Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,235,258:1	+A	10.3%	coding (353/1542 nt)	PP_2834 →	D‑galactarate dehydratase/altronate dehydratase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,235,258	1	.	A	10.3%	134.8 / 12.4	39	coding (353/1542 nt)	PP_2834	D‑galactarate dehydratase/altronate dehydratase
Reads supporting (aligned to +/- strand):  ref base . (17/18);  new base A (2/2);  total (19/20)
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

ATCGGATTTGCGTCCCAGGCGATCGACGCTGGCGACCATGTGCATGTGCACAACGTGCAGATGGGCGATTTTGCCCGCGACTATGCGTTTGGTGTCGATACCCGCAGCCTGCCAGGCAGCGCCGCGCAGTTCCAGGGCATCGTGCGCGC‑CGATGGCCGTGTCGCCACCCGCAA‑‑CTACATCGGCATT‑CT‑‑CACCTCGGTGAACTGTTCGGCGACCGTGGCCCGGGCCGTGGCCGACCATTTCCGCCGTGACATTCACCCCGAGGTGCTGGCCGACTACCCG  >  NC_002947/3235110‑3235388                                                                                                                                                      |                                                                                                                                        ctcGGATTTGCGTCCCAGGCGATCGACGCTGGCGACCATGTGCATGTGCACAACGTGCAGATGGGCGATTTTGCCCGCGACTATGCGTTTGGTGTCGATACCCGCAGCCTGCCAGGCAGCGCCGCGCAGTTCCAGGGCATCGTgcgcgc                                                                                                                                          <  8:121115/148‑1 (MQ=255) atcGGATTTGCGTCCCAGGCGATCGACGCTGGCGACCATGTGCATGTGCACAACGTGCAGATGGGCGATTTTGCCCGCGACTATGCGTTTGGTGTCGATACCCGCAGCCTGCCAGGCAGCGCCGCGCAGTTCCAGGGCATCGTgcgcgc                                                                                                                                          >  3:62360/1‑149 (MQ=255)    ggATTTGCGTCCCAGGCGATCGACGCTGGCGACCATGTGCATGTGCACAACGTGCAGATGGGCGATTTTGCCCGCGACTATGCGTTTGGTGTCGATACCCGCAGCCTGCCAGGCAGCGCCGCGCAGTTCCAGGGCATCGTGCGCGC‑CGa                                                                                                                                      <  6:259897/149‑1 (MQ=255)          gCGTCCCAGGCGATCGACGCTGGCGACCATGTGCATGTGCACAACGTGCAGATGGGCGATTTTGCCCGCGACTATGCGTTTGGTGTCGATACCCGCAGCCTGCCAGGCAGCGCCGCGCAGTTCCAGGGCATCGTGCGCGC‑CGATGGcc                                                                                                                                 <  4:211514/148‑1 (MQ=255)               ccAGGCGATCGACGCTGGCGACCATGTGCATGTGCACAACGTGCAGATGGGCGATTTTGCCCGCGACTATGCGTTTGGTGTCGATACCCGCAGCCTGCCAGGCAGCGCCGCGCAGTTCCAGGCCATCG‑GCGCGCACGATGccctgg                                                                                                                              <  4:195535/146‑4 (MQ=255)               ccAGGCGATCGACGCTGGCGACCATGTGCATGTGCACAACGTGCAGATGGGCGATTTTGCCCGCGACTATGCGTTTGGTGTCGATACCCGCAGCCTGCCAGGCAGCGCCGCGCAGTTCCAGGCCATCG‑GCGCGCACGATGccctgg                                                                                                                              >  3:195535/1‑143 (MQ=255)                  ggCGATCGTCGCTGGCGACCTTGTGGATGTGCAAAAAGTGCAGTTGGGCTATTTTGCGCGCGAGTATGCGTTTGGTGTCGATACCCGCAGCCTGCCAGGCAGCGCCGCGCAGTTCCAGGGCATCGTGCGCGC‑CGATGGCGGTGTCGGCa                                                                                                                        <  2:96582/149‑1 (MQ=255)                     gATCGACGCTGGCGACCATGTGCATGTGCACAACGTGCAGATGGGCGATTTTGCCCGCGACTATGCGTTTGGTGTCGATACCCGCAGCCTGCCAGGCAGCGCCGCGCAGTTCCAGGGCATCGTGCGCGC‑CGATGGCCGTGTCGCCAccc                                                                                                                     <  3:260248/149‑1 (MQ=255)                            gCTGGCGACCATGTGCATGTGCACAACGTGCAGATGGGCGATTTTGCCCGCGACTATGCGTTTGGTGTCGATACCCGCAGCCTGCCAGGCAGCGCCGCGCAGTTCCAGGGCATCGTGCGCGC‑CGATGGCCGTGTCGCCACCCGCAA‑‑CTa                                                                                                            >  5:11556/1‑149 (MQ=255)                                  gACCATGTGCATGTGCACAACGTGCAGATGGGCGATTTTGCCCGCGACTATGCGTTTGGTGTCGATACCCGCAGCCTGCCAGGCAGCGCCGCGCAGTTCCAGGGCATCGTGCGCGC‑CGATGGCCGTGTCGCCACCCGCAA‑‑CTACATCgg                                                                                                      <  4:62360/149‑1 (MQ=255)                                     catgtgcatgtgCACAACGTGCAGATGGGCGATTTTGCCCGCGACTATGCGTTTGGTGTCGATACCCGCAGCCTGCCAGGCAGCGCCGCGCAGTTCCAGGGCATCG‑GCGCGCACGATgc                                                                                                                                   <  8:54117/119‑2 (MQ=255)                                     catgtgcatgtgCACAACGTGCAGATGGGCGATTTTGCCCGCGACTATGCGTTTGGTGTCGATACCCGCAGCCTGCCAGGCAGCGCCGCGCAGTTCCAGGGCATCG‑GCGCGCACGATgc                                                                                                                                   >  7:54117/1‑118 (MQ=255)                                       tgtgcatgtgcaCAACGTGCAGATGGGCGATTTTGCCCGCGACTATGCGTTTGGTGTCGATACCCGCAGCCTGCCAGGCAGCGCCGCGCAGTTCCAGGGCATCGTGCGCGC‑CGATGTCCGTGTCCCAAACATCAA‑‑ATACATctcaatt                                                                                                  >  6:187953/1‑142 (MQ=255)                                         tgcatgtgcaCAACGTGCAGATGGGCGATTTTGCCCGCGACTATGCGTTTGGTGTCGATACCCGCAGCCTGCCAGGCAGCGCCGCGCAGTTCCAGGGCATCGTGCGCGC‑CGATGGCCGTGTCGCCACCCGCAA‑‑CTACATCGGCATt‑ct‑‑c                                                                                            <  6:11556/149‑1 (MQ=255)                                                 cacaACGTGCAGATGGGCGATTTTGCCCGCGACTATGCGTTTGGTGTCGATACCCGCAGCCTGCCAGGCAGCGCCGCGCAGTTCCAGGGCATGGTGCGCGC‑CGATGGCCGTGTCGCCACCCGCAA‑‑CTACATCGGCATT‑CT‑‑CACCTCGGt                                                                                    <  5:152563/149‑1 (MQ=255)                                                  acaACGTGCAGATGGGCGATTTTGCCCGCGACTATGCGTTTGGTGTCGATACCCGCAGCCTGCCAGGCAGCGCCGCGCAGTTCAAGGGCATCGTGCGCGC‑CGATGGCCGTGTCGCCACCCGCAA‑‑CTACATCGGCATT‑CT‑‑CACCTCGGTg                                                                                   <  5:187953/149‑1 (MQ=255)                                                           aGATGGGCGATTTTGCCCGCGACTATGCGTTTGGTGTCGATACCCGCAGCCTGCCAGGCAGCGCCGCGCAGTTCCAGGGCATCGTGCGCGC‑CGATGGCCGTGTCGCCACCCGCAA‑‑CTACATCGGCATT‑CT‑‑CACCTCGGTGAACTGTTCg                                                                          <  7:177936/149‑1 (MQ=255)                                                                           ccGCGACTATGCGTTTGGTGTCGATACCCGCAGCCTGCCAGGCAGCGCCGCGCAGTTCCAGGGCATCGTGCGCGC‑CGATGGCCGTGTCGCCACCCGCAA‑‑CTACATCGGCATT‑CT‑‑CACCTCGGTGAACTGTTCGGCGACCGTGGCCCggg                                                          >  2:83917/1‑149 (MQ=255)                                                                                       gTTTGGTGTCGATACCCGCAGCCTGCCAGGCAGCGCCGCGCAGTTCCAGGGCATCGTGCGCGC‑CGATGGCCGTGTCGCCACCCGCAA‑‑CTACATCGGCATT‑CT‑‑CACCTCGGTGAACTGTTCGGCGACCGTGGCCCGGGCCGTGGCCGAc                                               >  4:237145/1‑148 (MQ=255)                                                                                              gtCGATACCCGCAGCCTGCCAGGCAGCGCCGCGCAGTTCCAGGGCATCGTGCGCGC‑CGATGGCCGTGTCGCCACCCGCAA‑‑CTACATCGGCATT‑CT‑‑CACCTCGGTGAACTGTTCGGCGACCGTGGCCCGGGCCGTGGCCGACCATTTccg                                       >  1:172382/1‑149 (MQ=255)                                                                                                 gATACCCGCAGCCTGCCAGGCAGCGCCGCGCAGTTCCAGGGCATCGTGCGCGC‑CGATGGCCGTGTCGCCACCCGCAA‑‑CTACATCGGCATT‑CT‑‑CACCTCGGTGAACTGTTCGGCGACCGTGGCCCGGGCCGTGGCCg                                                 <  4:183929/136‑1 (MQ=255)                                                                                                 gATACCCGCAGCCTGCCAGGCAGCGCCGCGCAGTTCCAGGGCATCGTGCGCGC‑CGATGGCCGTGTCGCCACCCGCAA‑‑CTACATCGGCATT‑CT‑‑CACCTCGGTGAACTGTTCGGCGACCGTGGCCCGGGCCGTGGCCg                                                 >  3:183929/1‑136 (MQ=255)                                                                                                   tACCCGCAGCCTGCCAGGCAGCGCCGCGCAGTTCCAGGGCATCGTGCGCGC‑CGATGGCCGTGTCGCCACCCGCAA‑‑CTACATCGGCATT‑CT‑‑CACCTCGGTGAACTGTTCGGCGACCGTGGCCCGGGCCGTGGCCGACCATTTCCGCCGTg                                  <  3:237145/149‑1 (MQ=255)                                                                                                    cggcGCTGCCTGGCAGGCTGCGCCGCGCAGTTCCAGGGCATCGTGCGCGC‑CGATGGCCGTGTCGCCACCCGCAA‑‑CTACATCGGCATT‑CT‑‑CACCTCGGTGAACTGTTCGGCGACCGTGGCCCGGGCCGTGGCCGACCATTTCCGCCGTGa                                 >  2:241821/4‑149 (MQ=255)                                                                                                     cccGCAGCCTGCCAGGCAGCGCCGCGCAGTTCCAGGGCATCGTGCGCGC‑CGATGGCCGTGTCGCCACCCGCAA‑‑CTACATCGGCATT‑CT‑‑CACCTCGGTGAACTGTTCGGCGACCGTGGACCGGGCCGTGGCCGACCATTTCCGCCGTGa                                 >  3:31810/1‑148 (MQ=255)                                                                                                      ccGCAGCCTGCCAGGCAGCGCCGCGCAGTTCCAGGGCATCGTGCGCGC‑CGATGGCCGTGTCGCCACCCGCAA‑‑CTACATCGGCATT‑CT‑‑CACCTCGGTGAACTGTTCGGCGACCGTGGCCCGGGCCGTGGCCGAcc                                              >  5:112119/1‑134 (MQ=255)                                                                                                      ccGCAGCCTGCCAGGCAGCGCCGCGCAGTTCCAGGGCATCGTGCGCGC‑CGATGGCCGTGTCGCCACCCGCAA‑‑CTACATCGGCATT‑CT‑‑CACCTCGGTGAACTGTTCGGCGACCGTGGCCCGGGCCGTGGCCGAcc                                              <  6:112119/134‑1 (MQ=255)                                                                                                      ccGCAGCCTGCCAGGCAGCGCCGCGCAGTTCCAGGGCATCGTGCGCGC‑CGATGGCCGTGTCGCCACCCGCAA‑‑CTACATCGGCATT‑CT‑‑CACCTCGGTGAACTGTTCGGCGACCGTGGCCCGGGCCGTGGCCGACCATTTCCGCCGTGACa                               >  1:26173/1‑149 (MQ=255)                                                                                                       cGCAGCCTGCCAGGCAGCGCCGCGCAGTTCCAGGGCATCGTGCGCGC‑CGATGGCCGTGTCGCCACCCGCAA‑‑CTACATCGGCATT‑CT‑‑CACCTCGGTGAACTGTTCGGCGACCGTGGCCCGGGCCGTGGCCGACCATTTCCGCCGTGACAt                              >  8:172530/1‑149 (MQ=255)                                                                                                             cTGCCAGGCAGCGCCGCGCAGTTCCAGGGCATCGTGCGCGC‑CGATGGCCGTGTCGCCACCCGCAA‑‑CTACATCGGCATT‑CT‑‑CACCTCGGTGAACTGTTCGGCGACCGTGGCCCGGGCCGTGGCCGACCATTTCCGCCGTGACATTCAccc                        >  5:94598/1‑149 (MQ=255)                                                                                                               gCCAGGCAGCGCCGCGCAGTTCCAGGGCATCGTGCGCGC‑CGATGGCCGTGTCGCCACCCGCAA‑‑CTACATCGGCATT‑CT‑‑CACCTCGGTGAACTGTTCGGCGACCGTGGCCCGGGCCGTGGCCGACCATTTCCGCCGTGACATTCAcccc                       >  2:256763/1‑148 (MQ=255)                                                                                                                ccAGGCAGCGCCGCGCAGTTCCAGGGCATCGTGCGCGC‑CGATGGCCGTGTCGCCACCCGCAA‑‑CTACATCGGCATT‑CT‑‑CACCTCGGTGAACTGTTCGGCGACCGTGGCCCGGGCCGTGGCCGACCATTTCCGCCGTGACATTCAcccc                       >  3:180595/1‑147 (MQ=255)                                                                                                                ccAGGCAGCGCCGCGCAGTTCCAGGGCATCGTGCGCGC‑CGATGGCCGTGTCGCCACCCGCAA‑‑CTACATCGGCATT‑CT‑‑CACCTCGGTGAACTGTTCGGCGACCGTGGCCCGGGCCGTGGCCGACCATTTCCGCCGTGACATTCACCCCGa                     <  2:172382/149‑1 (MQ=255)                                                                                                                    gCAGCGCCGCGCAGTTCCAGGGCATCGTGCGCGC‑CGATGGCCGTGTCGCCACCCGCAA‑‑CTACATCGGCATT‑CT‑‑CACCTCGGTGAACTGTTCGGc                                                                        <  4:197336/94‑1 (MQ=255)                                                                                                                    gCAGCGCCGCGCAGTTCCAGGGCATCGTGCGCGC‑CGATGGCCGTGTCGCCACCCGCAA‑‑CTACATCGGCATT‑CT‑‑CACCTCGGTGAACTGTTCGGc                                                                        >  3:197336/1‑94 (MQ=255)                                                                                                                    gCAGCGCCGCGCAGTTCCAGGGCATCGTGCGCGC‑CGATGGCCGTGTCGCCACCCGCAA‑‑CTACATCGGCATT‑CT‑‑CACCTCGGTGAACTGTTCGGCGACCGTGGCCCGGGCCGTGGCCGACCATTTCCGCCGTGACATTCACCCCGAGGTg                 <  4:180595/149‑1 (MQ=255)                                                                                                                      aGCGCCGCGCAGTTCCAGGGCATCGTGCGCGC‑CGATGGCCGTGTCGCCACCCGCAACTCTACATCGGCATTCCTCCCTCCTCGGTGAACTGTTCGGCGACCGTGGCCCGGGCCGTGGCCGACCATTTCCGCCGTGACATTCACCCCGAg                    <  1:83917/149‑1 (MQ=255)                                                                                                                        cgccgcGCAGTTCCAGGGCATCGTGCGCGC‑CGATGGCCGTGTCGCCACCCGCAA‑‑CTACATCGGCATT‑CT‑‑CACCTCGGTGAACTGTTCGGCGACCGTGGCCCGGGCCGTGGCCGACCATTTCCGCCGt                                   <  3:230146/127‑1 (MQ=255)                                                                                                                        cgccgcGCAGTTCCAGGGCATCGTGCGCGC‑CGATGGCCGTGTCGCCACCCGCAA‑‑CTACATCGGCATT‑CT‑‑CACCTCGGTGAACTGTTCGGCGACCGTGGCCCGGGCCGTGGCCGACCATTTCCGCCGt                                   >  4:230146/1‑127 (MQ=255)                                                                                                                             cgcAGTTCCAGGGCATCGTGCGCGC‑CGATGGCCGTGTCGCCACCCGCAA‑‑CTACATCGGCATT‑CT‑‑CACCTCGGTGAACTGTTCGGCGACCGTGGCCCGGGCCGTGGCCGACCATTTCCGCCGTGACATTCACCCCGAGGTGCTGGCCGAc        <  1:256763/149‑1 (MQ=255)                                                                                                                                    ccAGGGCATCGTGCGCGC‑CGATGGCCGTGTCGCCACCCGCAA‑‑CTACATCGGCATT‑CT‑‑CACCTCGGTGAACTGTTCGGCGACCGTGGCCCGGGCCGTGGCCGACCATTTCCGCCGTGACATTCACCCCGAGGTGCTGGCCGACTACCCg  >  1:97573/1‑148 (MQ=255)                                                                                                                                                      |                                                                                                                                        ATCGGATTTGCGTCCCAGGCGATCGACGCTGGCGACCATGTGCATGTGCACAACGTGCAGATGGGCGATTTTGCCCGCGACTATGCGTTTGGTGTCGATACCCGCAGCCTGCCAGGCAGCGCCGCGCAGTTCCAGGGCATCGTGCGCGC‑CGATGGCCGTGTCGCCACCCGCAA‑‑CTACATCGGCATT‑CT‑‑CACCTCGGTGAACTGTTCGGCGACCGTGGCCCGGGCCGTGGCCGACCATTTCCGCCGTGACATTCACCCCGAGGTGCTGGCCGACTACCCG  >  NC_002947/3235110‑3235388

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: ‑