Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,508,225	A→G	10.5%	intergenic (+79/‑171)	cycA → / → urtA	D‑alanine/beta‑alanine/D‑serine/glycine permease/urea ABC transporter substrate‑binding protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,508,225	0	A	G	10.5%	118.5 / 3.8	47	intergenic (+79/‑171)	cycA/urtA	D‑alanine/beta‑alanine/D‑serine/glycine permease/urea ABC transporter substrate‑binding protein
Reads supporting (aligned to +/- strand):  ref base A (19/23);  new base G (3/2);  total (22/25)
Fisher's exact test for biased strand distribution p-value = 6.54e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGTGACCTACCAGCTCGTACGCAGCAGGCGCCATCCCCGCACGGCCGTGCGTAACGGCTGATGGCCTCGGGGGCTGTTCCCACGAAGGCACGGTGTACGCCGTCCGATGTGGGAGCGCCCTTGTGTCGCGATGGGCCGCACCGCGGCCCCAATCCTGTGCACACAAATCCATCAGGCACCAACCTGGATCCAACCAACGCCCCAAGACCTCGCACAGCCCCTCTAAACCGTACCTTTCGCCACTAGGCACAGCCCTTGCAACGCCCTCCCCGCTTGCCCAA  >  NC_002947/5508086‑5508366                                                                                                                                            |                                                                                                                                              ggTGACCTACCAGCTCGTACGCAGCAGGCGCCATCCCCGCACGGCCGTGCGTAACGGCTGATGGCCTCGGGGGCTGTTCCCACGAAGGCACGGTGTACGCCGTCCGATGTGGGAGCGCCCTTGTGTCGCGATGGGCCGCACCGCGGccc                                                                                                                                      >  8:110717/1‑149 (MQ=255)     aCCTACCAGCTCGTACTGAGCAGGCGCCATCCCCGCACGGCCGTGCGTAACGGCTGATGGCCTCGGGGGCTGTTCCCACGAAGGCACGGTGTACGCCGTCCGATGTGGGAGCGCCCTTGTGTCGCGATGGGCCGCACCGCGGCCCCaa                                                                                                                                   <  7:52007/148‑1 (MQ=255)       cTACCAGCTCGTACGCAGCAGGCGCCATCCCCGCACGGCCGTGCGTAACGCCTGATGGCCTCGGGGGCTGTTCCCACGAAGGCACGGTGTACGCCGTCCGATGTGGGAGCGCCCTTGTGTCGCGATGGGCCGCACCGCGGCCCCAATcc                                                                                                                                >  2:335492/1‑149 (MQ=255)           caagtCGTACGCCGGAGGCCGCATCCCCGCACGGCCTGGCGTAACGGGTGATGGCCTGGGGGGCTGTTCCCACGAAGGCACGGTGTACGCCGTCCGATGTGGGAGCGCCCTTGTGTCGCGATGGGCCGCACCGCGGCCCCAATCCtgtg                                                                                                                            <  4:192046/145‑1 (MQ=38)           cAGCTCGTACGCAGCAGGCGCCATCCCCGCACGGCCGTGCGTAACGGCTGATGGCCTCGGGGGCTGTTCCCACGAAGGCACGGTGTACGCCGTCCGATGTGGGAGCGCCCTTGTGTCGCGATGGGCCGCACCGCGGCCCCAATCCtgtg                                                                                                                            >  5:263178/1‑149 (MQ=255)           cAGCTCGTACGCAGCAGGCGCCATCCCCGCACGGCCGTGCGTAACGGCTGATGGCCTCGGGGGCTGTTCCCACGAAGGCACGGTGTACGCCGTCCGATGTGGGAGCGCCCTTGTGTCGCGATGGGCCGCACCGCGGCCCCAATCCtgtg                                                                                                                            <  6:9078/149‑1 (MQ=255)              cTCGTACGCAGCAGGCGCCATCCCCGCACGGCCGTGCGTAACGGCTGATGGCCTCGGGGGCTGTTCCCACGAAGGCACGGTGTACGCCGTCCGATGTGGGAGCGCCCTTGTGTCGCGATGGGCCGCACCGCGGCCCCAATCCTGTGcac                                                                                                                         <  5:244166/149‑1 (MQ=255)                 gTACGCAGCAGGCGCCATCCCCGCACGGCCGTGCGTAACGGCTGATGGCCTCGGGGGCTGTTCCCACGAAGGCACGGTGTACGCCGTCCGATGTGGGAGCGCCCTTGTGTCGCGATGGGCCGCACCGCGGCCCCAATCCTGTGcccac                                                                                                                       >  3:47333/1‑148 (MQ=255)                  tACGCAGCAGGCGCCATCCCCGCACGGCCGTGCGTAACGGCTGATGGCCTCGGGGGCTGTTCCCACGAAGGCACGGTGTACGCCGTCCGATGTGGGAGCGCCCTTGTGTCGCGATGGGCCGCGGTGCGGccca                                                                                                                                     >  4:214942/1‑132 (MQ=255)                  tACGCAGCAGGCGCCATCCCCGCACGGCCGTGCGTAACGGCTGATGGCCTCGGGGGCTGTTCCCACGAAGGCACGGTGTACGCCGTCCGATGTGGGAGCGCCCTTGTGTCGCGATGGGCCGCGGTGCGGccca                                                                                                                                     <  3:214942/133‑2 (MQ=255)                                cATCCCCGCACGGCCGTGCGTAACGGCTGATGGCCTCGGGGGCTGTTCCCACGAAGGCACGGTGTACGCCGTCCGATGTGGGAGCGCCCTTGTGTCGCGATGGGCCGCACCGCGGCCCCAATCCTGTGCACACAAATCCATCAGGCAcc                                                                                                       >  4:352730/1‑149 (MQ=255)                                   ccccGCACGGCCGTGCGTAACGGCTGATGGCCTCGGGGGCTGTTCCCACGAAGGCACGGTGTACGCCGTCCGATGTGGGAGCGCCCTTGTGTCGCGATGGGCCGCACCGCGGCCCCAATCCTGTGCACACAAATCCATCAGGCACCAAc                                                                                                    >  3:328763/1‑149 (MQ=255)                                      cGCACGGCCGTGCGTAACGGCTGATGGCCTCGGGGGCTGTTCCCACGAAGGCACGGTGTACGCCGTCCGATGTGGGAGCGCCCTTGTGTCGCGATGGGCCGCACCGCGGCCCCAATCCTGTGCACACAAATCCATCAGGCACCAACCTg                                                                                                 >  5:192111/1‑149 (MQ=255)                                       gCACGGCCGTGCGTAACGGCTGATGGCCTCGGGGGCTGTTCCCACGAAGGCACGGTGTACGCCGTCCGATGTGGGAGCGCCCTTGTGTCGCGATGGGCCGCACCGCGGCCCCAATCCTGTGCACACAAATCCATCAGGCACCAACCTgg                                                                                                <  8:133133/149‑1 (MQ=255)                                         aCGGCCGTGCGTAACGGCTGATGGCCTCGGGGGCTGTTCCCACGAAGGCACGGTGTACGCCGTCCGATGTGGGAGCGCCCTTGTGTCGCGATGGGCCGCACCGCGGCCCCAATCCTGTGCACACAAATCCATCAGGCACCAACCTGGAt                                                                                              >  7:223600/1‑149 (MQ=255)                                               gTGCGTAACGGCTGATGGCCTCGGGGGCTGTTCCCACGAAGGCACGGTGTACGCCGTCCGATGTGGGAGCGCCCTTGTGTCGCGATGGGCCGCACCGCGGCCCCAATCCTGTGCACACAAATCCATCAGGCACCAACCTGGATccaac                                                                                         >  6:165597/1‑148 (MQ=255)                                                   gTAACGGCTGATGGCCTCGGGGGCTGTTCCCACGAAGGCACGGTGTACGCCGTCCGATGTGGGAGCGCCCTTGTGTCGCGATGGGCCGCACCGCGGCCCCAATCCTGTGCACACAAATCCATCAGGCACCAACCTGGATccaacc                                                                                        <  2:354517/145‑1 (MQ=255)                                                   gTAACGGCTGATGGCCTCGGGGGCTGTTCCCACGAAGGCACGGTGTACGCCGTCCGATGTGGGAGCGCCCTTGTGTCGCGATGGGCCGCACCGCGGCCCCAATCCTGTGCACACAAATCCATCAGGCACCAACCTGGATccaacc                                                                                        >  1:354517/1‑145 (MQ=255)                                                     aaCGGCTGATGGCCTCGGGGGCTGTTCCCACGAAGGCACGGTGTACGCCGTCCGATGTGGGAGCGCCCTTGTGTCGCGATGGGCCGCACCGCGGCCCCAATCCTGTGCACACAAATCCATCAGGCACCAACCTGGATCCAACCAACGcc                                                                                  >  4:222150/1‑149 (MQ=255)                                                       cGGCTGATGGCCTCGGGGGCTGTTCCCACGAAGGCACGGTGTACGCCGTCCGATGTGGGAGCGCCCTTGTGTCGCGATGGGCCGCACCGCGGCCCCAATCCTGTGCACACAAATCCATCAGGCACCAACCTGGATCCAACCAACGcccc                                                                                <  7:110717/149‑1 (MQ=255)                                                                gCCTCGGGGGCTGTTCCCACGAAGGCACGGTGTACGCCGTCCGATGTGGGAGCGCCCTTGTGTCGCGATGGGCCGCACCGCGGCCCCAATCCTGTGCACACAAATCCATCAGGCACCAACCTGGATCCAACCAACGCCCCAAGACCTCg                                                                       >  7:292952/1‑149 (MQ=255)                                                                gCCTCGGGGGCTGTTCCCACGAAGGCACGGTGTACGCCGTCCGATGTGGGAGCGCCCTTGTGTCGCGATGGGCCGCACCGCGGCCCCAATCCTGTGCACACAAATCCATCAGGCACCAACCTGGATCCAACCAACGCCCCAAGACCTCg                                                                       <  5:260521/149‑1 (MQ=255)                                                                     gggggCTGTTCCCACGAAGGCACGGTGTACGCCGTCCGATGTGGGAGCGCCCTTGTGTCGCGATGGGCCGCACCGCGGCCCCAATCCTGTGCACACAAATCCATCAGGCACCAACCTGGATCCAACCAACGCCCCAAGACCTCGCACAg                                                                  <  4:328763/149‑1 (MQ=255)                                                                               cccACGAAGGCACGGTGTACGCCGTCCGATGTGGGAGCGCCCTTGTGTCGCGATGGGCCGCACCGCGGCCCCAATCCTGTGcaca                                                                                                                        >  4:269013/1‑85 (MQ=255)                                                                               cccACGAAGGCACGGTGTACGCCGTCCGATGTGGGAGCGCCCTTGTGTCGCGATGGGCCGCACCGCGGCCCCAATCCTGTGcaca                                                                                                                        <  3:269013/85‑1 (MQ=255)                                                                                ccACGAAGGCACGGTGTACGCCGTCCGATGTGGGAGCGCCCTTGTGTCGCGATGTGCCGCACCGCGGCCCCAATCCTGTGCACACAAATCCATCAGGCACCAACATGGATAAAACCAACGCCCCAAGCCCTCGCACAGCCCCTCTAAAc                                                       >  2:207091/1‑149 (MQ=39)                                                                                ccACGAAGGCACGGTGTACGCCGTCCGATGTGGGAGCGCCCTTGTGTCGCGATGGGCCGCACCGCGGCCCCAATCCTGTGCACACAAATCCATCAGGCACCAACCTGGATCCAACCAACGCCCCAAGACCTCGCACAGCCCCTCTaaa                                                        <  3:352730/148‑1 (MQ=255)                                                                                     aaGGCACGGTGTACGCCGTCCGATGTGGGAGCGCCCTTGTGTCGCGATGGGCCGCACCGCGGCCCCAATCCTGTGCACACAAATCCATCAGGCACCAACCTGGATCCAACCAACGCCCCAAGACCTCGCACAGCCCCTCTAAACCGTAc                                                  <  6:263178/149‑1 (MQ=255)                                                                                        gCACGGTGTACGCCGTCCGATGTGGGAGCGCCCTTGTGTCGCGATGGGCCGCACCGCGGCCCCAATCCTGTGCACACAAATCCATCAGGCACCAACCT‑GATCCAACCAACGCCCCAAGACCTCGCACAGCCCCTCTAAACCGTACCttt                                              <  1:214871/149‑1 (MQ=255)                                                                                         cACGGTGTACGCCGTCCGATGTGGGAGCGCCCTTGTGTCGCGATGGGCCGCACCGCGGCCCCAATCCTGTGCACACAAATCCATCAGGCACCAACCTGGATCCAACCAACGCCCCAAGACCTCGCACAGCCCCTCTAAACCGTACCttt                                              <  1:335492/149‑1 (MQ=255)                                                                                                  cGCCGTCCGATGTGGGAGCGCCCTTGTGTCGCGATGGGCCGCACCGCGGCCCCAATCCTGTGCACACAAATCCATCAGGCACCAACCTGGATCCAACCAACGCCCCAAGACCTCGCACAGCCCCTCTAAACCGTACCTTTCGCCACTa                                      <  3:222150/148‑1 (MQ=255)                                                                                                       tCCGATGTGGGAGCGCCCTTGTGTCGCGATGGGCCACACCGCGGCCCCAATCCTGTGCACACAAATCCATCAGGCACCAACCTGGATCCAACCAACGCCCCAAGACCTCGCACAGCCCCTCTAAACCGTACCTTTCGCCACTAGGca                                  >  1:319940/1‑147 (MQ=255)                                                                                                          gATGTGGGAGCGCCCTTGTGTCGCGATGGGCCGCACCGCGGCCCCAATCCTGTGCACACAAATCCATCAGGCACCAACCTGGATCCAACCAACGCCCCAAGACCTCGCACAGCCCCTCTAAACCGTACCTTTCGCCACTAGGCACAGcc                             <  8:223600/149‑1 (MQ=255)                                                                                                           aTGTGGGAGCGCCCTTGTGTCGCGATGGGCCGCACCGCGGCCCCAATCCTGTGCACACAAATCCATCAGGCACCAACCTGGATCCAACCAACGCCCCAAGACCTCGCACAGCCCCTCTAAACCGTACCTTTCGCCACTAGGCACAGccc                            <  5:165597/149‑1 (MQ=255)                                                                                                               cgaagttcccTTGTGTCGCGATGGGCCGCACCGCGGCCCCAATCCTGTGCACACAAATCCATCAGGCACCAACCTGGATCCAACCAACGCCCCAAGACCTCGCACAGCCCCTCTAAACCGTACCTTTCGCCACTAGGCACAGCCCTTGc                        <  1:133670/142‑1 (MQ=255)                                                                                                                 gAGCGCCCTTGTGTCGCGATGGGCCGCACCGCGGCCCCAATCCTGTGCACACAAAt                                                                                                                   >  4:337017/1‑56 (MQ=255)                                                                                                                 gAGCGCCCTTGTGTCGCGATGGGCCGCACCGCGGCCCCAATCCTGTGCACACAAAt                                                                                                                   <  3:337017/56‑1 (MQ=255)                                                                                                                     gcCCTTGTGTCGCGATGGGCCGCACCGCGGCCCCAATCCTGTGCACACAAATCCATCAGGCACCAACCTGGATCCAACCAACGCCCCAAGACCTCGCACAGCCCctct                                                           >  2:126408/1‑108 (MQ=255)                                                                                                                     gcCCTTGTGTCGCGATGGGCCGCACCGCGGCCCCAATCCTGTGCACACAAATCCATCAGGCACCAACCTGGATCCAACCAACGCCCCAAGACCTCGCACAGCCCctct                                                           <  1:126408/108‑1 (MQ=255)                                                                                                                     gcCCTTGTGTCGCGATGGGCCGCACCGCGGCCCCAATCCTGTGCACACAAATCCATCAGGCACCAACCTGGATCCAACCAACGCCCCAAGACCTCGCACAGCCCCTCTAAACCGTACCTTTCGCCACTAGGCACAGCCCTTGCAACGcc                  <  8:338079/149‑1 (MQ=255)                                                                                                                       ccTTGTGTCGCGATGGGCCGCACCGCGGCCCCAATCCTGTGCACACAAATCCATCAGGCACCAACCTGGATCCAACCAACGCCCCAAGACCTCGCACAGCCCCTCTAAACCGTACCTTTCGCCACTAGGCACAGCCCTTGCAACGCCCt                >  2:247836/1‑149 (MQ=255)                                                                                                                                gcgATGGGCCGCACCGCGGCCCCAATCCTGTGCACACAAATCCATCAGGCACCAACCTGGATCCAACCAACGCCCCAAGACCTCGCACAGCCCCTCTAAACCGTACCTTTCGCCACTAGGCACAGCCCTTGCAACGCCCTCCCCGCTTg       >  8:15505/1‑149 (MQ=255)                                                                                                                                 attggggCCGCGGTGCGGCCCCAATCCTGTGCACACAAATCCATCAGGCACCAACCTGGATCCAACCAACGCCCCAAGACCt                                                                         >  2:232784/5‑82 (MQ=255)                                                                                                                                 attggggCCGCGGTGCGGCCCCAATCCTGTGCACACAAATCCATCAGGCACCAACCTGGATCCAACCAACGCCCCAAGACCt                                                                         <  1:232784/78‑1 (MQ=255)                                                                                                                                 attggggCCGCGGTGCGGCCCCAATCCTGTGCACACAAATCCATCAGGCACCAACCTGGATCCAACCAACGCCCCAAGACCTCGCACAGCCCCGCTAAACCGTACCTTTCGCCGCTAGGGACAGCCCTTGCGGCGCGCGGCCCGCGTGc      >  4:268117/5‑149 (MQ=255)                                                                                                                                      ggCCGCACCGCGGCCCCAATCCTGTGCACACAAATCCATCAGGCACCAACCTGGATCCAACCAACGCCCCAAGACCTCGCACAGCCCCTCTAAACCGTACCTTTCGCCACTAGGCACAGCCCTTGCAACGCCCTCCCCGCTTGCCCaa  <  4:341092/148‑1 (MQ=255)                                                                                                                                      ggCCGCACCGCGGCCCCAATCCTGTGCACACAAATCCATCAGGCACCAACCTGGATCCAACCAACGCCCCAAGACCTCGCACAGCCCCTCTAAACCGTACCTTTCGCCACTAGGCACAGCCCTTGCAACGCCCTCCCCGCTTGCCCaa  <  1:247836/148‑1 (MQ=255)                                                                                                                                            |                                                                                                                                              GGTGACCTACCAGCTCGTACGCAGCAGGCGCCATCCCCGCACGGCCGTGCGTAACGGCTGATGGCCTCGGGGGCTGTTCCCACGAAGGCACGGTGTACGCCGTCCGATGTGGGAGCGCCCTTGTGTCGCGATGGGCCGCACCGCGGCCCCAATCCTGTGCACACAAATCCATCAGGCACCAACCTGGATCCAACCAACGCCCCAAGACCTCGCACAGCCCCTCTAAACCGTACCTTTCGCCACTAGGCACAGCCCTTGCAACGCCCTCCCCGCTTGCCCAA  >  NC_002947/5508086‑5508366

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: ‑