Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,734,866	C→A	9.3%	intergenic (+68/+45)	tcdA → / ← PP_1528	tRNA cyclic N6‑threonylcarbamoyladenosine(37) synthase TcdA/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,734,866	0	C	A	9.3%	114.8 / 4.3	43	intergenic (+68/+45)	tcdA/PP_1528	tRNA cyclic N6‑threonylcarbamoyladenosine(37) synthase TcdA/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (22/17);  new base A (2/2);  total (24/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.93e-01

ATGGTAGCGGCGAGCAAGGCGATAGAAAAACTGGTGGCTGGAGCGCGCCGGCCGTCGGAACGGGTCAAGCCTGAATAAGACCGCGTGGGTTTCTTCGCGGGCCTGCCCGCTCCCACAGATACTGCATC‑T‑CTTCCAAGCATGATGCCGTACCTGTGGGAGCGGGCGGGCCCGCGAAGCAACCAGCGCCGATTCAGCGGTTGGACGCCAACTCCGCCATCCGCTGCAACACCGCATGCAGCCCATTGCTGCGCGACGGCGACAATTGGCGCTCCAGCCCGAGCTGGGTAAACCACT  >  NC_002947/1734721‑1735014                                                                                                                                                    |                                                                                                                                                     aTGGTAGCGGCGAGCAAGGCGATAGAAAAACTGGTGGCTGGAGCGCGCCGGCCGTCGGAACGGGTCAAGCCTGAATAAGACCGCGTGGGTTTCTTCGCGGGCCTGCCCGCTCCCACAGATACTGCATC‑T‑CTTCCAAGCATGATGCCGTa                                                                                                                                                   >  5:363818/1‑149 (MQ=255)          gcgAGCAAGGCGATAGAAAAACTGGTGGCTGGAGCGCGCCGGCCGTCGGAACGGGTCAAGCCTGAATAAGACCGCGTGGGTTTCTTCGCGGGCCTGCCCGCTCCCACAGATACTGCATC‑T‑CTTCCAAGCATGATGCCGTACCTGTgg                                                                                                                                            <  8:197497/147‑1 (MQ=255)          gcgAGCAAGGCGATAGAAAAACTGGTGGCTGGAGCGCGCCGGCCGTCGGAACGGGTCAAGCCTGAATAAGACCGCGTGGGTTTCTTCGCGGGCCTGCCCGCTCCCACAGATACTGCATC‑T‑CTTCCAAGCATGATGCCGTACCTGTgg                                                                                                                                            >  7:197497/1‑147 (MQ=255)            gAGCAAGGCGATAGAAAAACTGGTGGCTGGAGCGCGCCGGCCGTCGGAACGGGTCAAGCCTGAATAAGACCGCGTGGGTTTCTTCGCGGGCCTGCCCGCTCCCACAGATACTGCATC‑T‑CTTCCAAGCATGATGCCGTACCTGTGGGAgc                                                                                                                                        <  7:297619/149‑1 (MQ=255)            gAGCAAGGCGATAGAAAAACTGGTGGCTGGAGCGCGCCGGCCGTCGGAACGGGTCAAGCCTGAATAAGACCGCGTGGGTTTCTTCGCGGGCCTGCCCGCTCCCACAGATACTGCATC‑T‑CTTCCAAGCATGATGCCGTACCTGTGGGAgc                                                                                                                                        >  6:369922/1‑149 (MQ=255)               cAAGGCGATAGAAAAACTGGTGGCTGGAGCGCGCCGGCCGTCGGAACGGGTCAAGCCTGAATAAGACCGCGTGGGTTTCTTCGCGGGCCTGCCCGCACCCACAGATACTCCATC‑T‑CTTCCAAGCATGATGCCCTACCTGTGGGAgcggg                                                                                                                                     >  8:33529/1‑149 (MQ=255)                   gCGATAGAAAAACTGGTGGCTGGAGCGCGCCGGCCGTCGGAACGGGTCAAGCCTGAATAAGACCGCGTGGGTTTCTTCGCGGGCCTGCCCGCTCCCACAGGTACGGCATCATGCTTGGAAG‑A‑GATGCAGTATCTGTGGGAgcgg                                                                                                                                      <  2:150296/144‑1 (MQ=18)                   gCGATAGAAAAACTGGTGGCTGGAGCGCGCCGGCCGTCGGAACGGGTCAAGCCTGAATAAGACCGCGTGGGTTTCTTCGCGGGCCTGCCCGCTCCCACAGGTACGGCATCATGCTTGGAAG‑A‑GATGCAGTATCTGTGGGAgcgg                                                                                                                                      >  1:150296/1‑144 (MQ=18)                    cGATAGAAAAACTGGTGGCTGGAGCGCGCCGGCCGTCGGAACGGGTCAAGCCTGAATAAGACCGCGTGGGTTTCTTCGCGGGCCTGCCCGCTCCCACAGATACTGCATC‑T‑CTTCCAAGCATGATGCCGTACCTGTGGGAGCgggcgggc                                                                                                                                <  5:369922/149‑1 (MQ=255)                           aaaaCTGGGGCCTGCAGCGCGCCGGCCGTCGGAACGGGTCAAGCCTGAATAAGACCGCGGGGGTTTCTTCGCGCGCCTGCCCGCTCCCACAGATCCTGCATC‑T‑CTTCCAACCATGATGCCGTACCTGGGGGAGCGGGCGGGCCCGCGaa                                                                                                                         <  7:235658/149‑1 (MQ=255)                                    ggCTGGAGCGCGCCGGCCGTCGGAACGGGTCAAGCCTGAATAAGACCGCGTGGGTTTCTTCGCGGGCCTGCCCGCTCCCACAGATACTGCATC‑T‑CTTCCAAGCATGATGCCGTTCCTGTGGGAGCGGGCGGGCCCGCGCAGcgatcgg                                                                                                                 >  3:232121/1‑142 (MQ=255)                                      cTGGAGCGCGCCGGCCGTCGGAACGGGTCAAGCCTGAATAAGACCGCGTGGGTTTCTTCGCGGGCCTGCCCGCTCCCACAGATACTGCATC‑T‑CTTCCAAGCATGATGCCGTACCTGTGGGAGCGGGCGGGCCCGCGAAGCAACCAgcgc                                                                                                              >  6:178787/1‑149 (MQ=255)                                         gAGCGCGCCGGCCGTCGGAACGGGTCAAGCCTGAATAAGACCGCGTGGGTTTCTTCGCGGGCCTGCCCGCTCCCACAGATACTGCATC‑T‑CTTCCAAGCATGATGCCGTACCTGTGGGAGCGGGCGGGCCCGCGAAGCAACCAGCGCCgc                                                                                                           >  7:322516/1‑148 (MQ=255)                                                     cgTCGGAACGGGTCAAGCCTGAATAAGACCGCGTGGGTTTCTTCGCGGGCCTGCCCGCTCCCACAGATACTGCATC‑T‑CTTCCAAGCATGATGCCGTACCTGTGGGAGCGGGCGGGCCCGCGAAGCAACCAGCGCCGATTAAGCGGTTgg                                                                                               >  7:30317/1‑149 (MQ=255)                                                          gAACGGGTCAAGCCTGAATAAGCCCGCGTGGGTTTCTTCGCGGGCCTCCCCGCTCCCACATATACTGCATC‑T‑CTTCCAAGCATGATGCCGTACCTGTGGGAGCGGGCGGGCCCGCGAAGCAACCAGCGCCGATTCAGCGGTTGGACGcc                                                                                          <  7:33529/149‑1 (MQ=255)                                                          gAACGGGTCAAGCCTGAATAAGACCGCGTGGGTTTCTTCGCGGGCCTGCCCGCTCCCACAGATACTGCATC‑T‑CTTCCAAGCATGATGCCGTACCTGTGGGAGCGGGCGGGCCCGCGAAGCAACCCGCGCCGCTTCAGCGGTTGGACGc                                                                                           >  2:222211/1‑148 (MQ=255)                                                                          aaTAAGACCGCGTGGGTTTCTTCGCGGGCCTGCCCGCTCCCACAGATACTGCATC‑T‑CTTCCAAGCATGATGCCGTACCTGTGGGAGCGGGCGGGCCCGCGAAGCAACCAGCGCCGATTCAGCGGTTGGACGCCAACTCCGCCATCCGCt                                                                          <  5:178787/149‑1 (MQ=255)                                                                            tccccccGCGTGGGTTTCTGCCCGGGCCGCCCCGCGCCCACAGACACTCCATC‑G‑CTCCCAAGCAGCCTGCCGTCCCTGTGGGAGCGGGCGGGCCCGCGAAGCAACCAGCGCCGATTCAGCGGTTGGACGCCAACTCCGCCATCCGCTGc                                                                        <  7:292024/144‑1 (MQ=255)                                                                            tAAGACCGGGTGGGTGTCTTCGCGGGCCTGCCCGCCCCCACAGATCCTGCATC‑T‑CTCCCACGCATGAGGCCGAACCTGGGGCAGGGGGGGGGCCCGCGAAGCAACCAGCGCCGATTCAGCGGTTGGACGCCAACTCCGCCATCCGCTGc                                                                        <  1:222211/149‑1 (MQ=255)                                                                                      tGGGTTTCTTCGCGGGCCTGCCCGCTCCCACAGATACTGCATC‑T‑CTTCCAAGCATGATGCCGTACCTGTGGGAGCGGGCGGGCCCGCGAAGCAACCAGCGCCGATTCa                                                                                                       <  5:290798/108‑1 (MQ=255)                                                                                      tGGGTTTCTTCGCGGGCCTGCCCGCTCCCACAGATACTGCATC‑T‑CTTCCAAGCATGATGCCGTACCTGTGGGAGCGGGCGGGCCCGCGAAGCAACCAGCGCCGATTCa                                                                                                       >  6:290798/1‑108 (MQ=255)                                                                                             attcGCGGGCCTGCCGGCTCCCACATATACTGCATC‑T‑CTTCCAAGCATGATGCCGTACCTGTGGTTGCGGGCGGGCCCGCGAAGCAACCAGCGCCGATTCAGCGGTTGGACGCCAACTCCGCCATCCGCTGCAACACCGCATGCAGcc                                                        <  8:30317/147‑1 (MQ=255)                                                                                               tcGCGGGCCTGCCCGCTCCCACAGATACTGCATC‑T‑CTTCCAAGCATGATGCCGTACCTGTGGGAGCGGGCGGGCCCGCGAAGCAACCAGCGCCGATTCAGCGGTTGGACGCCAACTCCGCCATCCGCTGCAACACCGCATg                                                             >  2:76720/1‑141 (MQ=255)                                                                                               tcGCGGGCCTGCCCGCTCCCACAGATACTGCATC‑T‑CTTCCAAGCATGATGCCGTACCTGTGGGAGCGGGCGGGCCCGCGAAGCAACCAGCGCCGATTCAGCGGTTGGACGCCAACTCCGCCATCCGCTGCAACACCGCATg                                                             <  1:76720/141‑1 (MQ=255)                                                                                                   gggCCCGCCCGCTCCCACAGGTACGGCATCATGCTTGGAAG‑A‑GATGCAGTATCTGTGGGAGCGGGCAGGCCCGCGAAGCAACCAGCGCCGATTCAGCGGTTGGACGCCAACTCCGCCATCCGCTGCAACACCGCATGCAGCCCATtgct                                                 >  8:155936/1‑149 (MQ=17)                                                                                                         gCCCGCTCCCACAGATACTGCATC‑T‑CTTCCAAGCATGATGCCGTACCTGTGGGAGCGGGCGGGACCGCGAACCAAACAGCGCCGATTCAGCGGTTGGACGCCAACTCCGCCATACGCTGCAACACCGCATGCAGCCCATTGCTGAGCGa                                           >  6:130190/1‑149 (MQ=255)                                                                                                                 ccACAGATACTGCATC‑T‑CTTCCAAGCATGATGCCGTACCTGTGGGAGCGGGCGGGCCCGCGAAGCAACCAGCGCCGATTCAGCGGTTGGACGCCAACTCCGCCATCCGCTGCAACACCGCATGCAGCCCATTGCTGCGCGACGGCGAc                                    >  8:315695/1‑148 (MQ=255)                                                                                                                   acaGATACTGCATC‑T‑CTTCCAAGCATGATGCCGTACCTGTGGGAGCGGGCGGGCCCGCGAAGCAACCAGCGCCGATTCAGCGGTTGGACGCCAACTCCGCCATCCGCTGCGACACCACATGCAGCCCATTGCTGCGCGACGGCGACAAt                                 >  2:314718/1‑149 (MQ=255)                                                                                                                           tGCATC‑T‑CTTCCAAGCATGATGCCGTACCTGTGGGAGCGGGCGGGCCCGCGAAGCAACCAGCGCCGATTCAGCGGTTGGACGCCAACTCCGCCATCCGCTGCAACACCGCATGCAGCCCATTGCTGCGCGACGGCGACAATTgg                              >  4:281191/1‑144 (MQ=255)                                                                                                                           tGCATC‑T‑CTTCCAAGCATGATGCCGTACCTGTGGGAGCGGGCGGGCCCGCGAAGCAACCAGCGCCGATTCAGCGGTTGGACGCCAACTCCGCCATCCGCTGCAACACCGCATGCAGCCCATTGCTGCGCGACGGCGACAATTgg                              <  3:281191/144‑1 (MQ=255)                                                                                                                           tGCATC‑T‑CTTCCAAGCATGATGCCGTACCTGTGGGAGCGGGCGGGCCCGCGAAGCAACCAGCGCCGATTCAGCGGTTGGACGCCAACTCCGCCATCCGCTGCAACACCGCATGCAGCCCATTGCTGCGCGACGGCGACAATTGGCGCTc                         >  6:138574/1‑149 (MQ=255)                                                                                                                            gCATC‑T‑CTTCCAAGCATGATGCCGTACCTGTGGGAGCGGGCGGGCCCGCGAAGCAACCAGCGCCGATTCAGCGGTTGGACGCCAACTCCGCCATCCGCTGCAACACCGCATGCAGCCCAt                                                     <  6:357415/120‑1 (MQ=255)                                                                                                                            gCATC‑T‑CTTCCAAGCATGATGCCGTACCTGTGGGAGCGGGCGGGCCCGCGAAGCAAACAGCGCCGATTCAGCGGTTGGACGCCAACTCCGCCATCCGCTGCAACACCGCATGCAGCCCAt                                                     >  5:357415/1‑120 (MQ=255)                                                                                                                               tc‑t‑cTTCCAAGCATGATGCCGTACCTGTGGGAGCGGGCGGGCCCGCGAAGCAACCAGCGCCGATTCAGCGGTTGGACGCCAACTCCGCCATCCGCTGCAACACCGCATGCAGCCCATTGCTGCGCGACGGCGACAATTGGCGCTCCAGc                     >  6:27251/1‑149 (MQ=255)                                                                                                                                c‑t‑ctTCCAAGCATGATGCCGTACCTGTGGGAGCGGGCGGGCCCGCGAAGCAACCAGCGCCGATTCAGCGGTTGGACGCCAACTCCGCCATCCGCTGCAACACCGCATGCAGCCCATTGCTGCGCGACGGCGACAATTGGCGCTCCAGcc                    >  6:245742/1‑149 (MQ=255)                                                                                                                                        cAAGCATGATGCCGTACCTGTGGGAGCGGGCGGGCCCGCGAAGCAACCAGCGCCGATTCAGCGGTTGGACGCCAACTCCGCCATCCGCTGCAACACCGCATGCAGCCCATTGCTGCGCGACGGCGACAATTGGCGCTCCAGCCCGAGCt              >  5:28506/1‑149 (MQ=255)                                                                                                                                         aaGCATGATGCCGTACCTGTGGGAGCGGGCGGGCCCGCGAAGCAACCAGCGCCGATTCAGCGGTTGGACGCCAACTCCGCCATCCGCTGCAACACCGCATGCAGCCCATTGCTGCGCGACGGCGACAATTGGCGCTCCAGCCCGAGCTg             >  3:269660/1‑149 (MQ=255)                                                                                                                                          aGCATGATGCCGTACCTGTGGGAGCGGGCGGGCCCGCGAAGCAACCAGCGCCGATTCAGCGGTTGGACGCCAACTCCGCCATCCGCTGCAACACCGCATGCAGCCCATTGCTGCGCGACGGCGACAATTGGCGCTCCAGCCCGAGCTgg            <  4:269660/149‑1 (MQ=255)                                                                                                                                              tgatgCCGTACCTGTGGGAGCGGGCGGGCCCGCGAAGCAACCAGCGCCGATTCAGCGGTTGGACGCCAACTCCGCCATCCGCTGCAACACCGCATGCAGCCCATTGCTGCGCGACGGCGACAATTGGCGCTCCAGCCCGAGCTGGGTaa        <  5:138574/149‑1 (MQ=255)                                                                                                                                                atgCCGTACCTGTGGGAGCGGGCGGGCCCGCGAAGCAACCAGCGCCGATTCAGCGGTTGGACGCCAACTCCGCCATCCGCTGCAACACCGCATGCAGCCCATTGCTGCGCGACGGCGACAATTGGCGCTCCAGCCCGAGCTGGGTAAAc      <  5:27251/149‑1 (MQ=255)                                                                                                                                                atgCCGTACCTGTGGGAGCGGGCGGGCCCGCGAAGCAACCAGCGCCGATTCAGCGGTTGGACGCCAACTCCGCCATCCGCTGCAACACCGCATGCAGCCCATTGCTGCGCGACGGCGACAATTGGCGCTCCAGCCCGAGCTGGGTAAAc      <  5:245742/149‑1 (MQ=255)                                                                                                                                                atgCAGTATCTGTGGGAGCGGGCAGGCCCGCGAAGCAACCAGCGCCGATTCAGCGGTTGGACGCCAACTCCGCCATCCGCTGCAACACCGCATGCAGCCCATTGCTGCGCGACGGCGACAATTGGCGCTCCAGCCCGAGCTGGGTAAAc      <  7:155936/149‑1 (MQ=255)                                                                                                                                                  gCCGTACCTGTGGGAGCGGGCGGGCCCGCGAAGCAACCAGCGCCGATTCAGCGGTTGGACGCCAACTCCGCCATCCGCTGCAACACCGCATGCAGCCCATTGCTGCGCGACGGCGACAATTGGCGCTCCAGCCCGAGCTGGGTAACCCa    >  1:236554/1‑149 (MQ=255)                                                                                                                                                    cGTACCTGTGGGAGCGGGCGGGCCCGCGAAGCAACCAGCGCCGATTCAGCGGTTGGACGCCAACTCCGCCATCCGCTGCGACACCACATGCAGCCCATTGCTGCGCGACGGCGACAATTGGCGCTCCAGCCCGAGCTGGGTAAACCACt  <  1:314718/149‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                     ATGGTAGCGGCGAGCAAGGCGATAGAAAAACTGGTGGCTGGAGCGCGCCGGCCGTCGGAACGGGTCAAGCCTGAATAAGACCGCGTGGGTTTCTTCGCGGGCCTGCCCGCTCCCACAGATACTGCATC‑T‑CTTCCAAGCATGATGCCGTACCTGTGGGAGCGGGCGGGCCCGCGAAGCAACCAGCGCCGATTCAGCGGTTGGACGCCAACTCCGCCATCCGCTGCAACACCGCATGCAGCCCATTGCTGCGCGACGGCGACAATTGGCGCTCCAGCCCGAGCTGGGTAAACCACT  >  NC_002947/1734721‑1735014

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑