325303/1‑149 (MQ=255)                                                                                                                   cTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGTGA‑ACGCTGGCCTGCATCGATTCGGCGCCGCCGCCGCGGCGTACGCCCCTGACCGGGCAGGCATCAAgg                           <  2:325303/149‑1 (MQ=255)                                                                                                                      gggtTGCGGGTGGACGGGTC‑GTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGTGA‑ACGCTGGCCTGCATCGATTTGGCGCCGCCGCCGCGGCGTACGCCCCTGACCGGGCAGGCATCAAGGTa                         <  4:353319/146‑1 (MQ=255)                                                                                                                              tgtgGAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGTGA‑ACGCTGGCCTGCATCGATTCGGCGCCGCCGCCGCGGCGTACGCCCCTGACCGGGCAGGCATCAAGGTAGTCCAGGcc                >  4:147609/1‑149 (MQ=255)                                                                                                                              tgtgGAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGTGA‑ACGCTGGCCTGCATCGATTAGGCGCCGCCGCCGCGGCGTACGCCCCTGACCGGGCAGGCATCAAGGTAGTCCAGGcc                >  3:186669/1‑149 (MQ=255)                                                                                                                                tgGAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGTGA‑ACGCTGGCCTGCATCGATTCGGCGCCGCCGCCGCGGCGTACGCCCCTGACCGGGCAGGCATCAAGGTAGTCCAGGCCCa              >  1:286714/1‑149 (MQ=255)                                                                                                                                  gAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGTGA‑ACGCTGGCCTGCATCGATTCGGCGCCGCCGCCGCGGCGTACGCCCCTGACCGGGCAGGCATCAAGGTAGTCCAGGCCCAcc            >  5:347275/1‑149 (MQ=255)                                                                                                                                     gggTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGTGA‑ACGCTGGCCTGCATCGATTCGGCGCCGCCGCCGCGGCGTACGCCCCTGACCGGGCAGGCATCAAGGTAGTCCAGGCCCACCGc          >  3:161472/1‑148 (MQ=255)                                                                                                                                      ggTC‑TTGCCGCGCGAGTGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGTGA‑ACGCTGGCCTGCATCGATTCGGCGCCGCCGCCGCGGCGTACGCCCCTGACCGGGCAGGCATCAAGGTAGTCCAGGCCCACCGc          >  2:95385/1‑147 (MQ=255)                                                                                                                                        tC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGTGA‑ACGCTGGCCTGCATCGATTCGGCGCCGCCGCCGCGGCGTACGCCCCTGACCGGGCAGGCATCAAg                            <  2:211411/127‑1 (MQ=255)                                                                                                                                        tC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGTGA‑ACGCTGGCCTGCATCGATTCGGCGCCGCCGCCGCGGCGTACGCCCCTGACCGGGCAGGCATCAAg                            >  1:211411/1‑127 (MQ=255)                                                                                                                                           ttGCCGCGCGAGTGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGTGA‑ACGCTGGCCTGCATCGATTCGGCGCCGCCGCCGCGGCGTACGCCCCTGACCGGGCAGGCATCAAg                            <  3:315406/125‑1 (MQ=255)                                                                                                                                           ttGCCGCGCGAGTGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGTGA‑ACGCTGGCCTGCATCGATTCGGCGCCGCCGCCGCGGCGTACGCCCCTGACCGGGCAGGCATCAAg                            >  4:315406/1‑125 (MQ=255)                                                                                                                                              ccGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGTGA‑ACGCTGGCCTGCATCGATTCGGCGCCGCCGCCGCGGCGTACGCCCCTGACCGGGCAGGCATCAAGGTAGTCCAGGCCCACCGCCAGCTTCa  <  2:286714/148‑1 (MQ=255)                                                                                                                                              ccGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGTGA‑ACGCTGGCCTGCATCGATTCGGCGCCGCCGCCGCGGCGTACGCCCCTGACCGGGCAGGCATCAAGGTAGTCCAGGCCCACCGCCAGCTTCa  <  7:226435/148‑1 (MQ=255)                                                                                                                                               cGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGTGA‑ACGCTGGCCTGCATCGATTCGGCGCCGCCGCCGCGGCGTACGCCCCTGACCGGGCAGGCATCAAGGTa                         <  4:362340/124‑1 (MQ=255)                                                                                                                                               cGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGTGA‑ACGCTGGCCTGCATCGATTCGGCGCCGCCGCCGCGGCGTACGCCCCTGACCGGGCAGGCATCAAGGTa                         >  3:362340/1‑124 (MQ=255)                                                                                                                                                    |                                                                                                                                               GAACAACTTGGTGAACGTGGAGATCTGGTCGATGCCGGCATTAGTGCGTGAGTCGCTGATGAAGACAAGCCCGTCCTCCAGGTGCATGGCGACACAGTAAGTCATGCGGTTTCCCTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGTGA‑ACGCTGGCCTGCATCGATTCGGCGCCGCCGCCGCGGCGTACGCCCCTGACCGGGCAGGCATCAAGGTAGTCCAGGCCCACCGCCAGCTTCA  >  NC_002947/3075948‑3076235

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: ‑