Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_002947	1,419,549	+C	intergenic (‑38/+98)	PP_1242 ← / ← PP_1244	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,419,548	1	.	C	97.4%	121.4 / ‑3.3	38	intergenic (‑37/+99)	PP_1242/PP_1244	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base C (19/18);  total (19/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCAGGGGATGCCGGGTTCGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGG‑CTCTT‑CGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTG‑ACGGCTGTGGTGACCCTGTGGGAGCGGGCGTGCCCGCGAAGAGGCCTGACCTGCTAATGCAAGGTGTGAGGCTCTGTGGGTAAATGCGACCGCATCTG  >  NC_002947/1419404‑1419691                                                                                                                                                  |                                                                                                                                                  gCAGGGGATGCCGGGTTCGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGggctgg‑cctc                                                                                                                                               >  6:353526/1‑146 (MQ=255)      ggATGCCGGGTTCGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTT‑cgc                                                                                                                                          <  5:353526/149‑1 (MQ=255)       gaggCCGGGGTCGATCCGGAACAGCGGGTCAGGGTGGTTTTCGCCGTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGATTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTT‑cgcg                                                                                                                                         <  6:275921/146‑1 (MQ=255)                  cGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTT‑CGCGGGCACGCCCGc                                                                                                                              >  3:146009/1‑149 (MQ=255)                   gATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTT‑CGCGGGCACGCCCGCt                                                                                                                             >  8:118865/1‑149 (MQ=255)                        ggAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGGGGGTTCTGTTGGGGTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTT‑CGCGGGCACGCCCGCTCCcac                                                                                                                        <  5:181636/149‑1 (MQ=255)                         gAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTT‑CGCggg                                                                                                                                       <  8:352149/133‑1 (MQ=255)                         gAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTT‑CGCggg                                                                                                                                       >  7:352149/1‑133 (MQ=255)                                  gTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTT‑CGCGGGCACGCCCGCTCCCACAGGTACtgtg                                                                                                              <  4:146009/149‑1 (MQ=255)                                       tgttgtTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTT‑CGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTg                                                                                                         >  5:382341/1‑149 (MQ=255)                                       tgttgtTTTCGACTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTT‑CGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTg                                                                                                         >  8:66099/1‑149 (MQ=255)                                         ttgttTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGggctgg‑c                                                                                                                                                  <  2:368563/106‑1 (MQ=255)                                         ttgttTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGggctgg‑c                                                                                                                                                  >  1:368563/1‑106 (MQ=255)                                                      ggTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTT‑CGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTG‑ACGGCTgtgg                                                                                          <  7:66099/148‑1 (MQ=255)                                                                 gTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTT‑CGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTG‑ACGGCTGTGGTGACCCTGTggg                                                                              >  8:331402/1‑149 (MQ=255)                                                                  tCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTT‑CGCgg                                                                                                                                        >  8:295012/1‑91 (MQ=255)                                                                  tCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTT‑CGCgg                                                                                                                                        <  7:295012/91‑1 (MQ=255)                                                                  tCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGGCGTTGGGCATTGTTTTGTTTCCCTGGATTCTGGGGTGCCTGGGCTGGCCTCTT‑CGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTG‑ACGGCTGTGGTGACCCTGTGGGa                                                                             <  3:289614/149‑1 (MQ=39)                                                                      gCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTT‑CGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTG‑ACGGCtgtg                                                                                           >  3:61747/1‑131 (MQ=255)                                                                      gCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTT‑CGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTG‑ACGGCtgtg                                                                                           <  4:61747/131‑1 (MQ=255)                                                                      gCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTT‑CGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTG‑ACGGCTGTGGTGACCCtgtg                                                                                <  7:140026/142‑1 (MQ=255)                                                                      gCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTT‑CGCGGGCACGCCCCCTACCACAGGTACTGTTCAGTGGGTT‑ACGGGTGTGGTGACCCTGTGGGAGCgg                                                                         >  3:21463/1‑149 (MQ=255)                                                                      gCCGACTGTGGTGGGTTCTGTTGTGTTGTAGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTT‑CGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTG‑ACGGCTGTGGTGACCCtgtg                                                                                >  8:140026/1‑142 (MQ=255)                                                                        cGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTT‑CGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTG‑ACGGCTGTGGTGACCCTGTGGGAGCGGGc                                                                       <  7:331402/149‑1 (MQ=255)                                                                        cGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTT‑CGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTG‑ACGGCTGTGGTGACCCTGTGGGAGCGGGc                                                                       <  7:118865/149‑1 (MQ=255)                                                                          aCTGTGGTGGGTGCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTT‑CGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTG‑ACGGCTGTGGTGACCCTGTGGGAGCGGGCGt                                                                     <  6:211506/149‑1 (MQ=255)                                                                              tggtggGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTT‑CGCGGGCACCCCCCCACCCAAAAGTTATTTGGAGTGGGTGAACGGGT‑TGGTGGACCTGTTGGAGCGGGCGttgcc                                                                 >  1:201972/1‑145 (MQ=255)                                                                                   ggTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTT‑CGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTG‑ACGGCt                                                                                              >  7:133625/1‑115 (MQ=255)                                                                                   ggTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTT‑CGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTG‑ACGGCt                                                                                              <  8:133625/115‑1 (MQ=255)                                                                                         gttgtgttgtCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTT‑CGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTG‑ACGGCTGTGGTGACCCTGTGGGAGCGGGCGTGCCCGCGAAGAGGcc                                                      >  4:313044/1‑149 (MQ=255)                                                                                         gttgtgttgtCGGTGGGCATTGTTATGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTT‑CGCCGGCACGCCCGCACCCCCAGGTAAAGTGCAGTGGGTG‑ACGGCGGTGGTGACCCGGTGGGATCGGGCGAGCCCGCGAACAGGc                                                       >  2:132790/1‑148 (MQ=255)                                                                                          ttgtgttgtCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTGGCCTGGGCTGGCCTCTT‑CGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTG‑ACGGCTGTGGTGACCCTGTGGGAGCGGGCGTGCCCGCGAAGAGGc                                                       <  5:154679/147‑1 (MQ=255)                                                                                                   cGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTT‑CGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTG‑ACgg                                                                                                <  2:33828/97‑1 (MQ=255)                                                                                                   cGGTGGGCATTGTTTTGTTTCCCTGGATTCAGGGTTGCCTGGGCTGGCCTCTT‑CGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTG‑ACgg                                                                                                >  1:33828/1‑97 (MQ=255)                                                                                                     gTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTT‑CGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTG‑ACGGGGGTGGTGACACTGTGGGAGCGGGCGTGCCAGCGAAGAGGCCTTCCCTGCTAAt                                          >  8:202998/1‑149 (MQ=37)                                                                                                           aTTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGGCCTCTT‑CGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTG‑ACGGCTGTGGTGACCCTGTGGGAGCGGGCGTGCCCGCGAAGAGGCCTGACCTGCTAATGCAAgg                                    <  6:382341/149‑1 (MQ=255)                                                                                                                        ccTGGATTCTGGGTTGCCTGGGCTGGCCTCTT‑CGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTG‑ACGGCTGTGGTGACCCTGTGGGAGCGGGCGTGCCCGCGAAGAGGCCTGACCTGCTAATGCAAGGTGTGAGGCTCtgt                       >  6:361607/1‑149 (MQ=255)                                                                                                                                 tGGGTTGCCTGGGCTGGCCTCTT‑CGCGGGCACGCCCGCTCCCCCAGGTACTGTGCAGTGCGTG‑GCGGCTGTGGTGACCCTGTGGGAGCGGGCGTGCCCGCGAAGAGGCCTGACCTGCTAATGCAAGGTGTGAGGCTCTGTGGGTAAATg              >  1:79054/1‑149 (MQ=255)                                                                                                                                        ctggggCTGG‑CTGTTGCGGGGGAACGCCCGCTCCCACTTTATTTGTGCTGGGGGTG‑CCGGTGGTGGTCCCCCTGGGGGCGGGGGGGTGCCCGCTAATAGGCCTGACCTGCTAATGCAAGGTGTGAGGCTCTGTGGGTAAATGCGACCGc       <  4:21463/146‑1 (MQ=255)                                                                                                                                        ccTGGGCTGGCCTCTT‑CGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTG‑ACGGCTGTGGTGACCCtgtg                                                                                <  6:244366/76‑1 (MQ=255)                                                                                                                                        ccTGGGCTGGCCTCTT‑CGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTG‑ACGGCTGTGGTGACCCtgtg                                                                                >  5:244366/1‑76 (MQ=255)                                                                                                                                             gctggccTCTT‑CGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTG‑ACGGCTGTGGTGACCCTGTGGGAGCGGGCGTGCCCGCGAAGAGGCCTGACCTGCTAATGCAAGGTGTGAGGCTCTGTGGGTAAATGCGACCGCATCTg  <  3:313044/149‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                  GCAGGGGATGCCGGGTTCGATGCGGAACAGCGGGTGAGTGTTGTTTTCGCCTTGGTAGAAGCAGGTCTTGCCGACTGTGGTGGGTTCTGTTGTGTTGTCGGTGGGCATTGTTTTGTTTCCCTGGATTCTGGGTTGCCTGGGCTGG‑CTCTT‑CGCGGGCACGCCCGCTCCCACAGGTACTGTGCAGTGCGTG‑ACGGCTGTGGTGACCCTGTGGGAGCGGGCGTGCCCGCGAAGAGGCCTGACCTGCTAATGCAAGGTGTGAGGCTCTGTGGGTAAATGCGACCGCATCTG  >  NC_002947/1419404‑1419691

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: ‑