Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,076,097	C→T	10.7%	intergenic (‑45/+29)	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	3,076,097	0	C	T	10.7%	126.8 / 4.7	48	intergenic (‑45/+29)	PP_2685/PP_2686	hypothetical protein/transglutaminase domain‑containing protein
Reads supporting (aligned to +/- strand):  ref base C (21/21);  new base T (3/2);  total (24/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AACGTGGAGATCTGGTCGATGCCGGCATTAGTGCGTGAGTCGCTGATGAAGACAAGCCCGTCCTCCAGGTGCATGGCGACACAGTAAGTCATGCGGTTTCCCTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGTGA‑ACGCTGGCCTGCATCGATTCGGCGCCGCCGCCGCGGCGTACGCCCCTGACCGGGCAGGCATCAAGGTAGTCCAGGCCCACCGCCAGCTTCAGGTGACGCT  >  NC_002947/3075961‑3076244                                                                                                                                          |                                                                                                                                                     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                                                                                                                                   >  6:115160/1‑134 (MQ=255)                       cGGCATTAGTGCGTGAGTCGCTGATGAAGACAAGCCCGTCCTCCAGGTGCATAGCGACACAGTAAGTCATGCGGTTTCCCTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGaa                                                                                                                                   <  5:115160/134‑1 (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                                                                                                                   >  8:128024/1‑117 (MQ=255)                                                        gCCCGTCCTCCAGGTGCATGGCGACACAGTAAGTCATGCGGTTTCCCTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTgg                                                                                                                   <  7:128024/117‑1 (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                                    <  2:325303/149‑1 (MQ=255)                                                                                                      cTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGTGA‑ACGCTGGCCTGCATCGATTCGGCGCCGCCGCCGCGGCGTACGCCCCTGACCGGGCAGGCATCAAgg                                    >  1:325303/1‑149 (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           <  7:226435/148‑1 (MQ=255)                                                                                                                                 ccGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGTGA‑ACGCTGGCCTGCATCGATTCGGCGCCGCCGCCGCGGCGTACGCCCCTGACCGGGCAGGCATCAAGGTAGTCCAGGCCCACCGCCAGCTTCa           <  2:286714/148‑1 (MQ=255)                                                                                                                                  cGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGTGA‑ACGCTGGCCTGCATCGATTCGGCGCCGCCGCCGCGGCGTACGCCCCTGACCGGGCAGGCATCAAGGTa                                  >  3:362340/1‑124 (MQ=255)                                                                                                                                  cGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGTGA‑ACGCTGGCCTGCATCGATTCGGCGCCGCCGCCGCGGCGTACGCCCCTGACCGGGCAGGCATCAAGGTa                                  <  4:362340/124‑1 (MQ=255)                                                                                                                                         gcgcgGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGTGA‑ACGCTGGCCTGCATCGATTCGGCGCCGCCGCCGCGGCGTACGCCCCTGACCGGGCAGGCATCAAGGTAGTCCAGGCCCACCGCCAGCTTCAGGTGACGct  >  3:77742/1‑149 (MQ=255)                                                                                                                                          |                                                                                                                                                     AACGTGGAGATCTGGTCGATGCCGGCATTAGTGCGTGAGTCGCTGATGAAGACAAGCCCGTCCTCCAGGTGCATGGCGACACAGTAAGTCATGCGGTTTCCCTTGTGTTGCGTGTGGAAGGGTC‑TTGCCGCACTCGCGCGGCAAGACCGGTCTGAAGCCAGTCTGTCACTGGCGATGCACGTGA‑ACGCTGGCCTGCATCGATTCGGCGCCGCCGCCGCGGCGTACGCCCCTGACCGGGCAGGCATCAAGGTAGTCCAGGCCCACCGCCAGCTTCAGGTGACGCT  >  NC_002947/3075961‑3076244

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: ‑