Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,250,655	C→G	8.9%	L14V (CTG→GTG)	ureJ →	urease accessory protein UreJ

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,250,655	0	C	G	8.9%	127.0 / 4.1	45	L14V (CTG→GTG)	ureJ	urease accessory protein UreJ
Reads supporting (aligned to +/- strand):  ref base C (24/17);  new base G (2/2);  total (26/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.27e-01

GCTTACCAAAGTGCACCGCATGGCCACAGCCACAGTCATGCCCATGGCCACGATCACCCGTTCGTACGCCTGCCTGCCCATTCCTGAACTGCCCTGGAGCAACCGATGAAAAAGACTTTCGCCTTGTTTCTGTTGATGCTGGCACTGCCAGCCTTTGC‑CCATCCGGGCCATGACAGCAACCCGCTGCAGGACGGCCTGCTGCACCCGCTGACCGGGCTCGATCACCTGCTGATGCTGCTGGGTACCGGCGTGCTCGCCGCGTTGACCCGTCGCAACCTGACATTGCCCCT  >  NC_002947/3250511‑3250800                                                                                                                                                 |                                                                                                                                                   gcTTACCAAAGTGCACCGCATGGCCACAGCCACAGTCATGCCCATGGCCACGATCACCCGTTCGTACGCCTGCCTGCCCATTCCTGAACTGCCCTGGAGCAACCGATGAAAAAGACTTTCGCCTTGTTTCTGTTGATGCTGGCACTGc                                                                                                                                                 >  4:224696/1‑148 (MQ=255)      ccAAAGTGCACCGCATGGCCACAGCCACAGTCATGCCCATGGCCACGATCACCCGTTCGTACGCCTGCCTGCCCATTCCTGAACTGCCCTGGAGCTACCGATGAAAAAGACTTTCGCCTTGTTTCTGTTGATGCTGGCAGTGCCAGcat                                                                                                                                           <  1:98728/149‑3 (MQ=255)                  gCATGGCCACAGCCACTGTCATGCCCATGGCCACTATCACCCTTTCGTACGCCTGCCTGCCCATTCCTGAACTGCCCTGGAGCAACCGATGAAAAAGACTTTCGCCTTGTTTCTGTTGATGCTGGCACTGCCAGCCTTTGC‑CCATCCgg                                                                                                                              <  3:189501/149‑1 (MQ=255)                       gccacagccacaGTCATGCCCATGGCCACGATCACCCGTTCGTACGCCTGCCTGCCCATTCCTGAACTGCCCTGGAGCAACCGATGAAAAAGACTTTCGCCTTGTTTCTGTTGATGCTGGCACTGCCAGCCTTTGC‑CCATCCGGGCCAt                                                                                                                         >  8:91609/1‑149 (MQ=255)                         cacagccacagTCATGCCCATGGCCACGATCACCCGTTCGTACGCCTGCCTGCCCATTCCTGAACTGCCCTGGAGCAACCGATGAAAAAGACTTTCGCCTTGTTTCTGTTGATGCTGGCACTGCCAGCCTTTGC‑CCATCCGGGCCATGa                                                                                                                       <  3:240342/149‑1 (MQ=255)                           cagccacagTCATGCCCATGGCCACGATCACCCGTTCGTACGCCTGCCTGCCCATTCCTGAACTGCCCTGGAGCAACCGATGAAAAAGACTTTCGCCTTGTTTCTGTTGATGCTGGCACTGCCAGCCTTTGC‑CCATCCGGGCCATGACa                                                                                                                     <  2:129540/149‑1 (MQ=255)                                      aTGCCCATGGCCACGATCACCCGTTCGTACGCCTGCCTGCCCATTCCTGAACTGCCCTGGAGCAACCGATGAAAAAGACTTTCGCCTTGTTTCTGTTGATGCTGGCACTGCCAGCCTTTGC‑CCATCCGGGCCATGACAGCAACCCGCTg                                                                                                          <  8:118471/149‑1 (MQ=255)                                         cccATGGCCACGATCACCCGTTCGTACGCCTGCCTGCCCATTCCTGAACTGCCCTGGAGCAACCGATGAAAAAGACTTTCGCCTTGTTTCTGTTGATGCTGGCACTGCCAGCCTTTGC‑CCATCCGGGCCATGACAGCAACCCGCTGCAg                                                                                                       >  2:360895/1‑149 (MQ=255)                                          ccATGGCCACGATCACCCGTTCGTACGCCTGCCTGCCCATTCCTGAACTGCCCTGGAGCAACCGATGAAAAAGACTTTCGCCTTGTTTCTGTTGATGCTGGCACTGCCAGCCTTTGC‑CCATCCGGGCCATGACAGCAACCCGCTGCAgg                                                                                                      >  6:269391/1‑149 (MQ=255)                                             tGGCCACGATCACCCGTTCGTACGCCTGCCTGCCCATTCCTGAACTGCCCTGGAGCAACCGATGAAAAAGACTTTCGCCTTGTTTCTGTTGATGCTGGCACTGCCAGCCTTTGC‑CCATCCGGGCCATGACAGCAACCCGCTGCAGGACg                                                                                                   <  8:314861/149‑1 (MQ=255)                                                    gATCACCCGTTCGTACGCCTGCCTGCCCATTCCTGAACTGCCCTGGAGCAACCGATGAAAAAGACTTTCGCCTTGTTTCTGTTGATGCTGGCACTGCCAGCCTTTGC‑CCATCCGGGCCATGACAGCAACCCGCTGCAGGACGGCctgct                                                                                            <  4:70451/149‑1 (MQ=255)                                                          ccGTTCGTACGCCTGCCTGCCCATTCCTGAACTGCCCTGGAGCAACCAATGAAAAAGACTTTCGCCTTGTTTCTGTTGATGCTGGCACTGCCAGCCTTTGc                                                                                                                                       >  6:85091/1‑101 (MQ=255)                                                          ccGTTCGTACGCCTGCCTGCCCATTCCTGAACTGCCCTGGAGCAACCAATGAAAAAGACTTTCGCCTTGTTTCTGTTGATGCTGGCACTGCCAGCCTTTGc                                                                                                                                       <  5:85091/101‑1 (MQ=255)                                                            gTTCGTACGCCTGCCTGCCCATTCCTGAACTGCCCTGGAGCAACCGATGAAAAAGACTTTCGCCTTGTTTCTGTTGATGCTGGCACTGCCAGCCTTTGC‑CCATCCGGGCCATGACAGCAACCCGCTGCAGGACGGCCTGCTGCACCCGc                                                                                    <  3:224696/149‑1 (MQ=255)                                                                gTACGCCTGCCTGCCCATTCCTGAACTGCCCTGGAGCAACCGATGAAAAAGACTTTCGCCTTGTTTCTGTTGATGCTGGCACTGCCAGCCTTTGC‑CCATCCGGGCCATGACAGCAACCCGCTGCAGGACGGCCTGCTGCACCCGCTGAc                                                                                >  6:305613/1‑149 (MQ=255)                                                                 tACGCCTGCCTGCCCATTCCTGAACTGCCCTGGAGCAACCGATGAAAAAGACTTTCGCCTTGTTTCTGTTGATGCTGGCACTGCCAGCCTTTGC‑CCATCCGGGCCATGACAGCAACCCGCTGCAGGACGGCCTGCTGCAc                                                                                        <  6:262404/140‑1 (MQ=255)                                                                 tACGCCTGCCTGCCCATTCCTGAACTGCCCTGGAGCAACCGATGAAAAAGACTTTCGCCTTGTTTCTGTTGATGCTGGCACTGCCAGCCTTTGC‑CCATCCGGGCCATGACAGCAACCCGCTGCAGGACGGCCTGCTGCAc                                                                                        >  5:262404/1‑140 (MQ=255)                                                                 tACGCCTGCCTGCCCATTCCTGAACTGCCCTGGAGCAACCGATGAAAAAGACTTTCGCCTTGTTTCTGTTGATGCTGGCACTGCCAGCCTTTGC‑CCATCCGGGCCATGACAGCAACCCGCTGCAGGACGGCCTGCTGCACCCGCTGAcc                                                                               >  2:303979/1‑149 (MQ=255)                                                                    gcctgcctGCCCATTCCTGAACTGCCCTGGAGCAACCGATGAAAAAGACTTTCGCCTTGTTTCTGTTGATGCTGGCACTGCCAGCCTTTGC‑CCATCCGGGCCATGACAGCAACCCGCTGCAGGACGGCCTGCTGCACCCGCTGACCggg                                                                            <  8:25689/149‑1 (MQ=255)                                                                      ctgcctgcCCATTCCTGAACTGCCCTGGAGCAACCGATGAAAAAGACTTTCGCCTTGTTTCTGTTGATGCTGGCACTGCCAGCCTTTGC‑CCATCCGGGCCATGACAGCAACCCGCTGCAGGACGGCCTGCTGCACCCGCTGACCGGGCt                                                                          >  4:201824/1‑149 (MQ=255)                                                                           tgccCATTCCTGAACTGCCCTGGAGCAACCGATGAAAAAGACTTTCGCCTTGTTTCTGTTGATGCTGGCACTGCCAGCCTTTGC‑CCATCCGGGCCATGACAGCAACCCGCTGCAGGACGGCCTGCTGCACCCGCTGACCGGGCTCGAt                                                                      >  6:366448/1‑148 (MQ=255)                                                                               cATTCCTGAACTGCCCTGGAGCAACCGATGAAAAAGACTTTCGCCTTGTTTCTGTTGATGCTGGCACTGCCAGCCTTTGC‑CCATCCGGGCCATGACAGCAACCCGCTGCAGGACGGCCTGCTGCACCCGCTGACCGGGCTCGATCACct                                                                 >  2:356915/1‑149 (MQ=255)                                                                                 ttCCTGAACTGCCCTGGAGCAACCGATGAAAAAGACTTTCGCCTTGTTTCTGTTGATGCTGGCACTGCCAGCCTTTGC‑CCATCCGGGCCATGACAGCAACCCGCTGCAGGACGGCCTGCTGCACCCGCTGACCGGGCTCGATCACctgc                                                               <  2:157681/149‑1 (MQ=255)                                                                                     tGAACTGCCCTGGAGCAACCGATGAAAAAGACTTTCGCCTTGTTTCTGTTGATGCTGGCACTGCCAGCCtcaa                                                                                                                                        >  4:339075/1‑70 (MQ=255)                                                                                     tGAACTGCCCTGGAGCAACCGATGAAAAAGACTTTCGCCTTGTTTCTGTTGATGCTGGCACTGCCAGCCtcaa                                                                                                                                        <  3:339075/73‑4 (MQ=255)                                                                                     tGAACTGCCCTGGAGCAACCGATGAAAAAGACTTTCGCCTTGTTTCTGTTGATGCTGGCACTGCCAGCCTTTGC‑CCATCCGGGCCATGACAGCAACCCGCTGCAGGACGGCCTGCTGCACCCGCTGACCGGGCTCGATCACCTGCTGAt                                                           >  6:298189/1‑149 (MQ=255)                                                                                       aaCTGCCCTGGAGCAACCGATGAAAAAGACTTTCGCCTTGTTTCTGTTGATGCTGGCACTGCCAGCCTTTGC‑CCATCCGGGCCATGACAGCAACCCGCTGCAGGACGGCCTGCTGCACCCGCTGACCGGGCTCGATCACCTGCTGAtgc                                                         >  5:234342/1‑149 (MQ=255)                                                                                                   gCAACCGATGAAAAAGACTTTCGCCTTGTTTCTGTTGATGCTGGCACTGCCAGCCTTTGC‑CCATCCGGGCCATGACAGCAACCCGCTGCAGGACGGCCTGCTGCACCCGCTGACCGGGCTCGATCACCTGCTGATGCTGCTGGGTACCg                                             <  7:2365/149‑1 (MQ=255)                                                                                                      aCCGATGAAAAAGACTTTCGCCTTGTTTCTGTTGATGCTGGCACTGCCAGCCTTTGC‑CCATCCGGGCCATGACAGCAACCCGCTGCAGGACGGCCTGCTGCACACGCTGACCGGGCTCGATCACCTGCTGATGCTGCTGGGTACCGGCg                                          >  1:148825/1‑149 (MQ=255)                                                                                                       ccGATGAAAAAGACTTTCGCCTTGTTTCTGTTGATGCTGGCACTGCCAGCCTTTGC‑CCATCCGGGCCATGACAGCAACCCGCTGCAGGACGGCCTGCTGCACCCGCTGACCGGGCTCGATCACCTGCTGTTGCTGCTGGGTACCGGCGt                                         >  2:72017/1‑149 (MQ=255)                                                                                                         gATGAAAAAGACTTTCGCCTTGTTTCTGTTGATGCTGGCACTGCCAGCCTTTGC‑CCATCCGGGCCATGACAGCAACCCGCTGCAGGACGGCCTGCTGCACCCGCTGACCGGGCTCGATCACCTGCTGATGCTGCTGGGTACCGGCGt                                         >  5:263750/1‑147 (MQ=255)                                                                                                         gATGAAAAAGACTTTCGCCTTGTTTCTGTTGATGCTGGCACTGCCAGCCTTTGC‑CCATCCGGGCCATGACAGCAACCCGCTGCAGGACGGCCTGCTGCACCCGCTGACCGGGCTCGATCACCTGCTGATGCTGCTGGGTACCGGCGt                                         <  6:263750/147‑1 (MQ=255)                                                                                                           tGAAAAAGACTTTCGCCTTGTTTCTGTTGATGCTGGCACTGCCAGCCTTTGC‑CCATCCGGGCCATGACAGCAACCCGCTGCAGGACGGCCTGCTGCACCCGCTGACCGGGCTCGATCACCTGCTGATGCTGCTGGGTACCGGCGTGCTc                                     <  1:356915/149‑1 (MQ=255)                                                                                                              aaaaGACTTTCGCCTTGTTTCTGTTGATGCTGGCACTGCCAGCCTTTGCGCCATCCGGGCCATGACAGCAACCCGCTGCAGGACGGCCTGCTGCACCCGCTGACCGGGCTCGATCACCTGCTGATGCTGCTGGGTACCGGCGTGCTcgc                                   >  1:88668/1‑149 (MQ=255)                                                                                                               aacgACTTTCGCCTTGTTTCTGTTGATGCTGGCACAGCCAGCGTTTGC‑CCATCCGGGCGAGGACAGCAACCCGCTGCAGGACGGCCTGCTGCACCCGCTGACCGGGCTCGCTCACCTGCTGATGCTGCTGGGTACCGGCGTGCTcgccg                                 >  6:206455/4‑149 (MQ=255)                                                                                                               aaaGACTTTCGCCTTGTTTCTGTTGATGCTGGCACTGCCAGCCTTTGC‑CCATCCGGGCCATGACAGCAACCCGCTGCAGGACGGCCTGCTGCACCCGCTGACCGGGCTCGATCACCTGCTGATGCTGCTGGGTACCGGCGTGCTcgccg                                 >  3:66460/1‑149 (MQ=255)                                                                                                                   aCTTTCGCCTTGTTTCTGTTGATGCTGGCACTGCCAGCCTTTGC‑CCATCCGGGCCATGACAGCAACCCGCTGCAGGACGGCCTGCTGCACCCGCTGACCGGGCTCGATCACCTGCTGATGCTGCTGGGTACCGGCGTGCTCGCCGCGtt                             <  5:298189/149‑1 (MQ=255)                                                                                                                                     caaaggCTGGCAGTGCCAGCCTTTGC‑CCATCCGGGCCATGACAGCAACCCGCTGCAGGACGGCCTGCTGCACCCGCTGACCGGGCTCGATCACCTGCTGATGCTGCTGGGTACCGGCGTGCTCGCCGCGTTGACCCGTCGCAACCTGa            >  5:380738/6‑148 (MQ=255)                                                                                                                                          gCTGGCAGTGCCAGCCTTTGC‑CCATCCGGGCCATGACAGCAACCCGCTGCAGGACGGCCTGCTGCACCCGCTGACCGGGCTCGATCACCTGCTGATGCTGCTGGGTACCGGCGTGCTCGCCGCGTTGACCCGTCGCAACCTGACATTGc      >  2:154873/1‑149 (MQ=255)                                                                                                                                            tGGCACTGCCAGCCTTTGC‑CCATCCGGGCCATGACAGCAACCCGCTGCAGGACGGCCTGCTGCACCCGCTGACCGGGCTCGATCACCTGCTGATGCTGCTGGGTACCGGCGTGCTCGCCGCGTTGACCCGTCGCAACCTGACATTGccc    >  2:116158/1‑149 (MQ=255)                                                                                                                                              gCAGTGCCAGCCTTTGC‑CCATCCGGGCCATGACAGCAACCCGCTGCAGGACGGCCTGCTGCACCCGCTGACCGGGCTCGATCACCTGCTGATGCTGCTGGGTACCGGCGTGCTCGCCGCGTTGACCCGTCGCAACCTGACATTGCCCCt  <  1:154873/149‑1 (MQ=255)                                                                                                                                              gCACTGCCAGCCTTTGC‑CCATCCGGGCCATGACAGCAACCCGCTGCAGGACGGCCTGCTGCACCCGCTGACCGGGCTCGATCACCTGCTGATGCTGCTGGGTACCGGCGTGCTCGCCGCGTTGACCCGTCGCAACCTGACATTGCCCCt  <  4:66460/149‑1 (MQ=255)                                                                                                                                              gCACTGCCAGCCTTTGC‑CCATCCGGGCCATGACAGCAACCCGCTGCAGGACGGCCTGCTGCACCCGCTGACCGGGCTCGATCACCTGCTGATGCTGCTGGGTACCGGCGTGCTCGCCGCGTTGACCCGTCGCAACCTGACATTGCCCCt  >  7:309123/1‑149 (MQ=255)                                                                                                                                              gCACTGCCAGCCTTTGC‑CCATCCGGGCCATGACAGCAACCCGCTGCAGGACGGCCTGCTGCACCCGCTGACCGGGCTCGATCACCTGCTGATGCTGCTGGGTACCGGCGTGCTCGCCGCGTTGACCCGTCGCAACCTGACATTGCCCCt  >  4:163447/1‑149 (MQ=255)                                                                                                                                              gCACTGCCAGCCTTTGC‑CCATCCGGGCCATGACAGCAACCCGCTGCAGGACGGCCTGCTGCACCCGCTGACCGGGCTCGATCACCTGCTGATGCTGCTGGGTACCGGCGTGCTCGCCGCGTTGACCCGTCGCAACCTGACATTGCCCCt  >  1:270130/1‑149 (MQ=255)                                                                                                                                                 |                                                                                                                                                   GCTTACCAAAGTGCACCGCATGGCCACAGCCACAGTCATGCCCATGGCCACGATCACCCGTTCGTACGCCTGCCTGCCCATTCCTGAACTGCCCTGGAGCAACCGATGAAAAAGACTTTCGCCTTGTTTCTGTTGATGCTGGCACTGCCAGCCTTTGC‑CCATCCGGGCCATGACAGCAACCCGCTGCAGGACGGCCTGCTGCACCCGCTGACCGGGCTCGATCACCTGCTGATGCTGCTGGGTACCGGCGTGCTCGCCGCGTTGACCCGTCGCAACCTGACATTGCCCCT  >  NC_002947/3250511‑3250800

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: ‑