Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,004,529	A→T	13.2%	Q184L (CAG→CTG)	PP_0866 →	transmembrane sensor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,004,529	0	A	T	13.2%	77.0 / 2.3	30	Q184L (CAG→CTG)	PP_0866	transmembrane sensor
Reads supporting (aligned to +/- strand):  ref base A (14/12);  new base T (2/2);  total (16/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.12e-01

TCGCATCTGGAGCTCAATGGCAACACGCAGTTGCAGGTCGAGTTCAGCGCCGGCCAGCGGCACGTGCGCCTGAACGCTGGTGAAGTGATGTTCAGCGTCGCCCATGACAGTAACCGGCCGTTTGTGGTCGACACTGCCCAGGGCAGTGTGATCGTCACAGGTACCCGCTTTGACGTCCGCCTGGACCCAGCCAGCACCCGTGTGGCGGTGGAACAGGGGTCGGTGCGGGTGCAGGGCAAGGGCGACTCGCCGGCGCAACTGACGGCCGGGCAGGGGTCGCATATAGAT  >  NC_002947/1004390‑1004677                                                                                                                                            |                                                                                                                                                     tCGCATCTGGAGCTCAATGGCAACACGCAGTTGCAGGTCGAGTTCAGCGCCGGCCAGCGGCACGTGCGCCTGAACGCTGGTGAAGTGATGTTCAGCGTCGCCCATGACAGTAACCGGCCGTTTGTGGTCGACACTGCCCTGGGCAgtgtc                                                                                                                                            <  1:445725/150‑2 (MQ=255) tCGCATCTGGAGCTCAATGGCAACACGCAGTTGCAGGTCGAGTTCAGCGCCGGCCAGCGGCACGTGCGCCTGAACGCTGGTGAAGTGATGTTCAGCGTCGCCCATGACAGTAACCGGCCGTTTGTGGTCGACACTGCCCAGGGCAGtgtg                                                                                                                                            >  2:355729/1‑150 (MQ=255)      tCTGGAGCTCAATGGCAACACGCAGTTGCAGGTCGAGTTCAGCGCCGGCCAGCGGCACGTGCGCCTGAACGCTGGTGAAGTGATGTTCAGCGTCGCCCATGACAGTAACCGGCCGTTTGTGGTCGACACTGCCCAGGGCAgtgtcga                                                                                                                                          >  2:328164/1‑144 (MQ=255)      tCTGGAGCTCAATGGCAACACGCAGTTGCAGGTCGAGTTCAGCGCCGGCCAGCGGCACGTGCGCCTGAACGCTGGTGAAGTGATGTTCAGCGTCGCCCATGACAGTAACCGGCCGTTTGTGGTCGACACTGCCCAGGGCAgtgtcga                                                                                                                                          <  1:328164/147‑4 (MQ=255)            gCTCAATGGCAACACGCAGTTGCAGGTCGAGTTCAGCGCCGGCCAGCGGCACGTGCGCCTGAACGCTGGTGAAGTGATGTTCAGCGTCGCCCATGACAGTAACCGGCCGTTTGTGGTCGACACTGCCCa                                                                                                                                                      >  1:453537/1‑129 (MQ=255)            gCTCAATGGCAACACGCAGTTGCAGGTCGAGTTCAGCGCCGGCCAGCGGCACGTGCGCCTGAACGCTGGTGAAGTGATGTTCAGCGTCGCCCATGACAGTAACCGGCCGTTTGTGGTCGACACTGCCCa                                                                                                                                                      <  2:453537/129‑1 (MQ=255)             cTCAATGGCAACACGCAGTTGCAGGTCGAGTTCAGCGCCGGCCAGCGGCACGTGCGCCTGAACGCTGGTGAAGTGATGTTCAGCGTCGCCCATGACAGTAACCGGCCGTTTGTGGTCGACACTGCCCAGGGCAGTGTGATCGTCACAGGt                                                                                                                                >  1:305420/1‑150 (MQ=255)              tCAATGGCAACACGCAGTTGCAGGTCGAGTTCAGCGCCGGCCAGCGGCACGTGCGCCTGAACGCTGGTGAAGTGATGTTCAGCGTCGCCCATGACAGTAACCGGCCGTTTGTGGTCGACACTGCCCAGGGCAGTGTGATCGTCACAGGTa                                                                                                                               >  2:359088/1‑150 (MQ=255)                aaTGGCAACACGCAGTTGCAGGTCGAGTTCAGCGCCGGCCAGCGGCACGTGCGCCTGAACGCTGGTGAAGTGATGTTCAGCGTCGCCCATGACAGTAACCGGCCGTTTGTGGTCGCCACTGCCCTGGGCAgtgtc                                                                                                                                            <  2:262259/135‑2 (MQ=255)                aaTGGCAACACGCAGTTGCAGGTCGAGTTCAGCGCCGGCCAGCGGCACGTGCGCCTGAACGCTGGTGAAGTGATGTTCAGCGTCGCCCATGACAGTAACCGGCCGTTTGTGGTCGACACTGCCCTGGGCAgtgtc                                                                                                                                            >  1:262259/1‑134 (MQ=255)                     cAACACGCAGTTGCAGGTCGAGTTCAGCGCCGGCCAGCGGCACGTGCGCCTGAACGCTGGTGAAGTGATGTTCAGCGTCGCCCATGACAGTAACCGGCCGTTTGTGGTCGACACTGCCCAGGGCAGTGTGATCGTCACAGGTACCCGCtt                                                                                                                        >  2:379976/1‑150 (MQ=255)                      aaCACGCAGTTGCAGGTCGAGTTCAGCGCCGGCCAGCGGCACGTGCGCCTGAACGCTGGTGAAGTGATGTTCAGCGTCGCCCATGACAGTAACCGGCCGTTTGTGGTCGACACTGCCCAGGGCAGTGTGATCGTCACAGGTACCCGCttt                                                                                                                       <  1:115474/150‑1 (MQ=255)                      aaCACGCAGTTGCAGGTCGAGTTCAGCGCCGGCCAGCGGCACGTGCGCCTGAACGCTGGTGAAGGGATGTTCAGCGTCGCCCATGACAGTAACCGGCCGTTTGTGGTCGACACTGCCCAGGGCAGTGTGATCGTCACAGGTAGCCGCttt                                                                                                                       <  1:184518/150‑1 (MQ=255)                         acGCAGTTGCAGGTCGAGTTCAGCGCCGGCCAGCGGCACGTGCGCCTGAACGCTGGTGAAGTGATGTTCAGCGTCGCCCATGACAGTAACCGGCCGTTTGTGGTCGACACTGCCCAGGGCAGTGTGATCGTCACAGGTACCCGCTTTGAc                                                                                                                    >  1:25530/1‑150 (MQ=255)                                 gCAGGTCGAGTTCAGCGCCGGCCAGCGGCACGTGCGCCTGAACGCTGGTGAAGTGATGTTCAGCGTCGCCCATGACAGTAACCGGCCGTTTGTGGTCGACACTGCCCAGGGCAGTGTGATCGTCACAGGTACCCGCTTTGACGTCCGCCt                                                                                                            <  1:355729/150‑1 (MQ=255)                                     gTCGAGTTCAGCGCCGGCCAGCGGCACGTGCGCCTGAACGCTGGTGAAGTGATGTTCAGCGTCGCCCATGACAGTAACCGGCCGTTTGTGGTCGACACTGCCCAGGGCAGTGTGATCGTCACAGGTACCCGCTTTGACGTCCGCCTGGAc                                                                                                        >  1:432423/1‑150 (MQ=255)                                         aGTTCAGCGCCGGCCAGCGGCACGTGCGCCTGAACGCTGGTGAAGTGATGTTCAGCGTCGCCCATGACAGTAACCGGCCGTTTGTGGTCGACACTGCCCAGGGCAGTGTGATCGTCACAGGTACCCGCTTTGACGTCCGCCTGGACccag                                                                                                    >  2:503726/1‑150 (MQ=255)                                           ttCAGCGCCGGCCAGCGGCACGTGCGCCTGAACGCTGGTGAAGTGATGTTCAGCGTCGCCCATGACAGTAACCGGCCGTTTGTGGTCGACACTGCCCAGGGCAGTGTGATCGTCACAGGTACCCGCttt                                                                                                                       <  2:135708/129‑1 (MQ=255)                                           ttCAGCGCCGGCCAGCGGCACGTGCGCCTGAACGCTGGTGAAGTGATGTTCAGCGTCGCCCATGACAGTAACCGGCCGTTTGTGGTCGACACTGCCCAGGGCAGTGTGATCGTCACAGGTACCCGCttt                                                                                                                       >  1:135708/1‑129 (MQ=255)                                                                      cTGAACGCTGGTGAAGTGATGTTCAGCGTCGCCCATGACAGTAACCGGCCGTTTGTGGTCGACACTGCCCAGGGCAGTGTGATCGTCACAGGTACCCGCTTTGACGTCCGCCTGGACCCAGCCAGCACCCGTGTGGCGGGGGAACAgggg                                                                       >  1:52980/1‑150 (MQ=255)                                                                          aCGCTGGTGAAGTGATGTTCAGCGTCGCCCATGACAGTAACCGGCCGTTTGTGGTCGACACTGCCCAGGGCAGTGTGATCGTCACAGGTACCCGCTTTGACGTCCGCCTGGACCCAGCCAGCACCCGTGTGGCGGTGGAACAGGGGTCgg                                                                   <  1:359088/150‑1 (MQ=255)                                                                             cTGGTGAAGTGATGTTCAGCGTCGCCCATGACAGTAACCGGCCGTTTGTGGTCGACACTGCCCAGGGCAGTGTGATCGTCACAGGTACCCGCTTTGACGTCCGCCTGGACCCAGCCAGCACCCGTGTGGCGGTGGAACAGGGGTCGGTGc                                                                <  1:503726/150‑1 (MQ=255)                                                                                     gTGATGTTCAGCGTCGCCCATGACAGTAACCGGCCGTTTGTGGTCGACACTGCCCAGGGCAGTGTGTTCGTCACAGGTACCCGCTGTGACGTCCGCCTGGACCCAGCCAGCACCCGTGTGGCGGTGGAACAGGGGTCGGTGCGGGTGCAg                                                        <  1:315613/150‑1 (MQ=255)                                                                                                      ccATGACAGTAACCGGCCGTTTGTGGTCGACACTGCCCAGGGCAGTGTGATCGTCACAGGTACCCGCTTTGACGTCCGCCTGGACCCAGCCAGCACCCGTGTGGCGGTGGAACAGGGGTCGGTGCGGGTGCAGGGCAAGGGCGACTCGcc                                       >  1:45738/1‑150 (MQ=255)                                                                                                                  ccGGCCGTTTGTGGTCGACACTGCCCAGGGCAGTGTGATCGTCACAGGTACCCGCTTTGACGTCCGCCTGGACCCAGCCAGCACCCGTGTGGCGGTGGAACAGGGGTCGGTGCGGGTGCAGGGCAAGGGCGACTCGCCGGCGCAACTGAc                           <  2:432423/150‑1 (MQ=255)                                                                                                                   cGGCCGTTTGTGGTCGACACTGCCCAGGGCAGTGTGATCGTCACAGGTACCCGCTTTGACGTCCGCCTGGACCCAGCCAGCACCCGTGTGGCGGTGGAACAGGGGTCGGTGCGGGTGCAGGGCAAGGGCGACTCGCCGGCGCAACTGACg                          <  2:305420/150‑1 (MQ=255)                                                                                                                             tgGTCGACACTGCCCAGGGCAGTGTGATCGTCACAGGTACCCGCTTTGACGTCCGCCTGGACCCAGCCAGCACCCGTGTGGCGGTGGAACAGGGGTCGGTGc                                                                >  1:42456/1‑102 (MQ=255)                                                                                                                             tgGTCGACACTGCCCAGGGCAGTGTGATCGTCACAGGTACCCGCTTTGACGTCCGCCTGGACCCAGCCAGCACCCGTGTGGCGGTGGAACAGGGGTCGGTGc                                                                <  2:42456/102‑1 (MQ=255)                                                                                                                                tCGACACTGCCCAGGGCAGTGTGATCGTCACAGGTACCCGCTTTGACGTCCGCCTGGACCCAGCCAGCACCCGTGTGGCGGTGGAACAGGGGTCGGTGCGGGTGCAGGGCAAGGGCGACTCGCCGGCGCAACTGACGGCCGGGCAGGGGt             >  2:257432/1‑150 (MQ=255)                                                                                                                                   acacTGCCCTGGGCAGTGTGATCGTCACAGGTACCCGCTTTGACGTCCGCCTGGACCCAGCCAGCACCCGTGTGGCGGTGGAACAGGGGTCGGTGCGGGTGCAGGGCAAGGGCGACTTGCCGGCGCAACTGACGGCCGGGCAGGGGTCGc          >  1:1680/1‑150 (MQ=255)                                                                                                                                         cccAGGGCAGTGTGATCGTCACAGGTACCCGCTTTGACGTCCGCCTGGACCCAGCCAGCACCCGTGTGGCGGTGGAAAAGCGGTTGGTGCGGGTGCAGGACAAGGGCGACTCGCCGGAACAACTGACTGCCGGGCAGGGGTCGCATATAg    >  1:138115/1‑150 (MQ=255)                                                                                                                                           cAGGGCAGTGTGATCGTCACAGGTACCCGCTTTGACGTCCGCCTGGACCCAGCCAGCACCCGTGTGGCGGTGGAACAGGGGTCGGTGCGGGTGCAGGGCAAGGGCGACTCGCCGGCGCAACTGACGGCCGGGCAGGGGTCGCATATAGAt  <  1:379976/150‑1 (MQ=255)                                                                                                                                            |                                                                                                                                                     TCGCATCTGGAGCTCAATGGCAACACGCAGTTGCAGGTCGAGTTCAGCGCCGGCCAGCGGCACGTGCGCCTGAACGCTGGTGAAGTGATGTTCAGCGTCGCCCATGACAGTAACCGGCCGTTTGTGGTCGACACTGCCCAGGGCAGTGTGATCGTCACAGGTACCCGCTTTGACGTCCGCCTGGACCCAGCCAGCACCCGTGTGGCGGTGGAACAGGGGTCGGTGCGGGTGCAGGGCAAGGGCGACTCGCCGGCGCAACTGACGGCCGGGCAGGGGTCGCATATAGAT  >  NC_002947/1004390‑1004677

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑