Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,734,870	C→T	9.1%	intergenic (+72/+41)	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	1,734,870	0	C	T	9.1%	120.3 / 2.6	44	intergenic (+72/+41)	tcdA/PP_1528	tRNA cyclic N6‑threonylcarbamoyladenosine(37) synthase TcdA/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (21/19);  new base T (2/2);  total (23/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.64e-01

GCGAGCAAGGCGATAGAAAAACTGGTGGCTGGAGCGCGCCGGCCGTCGGAACGGGTCAAGCCTGAATAAGACCGCGTGGGTTTCTTCGCGGGCCTGCCCGCTCCCACAGATACTGCATC‑T‑CTTCCAAGCATGATGCCGTACCTGTGGGAGCGGGCGGGCCCGCGAAGCAACCAGCGCCGATTCAGCGGTTGGACGCCAACTCCGCCATCCGCTGCAACACCGCATGCAGCCCATTGCTGCGCGACGGCGACAATTGGCGCTCCAGCCCGAGCTGGGTAAACCACTCGC  >  NC_002947/1734730‑1735017                                                                                                                                               |                                                                                                                                                    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         <  5:245742/149‑1 (MQ=255)                                                                                                                                       atgCCGTACCTGTGGGAGCGGGCGGGCCCGCGAAGCAACCAGCGCCGATTCAGCGGTTGGACGCCAACTCCGCCATCCGCTGCAACACCGCATGCAGCCCATTGCTGCGCGACGGCGACAATTGGCGCTCCAGCCCGAGCTGGGTAAAc         <  5:27251/149‑1 (MQ=255)                                                                                                                                       atgCAGTATCTGTGGGAGCGGGCAGGCCCGCGAAGCAACCAGCGCCGATTCAGCGGTTGGACGCCAACTCCGCCATCCGCTGCAACACCGCATGCAGCCCATTGCTGCGCGACGGCGACAATTGGCGCTCCAGCCCGAGCTGGGTAAAc         <  7:155936/149‑1 (MQ=255)                                                                                                                                         gCCGTACCTGTGGGAGCGGGCGGGCCCGCGAAGCAACCAGCGCCGATTCAGCGGTTGGACGCCAACTCCGCCATCCGCTGCAACACCGCATGCAGCCCATTGCTGCGCGACGGCGACAATTGGCGCTCCAGCCCGAGCTGGGTAACCCa       >  1:236554/1‑149 (MQ=255)                                                                                                                                           cGTACCTGTGGGAGCGGGCGGGCCCGCGAAGCAACCAGCGCCGATTCAGCGGTTGGACGCCAACTCCGCCATCCGCTGCGACACCACATGCAGCCCATTGCTGCGCGACGGCGACAATTGGCGCTCCAGCCCGAGCTGGGTAAACCACt     <  1:314718/149‑1 (MQ=255)                                                                                                                                             tACCTGTGGGAGCGGTCGGGCCCGCGAAGCAACCAGCGCCGATTCAGCGGTTGGACGCCAACTCCGCCATCCGCTGCAACACCGCATGCAGCCAATTGCTGCGCGACGGCTACATTTGGCGCTCCATCCCGAGCTGGGTAAACCACTcg   <  5:130190/149‑1 (MQ=255)                                                                                                                                               ccTGTGGGAGCGGGCGGGCCCGCGAAGCAACCAGCGCCGATTCAGCGGTTGGACGCCAACTCCGCCATCCGCTGCAACACCGCATGCAGCCCATTGCTGCGCGACGGCGACAATTGGCGCTCCAGCCCGAGCTGGGTAAACCACTcgc  <  6:28506/148‑1 (MQ=255)                                                                                                                                               |                                                                                                                                                    GCGAGCAAGGCGATAGAAAAACTGGTGGCTGGAGCGCGCCGGCCGTCGGAACGGGTCAAGCCTGAATAAGACCGCGTGGGTTTCTTCGCGGGCCTGCCCGCTCCCACAGATACTGCATC‑T‑CTTCCAAGCATGATGCCGTACCTGTGGGAGCGGGCGGGCCCGCGAAGCAACCAGCGCCGATTCAGCGGTTGGACGCCAACTCCGCCATCCGCTGCAACACCGCATGCAGCCCATTGCTGCGCGACGGCGACAATTGGCGCTCCAGCCCGAGCTGGGTAAACCACTCGC  >  NC_002947/1734730‑1735017

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: ‑