Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,886,166	T→A	12.9%	intergenic (+45/+78)	PP_4295 → / ← PP_4296	TetR family transcriptional regulator/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,886,166	0	T	A	12.9%	79.5 / 4.3	31	intergenic (+45/+78)	PP_4295/PP_4296	TetR family transcriptional regulator/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (12/15);  new base A (2/2);  total (14/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.58e-01

TGCGGTGACCGGTAAGGCCAAGCTGGCCGACAGTGATTATGACGCGGCGGCCGAGACCATCATTCGTATGGTCTTGAAAGGTTGTGAGCCTGAGGCAGCCTGAACCATCTCGAAGGGCCATTCGCGGGCAAGCCCGCTCCCACAGGATCACCACATGCCTGAAGGTTGTGGAGTCCCTGTGGGAGCGGGCTTGCCCGCGAATGGGCCAGAACAGGCAATAGAGATTTAGGCCGCTACCCCGGCATCTGCCCGCAGCCCCACCTCCTCGATCGCACTGATCGCACACTGCTCGTC  >  NC_002947/4886019‑4886312                                                                                                                                                    |                                                                                                                                                   tGCGGTGACCGGTAAGGCCAAGCTGGCCGACAGTGATTATGACGCGGCGGCCGAGACCATCATTCGTATGGTCTTGAAAGGTTGTGAGCCTGAGGCAGCCTGAACCATCTCGAAGGGCCATTCGCGGGCAAGCCCGCTCCCACAGGATc                                                                                                                                                   <  4:62526/149‑1 (MQ=255)  gCGGTGACCGGTAAGGCCAAGCTGGCCGACAGTGATTATGACGCGGCGGCCGAGACCATCATTCGTATGGTCTTGAAAGGTTGTGAGCCTGAGGCAGCCTGAACCATCTCGAAGGGCCATTCGCGGGCAAGCCCGCTCCCACAGGATca                                                                                                                                                  >  5:257419/1‑149 (MQ=255)   cGGTGACCGGTAAGGCCATGCTGGCCGACAGTGATTATGACGCGGCGGCCGAGACCATCATTCGTATGGTCTTGAAAGGTTGTGAGCCTGAGGCATCCTGAACCATCTCGAAGGGCCATTCGCGGGCAAGCCCGCTCCCACAGGATca                                                                                                                                                  <  2:180788/148‑1 (MQ=255)            gTAAGGCCAAGCTGGCCGACAGTGATTATGACGCGGCGGCCGAGACCATCATTCGTATGGTCTTGAAAGGTTGTGAGCCTGAGGCAGCCTGAACCATCTCGAAGGGCCATTCGCGGGCAAGCCCGCTCCCACAGGATCACCACATGCCt                                                                                                                                        >  2:153481/1‑149 (MQ=255)               aGGCCAAGCTGGCCGACAGTGATTATGACGCGGCGGCCGAGACCATCATTCGTATGGTCTTGAAAGGTTGTGAGCCTGAGGCAGCCTGAACCATCTCGAAGGGCCATTCGCGGGCAAGCCCGCTCCCACAGGATCACCACATGCCTGaa                                                                                                                                     <  2:200191/149‑1 (MQ=255)                   cAAGCTGGCCGACAGTGATTATGACGCGGCGGCCGAGACCATCATTCGTATGGTCTTGAAAGGTTGTGAGCCTGAGGCAGCCTGAACCATCTCGAAGGGCCATTCGCGGGCAAGCCCGCTCCCACAGGATCACCACATGCCTGAAGGtt                                                                                                                                 <  4:59538/149‑1 (MQ=255)                      gCTGGCCGACAGTGATTATGACGCGGCGGCCGAGACCATCATTCGTATGGTCTTGAAAGGTTGTGAGCCTGAGGCAGCCTGAACCATCTCGAAGGGCCATTCGCGGGCAAGCCCGCTCCCACAGGATCACCACATGCCTGAAGGTtgtg                                                                                                                              <  1:153481/149‑1 (MQ=255)                        tGGCCGACAGTGATTATGACGCGGCGGCCGAGACCATCATTCGTATGGTCTTGAAAGGTTGTGAGCCTGAGGCAGCCTGAACCATCTCGAAGGGCCATTCGCGGGCAAGCCCGCTCCCACACGATCACCACATGCCTGAAGGTTGTGGa                                                                                                                            <  1:16067/149‑1 (MQ=255)                             gACAGTGATTATGACGCGGCGGCCGAGACCATCATTCGTATGGTCTTGAAAGGTTGTGAGCCTGAGGCAGCCTGAACCATCTCGAAGGGCCATTCGCGGGCAAGCCCGCTCCCACAGGATCACCACATGCCTGAAGGTTGTGGAGTccc                                                                                                                       >  7:260735/1‑149 (MQ=255)                                 gTGATTATGACGCGGCGGCCGAGACCATCATTCGTATGGTCTTGAAAGGTTGTGAGCCTGAGGCAGCCTGAACCATCTCGAAGGGCCATTCGCGGGCAAGCCCGCTCCCACAGGATCACCACATGCCTGAAGGTTGTGGAGTCCCtgtg                                                                                                                   <  1:205957/149‑1 (MQ=255)                                 gTGATTAGGACGCGGCGGCCGAGACCATCATTCGTATGGTCTTGAAAGGTTGTGAGCCTGAGGCAGCCTGAACCATCTCGAAGGGCCATTCGCGGGCAAGCCCGCTCCCACAGGATCACCACATGCCTGAAGGTTGTGGAGTCCCtgtg                                                                                                                   <  8:128364/149‑1 (MQ=255)                                       aTGACGCGGCGGCCGAGACCATCATTCGTATTGTCTTGAAAGGTTGTGAGCCTGAGTCAGCCTGAACCATCTCGAAGGGCCATTCGCGGGCAAGCCCGCTCCCACAGGATCACCACATGCCTGAAGGTTGTGGAGTCCCTGTGGGAGc                                                                                                              <  8:99742/148‑1 (MQ=255)                                        tGACGCGGCGGCCGAGACCATCATTCGTATGGTCTTGAAAGGTTGTGAGCCTGAGGCAGCCTGAACCATCTCGAAGGGCCATTCGCGGGCAAGCCCGCTCCCACAGGATCACCACATGCCTGAAGGTTGTGGa                                                                                                                            >  5:56511/1‑133 (MQ=255)                                        tGACGCGGCGGCCGAGACCATCATTCGTATGGTCTTGAAAGGTTGTGAGCCTGAGGCAGCCTGAACCATCTCGAAGGGCCATTCGCGGGCAAGCCCGCTCCCACAGGATCACCACATGCCTGAAGGTTGTGGa                                                                                                                            <  6:56511/133‑1 (MQ=255)                                          aCGCGGCGGCCGAGACCATCATTCGTATGGTCTTGAAAGGTTGTGAGCCTGAGGCAGCCTGAACCATCTCGAAGGGCCATTCGCGGGCAAGCCCGCTCCCACAGGATCACCACATGCCTGAAGGTTGTGGAGTCCCTGTGGGAGCggg                                                                                                           <  6:257419/148‑1 (MQ=255)                                            gcggcgGCCGAGACCATCATTCGTATGGTCTTGAAAGGTTGTGAGCCTGAGGCAGCCTGAAACATCTCGAAGGGCCATTCGCGGGCAAGCCCGCTCCCACAGGATCACCACATGCCTGAAGGTtgt                                                                                                                               <  3:184267/126‑1 (MQ=255)                                            gcggcgGCCGAGACCATCATTCGTATGGTCTTGAAAGGTTGTGAGCCTGAGGCAGCCTGAAACATCTCGAAGGGCCATTCGCGGGCAAGCCCGCTCCCACAGGATCACCACATGCCTGAAGGTtgt                                                                                                                               >  4:184267/1‑126 (MQ=255)                                             cggcggCCGAGACCATCATTCGTATGGTCTTGAAAGGTTGTGAGCCTGAGGCAGCCTGAACCATCTCGAAGGGCCATTCGCGGGCAAGCCCGCTCCCACAGGGACTCCACAACCTTCAGGCATGTGGTGATCCTGTGGGAGCGGGCTTg                                                                                                       <  3:28623/149‑1 (MQ=17)                                                cggcCGAGACCATCATTCGTATGGTCTTGAAAGGTTGTGAGCCTGAGGCAGCCTGAACCATCTCGAAGGGCCATTCGCGGGCAAGCCCGCTCCCACAGGATCACCACATGCCTGAAGGTTGTGGAGTCCCTGTGGGAGCGGGCTTGccc                                                                                                    <  8:260735/149‑1 (MQ=255)                                                          catcatTCGTATGGTCTTGAAAGGTTGTGAGCCTGAGGCAGCCTGAACCATCTCGAAGGGCCATTCGCGGGCAAGCCCGCTCCCACAGGATCACCACATGCCTGAAGGTTGTGGa                                                                                                                            >  1:173319/1‑115 (MQ=255)                                                          catcatTCGTATGGTCTTGAAAGGTTGTGAGCCTGAGGCAGCCTGAACCATCTCGAAGGGCCATTCGCGGGCAAGCCCGCTCCCACAGGATCACCACATGCCTGAAGGTTGTGGa                                                                                                                            <  2:173319/115‑1 (MQ=255)                                                                                    gtgAGCCTGAGGCAGCCTGAACCATCTCGAAGGGCCATTCGCGGGCAAGCCCGCTACCACAGGATCACCACATGCCTGAAGGGTGTGGAGTCCCTGTGGGAGCGCGCTTGCCCGCGAATGGGCCAGAAGAGGCAATAGAGATTTAGGcc                                                                >  5:307782/1‑149 (MQ=255)                                                                                                                      ccATTCGCGGGCAAGCCCGCTCCCACAGGATCACCACATGCCTGAAGGTTGTGGAGTCCCTGTGGGAGCGGGCTTGCCCGCGAATGGGCCAGAACAGGCAATAGAGATTTAGGCCGCTACCCCGGCATCTGCCCGCAGCCCCAcctcct                              >  5:76713/1‑149 (MQ=255)                                                                                                                        aTTCGCGGGCAAGCCCGCTCCCACAGGATCACCACATGCCTGAAGGTTGTGGAGTCCCTGTGGGAGCGGGCTTGCCCGCGCATGGGGCAGAACAGGCAATAGAGCTTTAGGCCGCGACCCCGGCATCTGCCCGCCGCCCCCcctccgc                             >  2:310924/1‑146 (MQ=38)                                                                                                                                  aaGCCCGCTCCCACAGGATCACCACATGCCTGAAGGTTGTGGAGTCCCTGTGGGAGCGGGCTTGCCCGCGAATGGGCCAGAACAGGCAATAGAGATTTAGGCCGCTACCCCGGCATCTGCCCGCAGCCCCACCTCCTCGATCGCACTGa                  >  7:210794/1‑149 (MQ=255)                                                                                                                                      ccGCTCCCACAGGGACTCCACAACCTTCAGGCATGTGGTGATCCTGTGGGAGCGGGCTTGCCCGCGAATGGGCCAGAACAGGCAATAGAGATTTAGGCCGCTACCCCGGCATCTGCCCGCAGCCCCACCTCCTCGATCGCACTGATCg               >  5:181830/1‑148 (MQ=18)                                                                                                                                      ccGCTCCCACAGGATCACCACATGCCTGAAGGTTGTGGAGTCCCTGTGGGAGCGGGCTTGCCCGCGAATGGGCCAGAACAGGCAATAGAGATTTAGGCCGCTACCCCGGCATCTGCCCGCAGCCCCACCTCCTCGATCGCACTGATCg               >  6:54998/1‑148 (MQ=255)                                                                                                                                        gCTCCCACAGGGACTCCACAACCTTCAGGCATGTGGTGATCCTGTGGGAGCGGGCTTGCCCGCGAAT‑GGCCAGAACAGGCAATAGAGATTTAGGCCGCTACCCCGGCATCTGCCCGCAGCCCCACCTCCTCGATCg                        >  7:30873/1‑136 (MQ=17)                                                                                                                                        gCTCCCACAGGGACTCCACAACCTTCAGGCATGTGGTGATCCTGTGGGAGCGGGCTTGCCCGCGAAT‑GGCCAGAACAGGCAATAGAGATTTAGGCCGCTACCCCGGCATCTGCCCGCAGCCCCACCTCCTCGATCg                        <  8:30873/136‑1 (MQ=17)                                                                                                                                                  gATCACCACATGCCTGAAGGTTGTGGAGTCCCTGTGGGAGCGGGCTTGCCCGCGAATGGGCCAGAACAGGCAATAGAGATTTAGGCCGCTACCCCGGCATCTGCCCGCAGCCCCACCTCCTCGATCGCACTGATCGCACACTGCtcgtc  <  1:310924/149‑1 (MQ=255)                                                                                                                                                   aTCACAACATGCCTGAAGGTTGTGGAGTCACTGTGGGAGCGGGCTTGCCCGCGAATGGGCCAGAACAGGCAATAGAGAATTAGACCGCTACCCCg                                                       >  7:226981/1‑95 (MQ=38)                                                                                                                                                    |                                                                                                                                                   TGCGGTGACCGGTAAGGCCAAGCTGGCCGACAGTGATTATGACGCGGCGGCCGAGACCATCATTCGTATGGTCTTGAAAGGTTGTGAGCCTGAGGCAGCCTGAACCATCTCGAAGGGCCATTCGCGGGCAAGCCCGCTCCCACAGGATCACCACATGCCTGAAGGTTGTGGAGTCCCTGTGGGAGCGGGCTTGCCCGCGAATGGGCCAGAACAGGCAATAGAGATTTAGGCCGCTACCCCGGCATCTGCCCGCAGCCCCACCTCCTCGATCGCACTGATCGCACACTGCTCGTC  >  NC_002947/4886019‑4886312

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑