Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,134,325	A→T	10.2%	intergenic (+48/+15)	tolC → / ← PP_4520	agglutination protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,134,325	0	A	T	10.2%	107.1 / 2.3	39	intergenic (+48/+15)	tolC/PP_4520	agglutination protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (19/16);  new base T (2/2);  total (21/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.00e-01

CCATGGGTGAATTGCTGAGCAAACAGCATATTTCGTTGCCACCAGAGGCGCTGGCGACCACCGAAGTCCGCACCGAGGCGCGTCTGCCTGAGATGCGTTGAGCGGGTTTTAGGTAGCGGGGCCGCTTTGTGCTGCGAATGGGCTGCAAAGCAGCCCCCAACCCTCACTCGCGGCCATGATTACGCTGAAAGGTCTCTACGCCCATGGCCCTGATCTGCCCCTCGATCAACGTCTCGAACGGCGCCAGCAGTGCATCGAAGCAGGCCGGTTGCTCCAGCGTGTTCAATGCCCC  >  NC_002947/5134177‑5134468                                                                                                                                                     |                                                                                                                                                ccATGGGTGAATTGCTGAGCAAACAGCATATTTCGTTGCCACCAGAGGCGCTGGCGACCACCGAAGTCCGCACCGAGGCGCGTCTGCCTGAGATGCGTTGAGCGGGTTTTAGGTAGCGGGGCCGCTTTGTGCTGCGAATGGGCTGCaaa                                                                                                                                                 <  7:197333/149‑1 (MQ=255)               cTGAGCAAACAGCATATTTCGTTGGCTCCAGAGGCGCTGGCGACCACCGAAGTCCGCACCGAGGCGCGTCTGCCTGAGATGCGTTGAGCGGGTTTTAGGTAGCGGGGCCGCTTTGTGCTGCGAATGGGCTGCTTTGCAGcccattcgca                                                                                                                                   <  6:76489/149‑8 (MQ=255)                           cATATTTCGTTGCCACCAGAGGCGCTGGCGACCACCGAAGTCCGCACCGAGGCGCGTCTGCCTGAGATGCGTTGAGCGGGTTTTAGGTAGCGGGGCCGCTTTGTGCTGCGAATGGGCTGCAAagcagc                                                                                                                                            <  8:227143/128‑1 (MQ=255)                           cATATTTCGTTGCCACCAGAGGCGCTGGCGACCACCGAAGTCCGCACCGAGGCGCGTCTGCCTGAGATGCGTTGAGCGGGTTTGAGGTAGCGGGGCCGCTTTGTGCTGCGAATGGGCTGCAAagcagc                                                                                                                                            >  7:227143/1‑128 (MQ=255)                                           caGAGGCGCTGGCGACCACCGAAGTCCGCACCGAGGCGCGTCTGCCTGAGATGCGTTGAGCGGGTTTTAGGTAGCGGGGCCGCTTTGTGCTGCGAATGGGCTGCAAAGCAGCCCCCAACCCTCACTCGCGGCCATGATTACGCTGAAAg                                                                                                       >  5:274046/1‑149 (MQ=255)                                                            accGAAGTCCGCACCGAGGCGCGTCTGCCTGAGATGCGTTGAGCGGGTTTTAGGTAGCGGGGCCGCTTTGTGCTGCGAATGGGCTGCAAAGCAGCCCCCAACCCTCACTCGCGGCCATGATTACGCTGAAAGGTCTCTACGCCCATGGc                                                                                      <  6:274046/149‑1 (MQ=255)                                                             ccGAAGTCCGCACCGAGGCGCGTCTGCCTGAGATGCGTTGAGCGGGTTTTAGGTAGCGGGGCCGCTTTGTGCTGCGAATGGGCTGCAAAGCAGCCCCCAACCCTCACTCGCGGCCATGATTACGCTGAAAGGTCTCTACGCCCATGGcc                                                                                     >  7:157159/1‑149 (MQ=255)                                                              cGAAGTCCGCACCGAGGCGCGTCTGCCTGAGATGCGTTGAGCGGGTTTTAGGTAGAGGGGACGCTTTGTGCTGCGAAATGGCTGCAAAGCAGCCACCAACCCTCAATCGCGGCCATGATTACGCTGAATGGTCTCTACGCCCATGGcc                                                                                     >  8:147454/1‑148 (MQ=255)                                                                aaGTCCGCACCGAGGCGCGTCTGCCTGAGATGCGTTGAGCGGGTTTTAGGTAGCGGGGCCGCTTTGTGCTGCGAATGGGCTGCAAAGCAGCCCCCAACCCTCACTCGCGGCCATGATTACGCTGAAAGGTCTCTACGCCCATGGCCCt                                                                                   >  4:313235/1‑148 (MQ=255)                                                                      gCACCGAGGCGCGTCTGCCTGAGATGCGTTGAGCGGGTTTTAGGTAGCGGGGCCGCTTTGTGCTGCGAATGGGCTGCAAAGCAGCCCCCAACCCTCACTCGCGGCCATGATTACGCTGAAAGGTCTCTACGCCCATGGCCCTGATCTGc                                                                            >  1:187225/1‑149 (MQ=255)                                                                           gAGGCGCGTCTGCCTGAGATGCGTTGAGCGGGTTTTAGGTAGCGGGGCCGCTTTGTGCTGCGAATGGGCTGCAAAGCAGCCCCCAACCCTCACTCGCGGCCATGATTACGCTGAAAGGTCTCTACGCCCATGGCCCTGATCTGCCCCTc                                                                       >  4:18166/1‑149 (MQ=255)                                                                              gcgcGTCGGCCTGAGATGCGTTGAGCGGGTTTTAGGTAGCGGGGCCGCTTTGTGCTGCGAATGGGCTGCAAAGCAGCCCCCAACCCTCACTCGCGGCCATGATTACGCTGAAAGGTCACTACGCCCATGCCCCTGATCTGCCCCTCGAt                                                                    >  2:244705/1‑149 (MQ=255)                                                                                gcgTCTGCCTGAGATGCGTTGAGCGGGTTTTAGGTAGCGGGGCCGCTTTGTGCTGCGAATGGGCTGCAAAGCAGCCCCCAACCCTCACTCGCGGcc                                                                                                                       >  2:128312/1‑96 (MQ=255)                                                                                gcgTCTGCCTGAGATGCGTTGAGCGGGTTTTAGGTAGCGGGGCCGCTTTGTGCTGCGAATGGGCTGCAAAGCAGCCCCCAACCCTCACTCGCGGcc                                                                                                                       >  2:183120/1‑96 (MQ=255)                                                                                gcgTCTGCCTGAGATGCGTTGAGCGGGTTTTAGGTAGCGGGGCCGCTTTGTGCTGCGAATGGGCTGCAAAGCAGCCCCCAACCCTCACTCGCGGcc                                                                                                                       <  1:183120/96‑1 (MQ=255)                                                                                gcgTCTGCCTGAGATGCGTTGAGCGGGTTTTAGGTAGCGGGGCCGCTTTGTGCTGCGAATGGGCTGCAAAGCAGCCCCCAACCCTCACTCGCGGcc                                                                                                                       <  1:128312/96‑1 (MQ=255)                                                                                         tGAGATGCGTTGAGCGGGTTTTAGGTAGCGGGGCCGCTTTGTGCTGCGAATGGGCTGCAAAGCAGCCCCCAACCCTCACTCGCGGCCATGATTACGCTGAAAGGTCTCTACGCCCATGGCCCTGAt                                                                                <  6:363617/126‑1 (MQ=255)                                                                                         tGAGATGCGTTGAGCGGGTTTTAGGTAGCGGGGCCGCTTTGTGCTGCGAATGGGCTGCAAAGCAGCCCCCAACCCTCACTCGCGGCCATGATTACGCTGAAAGGTCTCTACGCCCATGGCCCTGAt                                                                                >  5:363617/1‑126 (MQ=255)                                                                                            gaTGCGTTGAGCGGGTTTTAGGTAGCGGGGCCGCTTTGTGCTGCGAATGGGCTGCAAAGCAGCCCCCAACCCTCACTCGCGGCCATGATTACGCTGAAAGGTCTCTACGCCCATGGCCCTGATCTGCCCCTCGATCAACGTCTCGAAc                                                       <  3:18166/148‑1 (MQ=255)                                                                                             aTGCGTTGAGCGGGTTTTAGGTAGCGGGGCCGCTTTGTGCTGCGAATGGGCTGCAAAGCAGCCCCCAACCCTCACTCGCGGCCATGATTACGCTGAAAGGTCTCTACGCCCATGGCCCTGATCTGCCCCTCGATCAACGTCTCGAACgg                                                     <  8:157159/149‑1 (MQ=255)                                                                                               gCGTTGAGCGGGTTTTAGGTAGCGGGGCCGCTTTGTGCTGCGAATGGGCTGCAAAGCAGCCCCCAACCCTCACTCGCGGCCATGATTACGCTGAAAGGTCTCTACGCCCATGGCCCTGATCTGCCCCt                                                                        >  8:150869/1‑128 (MQ=255)                                                                                               gCGTTGAGCGGGTTTTAGGTAGCGGGGCCGCTTTGTGCTGCGAATGGGCTGCAAAGCAGCCCCCAACCCTCACTCGCGGCCATGATTACGCTGAAAGGTCTCTACGCCCATGGCCCTGATCTGCCCCt                                                                        <  7:150869/128‑1 (MQ=255)                                                                                                           ttttAGGTAGCGGGGCCGCTTTGTGCTGCGAATGGGCTGCAAAGCAGCCCCCAACCCTCACTCGCGGCCATGATTACGCTGAAAGGTCTCTACGCCCATGGCCCTGATCTGCCCCTCGATCAACGTCTCGAACGGCGCCAGCAGTGCAt                                       >  5:70794/1‑149 (MQ=255)                                                                                                                 gTAGCGGGGCCGCTTTGTGCTGCGAATGGGCTGCAAAGCAGCCCCCAACCCTCACTCGCGGCCATGATTACGCTGAAAGGTCTCTACGCCCATGGCCCTGATCTGCCCCTCGATCAACGTCTCGAACGgcgc                                                  <  8:126376/132‑1 (MQ=255)                                                                                                                 gTAGCGGGGCCGCTTTGTGCTGCGAATGGGCTGCAAAGCAGCCCCCAACCCTCACTCGCGGCCATGATTACGCTGAAAGGTCTCTACGCCCATGGCCCTGATCTGCCCCTCGATCAACGTCTCGAACGgcgc                                                  >  7:126376/1‑132 (MQ=255)                                                                                                                 gTAGCGGGGCCGCTTTGTGCTGCGAATGGGCTGCAAAGCAGCCCCCAACCCTCACTCGCGGCCATGATTACGCTGAAAGGTCTCTACGCCCATGGCCCTGATCTGCCCCTCGATCAACGTCTCGAACGGCGCCAGCAGTGCATCGAAg                                  >  4:156164/1‑148 (MQ=255)                                                                                                                 gTAGCGGGGCCGCTTTGTGCTGCGAATGGGCTGCAAAGCAGCCCCCAACCCTCACTCGCGGCCATGATTACGCTGAAAGGTCTCTACGCCCATGGCCCTGATCTGCCCCTCGATCAACGTCTCGAACGGCGCCAGCAGTGCATCGAAg                                  >  1:309352/1‑148 (MQ=255)                                                                                                                 gTAGCGGGGCCGCTTTGTGCTGCGAATGGGCTGCAAAGCAGCCCCCAACCCTCACTCGCGGCCATGATTACGCTGAAAGGTCTCTACGCCCATGGCCCTGATCTGCCCCTCGATCAACGTCTCGAACGGCGCCAGCAGTGCATCGAAg                                  <  2:309352/148‑1 (MQ=255)                                                                                                                 gTAGCGGGGCCGCTTTGTGCTGCGAATGGGATGCAAAGCAGCCCCCAACCCTCACTCGCGGCCATGATTACGCTGAACGGTCTCTACGCCCATGGCCCTGATCTGCCCCTCGATCAACGTCTCGAACGGCGCCAGCAGTGCATCGAAGc                                 <  1:244705/149‑1 (MQ=255)                                                                                                                  tAGCGGGGCCGCTTTGTGCTGCGAATGGGCTGCAAAGCAGCCCCCAACCCTCACTCGCGGCCATGATTACGCTGAAAGGTCTCTACGCCCATGGCCCTGATCTGCCCCTCGATCAACGTCTCGAACGGCGCCAGCAGTGCATCGAAg                                  >  4:313917/1‑147 (MQ=255)                                                                                                                     cGGGGCCGCTTTGTGCTGCGAATGGGCTGCAAAGCAGCCCCCAACCCTCACTCGCGGCCATGATTACGCTGAAAGGTCTCTACGCCCATGGCCCTGATCTGCCCCTCGAt                                                                    <  6:79387/110‑1 (MQ=255)                                                                                                                     cGGGGCCGCTTTGTGCTGCGAATGGGCTGCAAAGCAGCCCCCAACCCTCACTCGCGGCCATGATTACGCTGAAAGGTCTCTACGCCCATGGCCCTGATCTGCCCCTCGAt                                                                    >  5:79387/1‑110 (MQ=255)                                                                                                                        ggCCGCTTTGTGCTGCGAATGGGCTGCAAAGCAGCCCCCAACCCTCACTCGCGGCCATGATTACGCTGAAAGGTCTCTACGCCCATGGCCCTGATCTGCCCCTCGATCAACGTCTCGAACGGCGCCAGCAGTGCATCGAAGCAGGCCgg                          <  2:187225/149‑1 (MQ=255)                                                                                                                                 gtgCTGCGAATGGGCTGCAAAGCAGCCCCCAACCCTCACTCGCGGCCATGATTACGCTGAAAGGTCTCTACGCCCATGGCCCTGATCTGCCCCTCGATCAACGTCTCGAACGGCGCCAGCAGTGCATCGAAGCAGGCCGGTTGCTCCa                  <  3:313235/148‑1 (MQ=255)                                                                                                                                       agAATTGGCTTCAAAGCAGCCCCCTACCGTCACTCGCGGCCATGATTACGCTTAAATGTCTCTACGCCCATGGCCCTGATCTGCCCCTCGATCAACGTCTCGAACGGCGCGAGCAGTGCATCGAAGCAGGCCGGTTGCTCCAGCGTGtt           <  7:147454/148‑1 (MQ=255)                                                                                                                                        gAATGGGCTGCAAAGCAGCCCCCAACCCTCACTCGCGGCCATGATTACGCTGAAAGGTCTCTACGCCCATGGCCCTGATCTGCCCCTCGATCAACGTCTCGAACGGCGCCAGCAGTGCATCGAAGCAGGCCGGTTGCTCCAGCGTGTTc          <  6:70794/149‑1 (MQ=255)                                                                                                                                          gggggCTGCTTTGCAGCCCCCAACCCTCACTCGCGGCCATGATTACGCTGAAAGGTCTCTACGCCCATGGCCCTGATCTGCCCCTCGATCAACGTCTCGAACGGCGCCAGCAGTGCATCGAAGCAGGCCGGTTGCTCCAGc                <  2:134140/139‑1 (MQ=255)                                                                                                                                          gggggCTGCTTTGCAGCCCCCAACCCTCACTCGCGGCCATGATTACGCTGAAAGGTCTCTACGCCCATGGCCCTGATCTGCCCCTCGATCAACGTCTCGAACGGCGCCAGCAGTGCATCGAAGCAGGCCGGTTGCTCCAGc                >  1:134140/3‑141 (MQ=255)                                                                                                                                            gggCTGCTTTGCAGCCCCCAACCCTCACTCGCGGCCATGATTACGCTGAAAGGTCTCTACGCCCATGGCCCTGATCTGCCCCTCGATCAACGTCTCGAACGGCGCCAGCAGTGCATCGAAGCAGGCCGGTTGCTCCAGCGTGTTCAATg      >  6:364461/1‑149 (MQ=255)                                                                                                                                                tGCAAAGCAGCCCCCAACCCTCACTCGCGGCCATGATTACGCTGAAAGGTCTCTACGCCCATGGCCCTGATCTGCCCCTCGATCAACGTCTCGAACGGCGCCAGCAGTGCATCGAAGCa                                >  6:345146/1‑119 (MQ=255)                                                                                                                                                tGCAAAGCAGCCCCCAACCCTCACTCGCGGCCATGATTACGCTGAAAGGTCTCTACGCCCATGGCCCTGATCTGCCCCTCGATCAACGTCTCGAACGGCGCCAGCAGTGCATCGAAGCa                                <  5:345146/119‑1 (MQ=255)                                                                                                                                                tGCAAAGCAGCCCCCAACCCTCACTCGCGGCCATGATTACGCTGAAAGGTCTCTACGCCCATGGCCCTGATCTGCCCCTCGATCAACGTCTCGAACGGCGCCAGCAGTGCATCGAAGCAGGCCGGTTGCTCCAGCGTGTTCAATGcccc  >  5:258465/1‑149 (MQ=255)                                                                                                                                                     |                                                                                                                                                CCATGGGTGAATTGCTGAGCAAACAGCATATTTCGTTGCCACCAGAGGCGCTGGCGACCACCGAAGTCCGCACCGAGGCGCGTCTGCCTGAGATGCGTTGAGCGGGTTTTAGGTAGCGGGGCCGCTTTGTGCTGCGAATGGGCTGCAAAGCAGCCCCCAACCCTCACTCGCGGCCATGATTACGCTGAAAGGTCTCTACGCCCATGGCCCTGATCTGCCCCTCGATCAACGTCTCGAACGGCGCCAGCAGTGCATCGAAGCAGGCCGGTTGCTCCAGCGTGTTCAATGCCCC  >  NC_002947/5134177‑5134468

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: ‑