Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	6,084,198	G→A	9.3%	P175S (CCG→TCG)	PP_5337 ←	LysR family transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	6,084,198	0	G	A	9.3%	115.4 / 3.2	43	P175S (CCG→TCG)	PP_5337	LysR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (20/19);  new base A (2/2);  total (22/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.88e-01

TATACCGCAGGTTGCGCTGGCGCAGCAGCAAGTTGACCGAGCGGCCGAGGAACGC‑‑GCCGGCGGTGTAGGCTAGCAACGGCACACTGCCCTCGCCCTCCAGGTCGAACAATGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGGCAGCATTTCAGTGGTGCCCATGTGCAGCGACGGGAAGATCTCGGCATCCATCTGCAAGGCCGCGTCCGGGTCGTAGAACGCCAGCATCAGGTCGCAGCCGCCTTCGCGCAGTGCATGTACGGCATCTCCGACGTTAGTCGCAAC  >  NC_002947/6084057‑6084342                                                                                                                                                 |                                                                                                                                                 tataCCGCAGGTTGCGCTGGCGCAGCAGCAAGTTGACCGAGCGGCCGAGGAACGC‑‑GCCGGCGGTGTAGGCTAGCAACGGCACACTGCCCTCGCCCTCCAGGTCGAACAATGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGGCAGCAtt                                                                                                                                           >  4:217654/1‑149 (MQ=255)      cGCAGGTTGCGCTGGCGCAGCAGCAAGTTGACCGAGCGGCCGAGGAACGC‑‑GCCGGCGGTGTAGGCTAGCAACGGCACACTGCCCTCGCCCTCCAGGTCGAACAATGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGGCAGCATTTCAgt                                                                                                                                      >  2:260370/1‑149 (MQ=255)      cGCAGGTTGCGCTGGCGCAGCAGCAAGTTGACCGAGCGGCCGAGGAACGC‑‑GCCGGCGGTGTAGGCTAGCAACGGCACACTGCCCTCGCCCTCCAGGTCGAACAATGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGGCAGCATTTCAgt                                                                                                                                      >  6:53504/1‑149 (MQ=255)       gCAGGTTGCGCTGGCGCAGCAGCAAGTTGACCGAGCGGCCGAGGAACGC‑‑GCCGGCGGTGTAGGCTAGCAACGGCACACTGCCCTCGCCCTCCAGGTCGAACAATGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGGCAGCATTTCAgtg                                                                                                                                     <  3:217654/149‑1 (MQ=255)            ttGCGCTGGCGCAGCAGCAAGTTGACCGAGCGGCCGAGGAACGC‑‑GCCGGCGGTGTAGGCTAGCAACGGCACACTGCCCTCGCCCTCCAGGTCGAACAATGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGGCAGCATTTCAGTGGTGcc                                                                                                                                <  8:89450/149‑1 (MQ=255)                gcTGGCGCAGCAGCAAGTTGACCGAGCGGCCGAGGAACGC‑‑GCCGGCGGTGTAGGCTAGCAACGGCACACTGCCCTCGCCCTCCAGGTCGAACAATGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGGCAGCATTTCAGTGGTGCCCAtg                                                                                                                            >  6:295117/1‑149 (MQ=255)                    gcgcAGCATCAAGTTGACCGAGCGGCCGAGGAACGCGTGTTGTCGGTGTAGGCTAGCAACGGCACACTGCCCTCGCCCTCCAGGTCGAACAATGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGGCAGCATTTCAGTGGTGCCCAtgt                                                                                                                           <  1:298148/148‑1 (MQ=255)                      gcagcagcaAGTTGACCGAGCGGCCGAGGAACGC‑‑GCCGGCGGTGTAGGCTAGCAACGGCACACTGCCCTCGCCCTCCAGGTCGAACAATGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGGCAGCATTTCAGTGGTGCCCATGTGCAGc                                                                                                                      >  8:8553/1‑149 (MQ=255)                       cagcagcaAGTTGACCGAGCGGCCGAGGAACGC‑‑GCCGGCGGTGTAGGCTAGCAACGGGACACTGCCCTCGCCCTCCAGGTCGAACAATGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGGCAGCATTTCAGTGGTGCCCATGTGCAGCg                                                                                                                     >  2:281828/1‑149 (MQ=255)                        agcagcaAGTTGACCGAGCGGCCGAGGAACGC‑‑GCCGGCGGTGTAGGCTAGCAACGGCACACTGCCCTCGCCCTCCAGGTCGAACAATGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGGCAGCATTTCAGTGGTGCCCATGTGCAGCGa                                                                                                                    >  3:99193/1‑149 (MQ=255)                             caAGTTGACCGAGCGGCCGAGGAACGC‑‑GCCGGCGGTGTAGGCTAGCAACGGCACACTGCCCTCGCCCTCCAGGTCGAACAATGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGGCAGCATTTCAGTGGTGCCCATGTGCAGCGACggg                                                                                                                >  5:242873/1‑148 (MQ=255)                                      cGAGCGGCCGAGGAACGC‑‑GCCGGCGGTGTAGGCTAGCAACGGCACACTGCCCTCGCCCTCCAGGTCGAACAATGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGGCAGCATTTCAGTGGTGCCCATGTGCAGCGACGGGAAGATCTCgg                                                                                                      >  1:41464/1‑149 (MQ=255)                                         gCGGCCGAGGAACGC‑‑GCCGGCGGTGTAGGCTAGCAACGGCACACTGCCCTCGCCCTCCAGGTCGAACAATGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGGCAGCATTTCAGTGGTGCCCATGTGCAGCGACGGGAAGATCTCGGcat                                                                                                   <  5:53504/149‑1 (MQ=255)                                               gAGGAACGC‑‑GCCGGCGGTGTAGGCTAGCAACGGCACACTGCCCTCGCCCTCCAGGTCGAACAATGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGGCAGCATTTCAGTGGTGCCCATGTGCAGCGACGGGAAGATCTCGGCATCCATCt                                                                                             <  4:99193/149‑1 (MQ=255)                                                aGGAACGC‑‑GCCGGCGGTGTAGGCTAGCAACGGCACACTGCCCTCGCCCTCCAGGTCGAACAATGGCTTGCCATCGGCATCCACAGCGCACTACCGGCAGCATTTCAGTGGTGCCCATGTGCAGCGACGGGAAGATCTCGGCATCCATCt                                                                                             <  1:281828/149‑1 (MQ=255)                                                 ggAACGC‑‑GCCGGCGGTGTAGGCTAGCAACGGCACACTGCCCTCGCCCTCCAGGTCGAACAATGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGGCAGCATTTCAGTGGTGCCCATGTGCAGCGACGGGAAGATCTCGGCATCCATCTg                                                                                            >  2:55710/1‑148 (MQ=255)                                                   aaCGC‑‑GCCGGCGGTGTAGGCTAGCAACGGCACACTGCCCTCGCCCTCCAGGTCGAACAATGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGGCAGCATTTCAGTGGTGCCCATGTGCAGCGATGGGTAGATCTCGGCATCCATCTGCaa                                                                                         <  7:8553/149‑1 (MQ=255)                                                              gcggTGTAGGCTAGCAACGGCACACTGCCCTCGCCCTCCAGGTCGAACAATGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGGCAGCATTTCAGTGGTGCCCATGTGCAGCGACGGGAAGATCTCGGCATCCATCTGCAAGGCCGCGTc                                                                                <  1:260370/149‑1 (MQ=255)                                                              gcggTGTAGGCTAGCAACGGCACACTGCCCTCGCCCTCCAGGTCGAACAATGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGGCAGCATTTCAGTGGTGCCCATGTGCAGCGACGGGAAGATCTCGGCATCCATCTGCAAGGCCGCGTc                                                                                >  3:37364/1‑149 (MQ=255)                                                               cggTGTAGGCTAGCAACGGCACACTGCCCTCGCCCTCCAGGTCGAACAATGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGGCAGCATTTCAGTGGTGCCCATGTGCAGCGACGGGAAGATCTCGGCATCCATCTGCAAGGCCGCGTcc                                                                               <  4:37364/149‑1 (MQ=255)                                                                   gtAGGCTAGCAACGGCACACTGCCCTCGCCCTCCAGGTCGAACAATGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGgcagca                                                                                                                                             <  8:70530/83‑1 (MQ=255)                                                                   gtAGGCTAGCAACGGCACACTGCCCTCGCCCTCCAGGTCGAACAATGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGgcagca                                                                                                                                             >  7:70530/1‑83 (MQ=255)                                                                     aGGCTAGCAACGGCACACTGCCCTCGCCCTCCAGGTCGAACAATGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGGCAGCATTTCAGTGGTGCCCATGTGCAGCGACGGGAAGATCTCGGCATCCATCTGCAAGGCCGCGTCCGGGTca                                                                         >  5:235574/1‑148 (MQ=255)                                                                       gCTAGCAACGGCACACTGCCCTCGCCCTCCAGGTCGAACAATGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGACAGCATTTCAGTGGTGCCCATGTGCAGCGACGGGAAGATCTCGGCATCCATCTGCAAGGCCGCGTCCGGGTCg                                                                         >  8:333149/1‑147 (MQ=255)                                                                       gCTAGCAACGGCACACTGCCCTCGCCCTCCAGGTCGAACAATGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGACAGCATTTCAGTGGTGCCCATGTGCAGCGACGGGAAGATCTCGGCATCCATCTGCAAGGCCGCGTCCGGGTCg                                                                         >  8:328442/1‑147 (MQ=255)                                                                       gCTAGCAACGGCACACTGCCCTCGCCCTCCAGGTCGAACAATGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGACAGCATTTCAGTGGTGCCCATGTGCAGCGACGGGAAGATCTCGGCATCCATCTGCAAGGCCGCGTCCGGGTCGTa                                                                       <  7:328442/149‑1 (MQ=255)                                                                       gCTAGCAACGGCACACTGCCCTCGCCCTCCAGGTCGAACAATGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGACAGCATTTCAGTGGTGCCCATGTGCAGCGACGGGAAGATCTCGGCATCCATCTGCAAGGCCGCGTCCGGGTCGTa                                                                       <  7:333149/149‑1 (MQ=255)                                                                           gCAACGGCACACTGCCCTCGCCCTCCAGGTCGAACAATGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGGCAGCATTTCAGTGGTGCCCATGTGCAGCGACGGGAAGATCTCGGCATCCATCTGCAAGGCCGCGTCCGGGTCGTAGaa                                                                    <  5:295117/148‑1 (MQ=255)                                                                               cGGCACACTGCCCTCGCCCTCCAGGTCGAACAATGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGGCAGCATTTCAGTGGTGCCCATGTGCAGCGACGGGAAGATCTCGGCATCCATCTGCAAGGCCGCGTCCGGGTCGTa                                                                       <  6:177854/141‑1 (MQ=255)                                                                               cGGCACACTGCCCTCGCCCTCCAGGTCGAACAATGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGGCAGCATTTCAGTGGTGCCCATGTGCAGCGACGGGAAGATCTCGGCATCCATCTGCAAGGCCGCGTCCGGGTCGTa                                                                       >  5:177854/1‑141 (MQ=255)                                                                                 gCACACTGCCCTCGCCCTCCAGGTCGAACAATGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGGCAGCATTTCAGTGGTGCCCATGTGCAGCGACGGGAAGATCTCGGCATCCATCTGCAAGGCCGCGTCCGGGTCGTAGAACGCCAg                                                              >  2:351540/1‑148 (MQ=255)                                                                                    cacTGCCCTCGCCCTCCAGGTCGAACAATGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGGCAGCATTTCAGTGGTGCCCATGTGCAGCGACGGGAAGATCTCGGCATCCATCTGCAAGGCCGCGTCCGGGTCGTAGAACGCCAGCATc                                                          <  6:242873/149‑1 (MQ=255)                                                                                       tGCCCTCGCCCTCCAGGTCGAACAATGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGGCAGCATTTCAGTGGTGCCCATGTGCAGCGACGGGAAGATCTCGGcatccatc                                                                                              >  5:249297/1‑110 (MQ=255)                                                                                       tGCCCTCGCCCTCCAGGTCGAACAATGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGGCAGCATTTCAGTGGTGCCCATGTGCAGCGACGGGAAGATCTCGGcatccatc                                                                                              <  6:249297/110‑1 (MQ=255)                                                                                               ccctcCAGGTCGAACAATGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGGCAGCATTTCAGTGGTGCCCATGTGCAGCGACGGGAAGATCTCGGCATCCATCTGCAAGGCCGCGTCCGGGTCGTAGAACGCCAGCATCAGGTCGCAgcc                                               <  2:41464/149‑1 (MQ=255)                                                                                                          gAACAATGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGGCAGCATTTCAGTGGTGCCCATGTGCAGCGACGGGAAGATCTCGGCATCCATCTGCAAGGCCGCGTCCGGGTCGTAGAACGCCAGCAt                                                           >  4:189706/1‑126 (MQ=255)                                                                                                          gAACAATGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGGCAGCATTTCAGTGGTGCCCATGTGCAGCGACGGGAAGATCTCGGCATCCATCTGCAAGGCCGCGTCCGGGTCGTAGAACGCCAGCAt                                                           <  3:189706/126‑1 (MQ=255)                                                                                                                tGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGGCAGCATTTCAGTGGTGCCCATGTGCAGCGACGGGAAGATCTCGGCATCCATCTGCAAGGCCGCGTCCGGGTCGTAGAACGCCAGCATCAGGTCGCAGCCGCCTTCGCGCAGTGCAt                              <  1:55710/149‑1 (MQ=255)                                                                                                                       ccATCGGCATCCACAGCGCAC‑ACCGGCAGCATTTCAGTGGTGCCCATGTGCAGCGACGGGAAGATCTCGGCATCCATCTGCAAGGCCGCGTCCGGGTCATAGAACGCCAGCATCAGGTCGCAGCCACCTTCGCGCAGTGCATGTACgg                        <  6:235574/148‑1 (MQ=255)                                                                                                                               aTCCACAGCGCAC‑ACCGGCAGCATTTCAGTGGTGCCCATGTGCAGCGACGGGAAGATCTCGGCATCCATCTGCAAGGCCGCGTCCGGGTCGTAGAACGc                                                                 >  6:126827/1‑99 (MQ=255)                                                                                                                               aTCCACAGCGCAC‑ACCGGCAGCATTTCAGTGGTGCCCATGTGCAGCGACGGGAAGATCTCGGCATCCATCTGCAAGGCCGCGTCCGGGTCGTAGAACGc                                                                 <  5:126827/99‑1 (MQ=255)                                                                                                                               aTCCACAGCGCAC‑ACCGGCAGCATTTCAGTGGTGCCCATGTGCAGCGACGGGAAGATCTCGGCATCCATCTGCAAGGCCGCGTCCGGGTCGTAGAACGCCAGCATCAGGTCGCAGCCGCCTTCGCGCAGTGCATGTACGGCAtc                    <  3:13932/144‑1 (MQ=255)                                                                                                                               aTCCACAGCGCAC‑ACCGGCAGCATTTCAGTGGTGCCCATGTGCAGCGACGGGAAGATCTCGGCATCCATCTGCAAGGCCGCGTCCGGGTCGTAGAACGCCAGCATCAGGTCGCAGCCGCCTTCGCGCAGTGCATGTACGGCAtc                    >  4:13932/1‑144 (MQ=255)                                                                                                                                          ac‑acCGGCAGCATTTCAGTGGTGCCCATGTGCAGCGACGGGAAGATCTCGGCATCCATCTGCAAGGCCGCGTCCGGGTCGTAGAACGCCAGCATCAGGTCGCAGCCGCCTTCGCGCAGTGCATGTACGGCATCTCCGACGTTAGTCGc     >  8:6833/1‑148 (MQ=255)                                                                                                                                             acCGGCAGCATTTCAGTGGTGCCCATGTGCAGCGACGGGAAGATCTCGGCATCCATCTGCAAGGCCGCGTCCGGGTCGTAGAACGCCAGCATCAGGTCGCAGCCGCCTTCGCGCAGTGCATGTACGGCATCTCCGACGTTAGTCGCAAc  >  4:293071/1‑149 (MQ=255)                                                                                                                                                 |                                                                                                                                                 TATACCGCAGGTTGCGCTGGCGCAGCAGCAAGTTGACCGAGCGGCCGAGGAACGC‑‑GCCGGCGGTGTAGGCTAGCAACGGCACACTGCCCTCGCCCTCCAGGTCGAACAATGGCTTGCCATCGGCATCCACAGCGCAC‑ACCGGCAGCATTTCAGTGGTGCCCATGTGCAGCGACGGGAAGATCTCGGCATCCATCTGCAAGGCCGCGTCCGGGTCGTAGAACGCCAGCATCAGGTCGCAGCCGCCTTCGCGCAGTGCATGTACGGCATCTCCGACGTTAGTCGCAAC  >  NC_002947/6084057‑6084342

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: ‑