Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,975,496	C→T	13.8%	A115T (GCC→ACC)	PP_2600 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,975,496	0	C	T	13.8%	72.2 / 4.2	29	A115T (GCC→ACC)	PP_2600	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (14/11);  new base T (2/2);  total (16/13)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.72e-01

GTCTTGCGCAAGCGTGGCAGCAGGGCGCCAACCTCGCGGGCATCGTAGGGCGCGGCGATCACCTGGTGGCCGCCAAGGGCTGCGCCTGGCGTATCGCCATGCATGTCCGGGATGCCGTTGCCGTCGGCAAACTGCAACGCCGTGTACTTCTCGAAAAACGCCACCATATGCGGGCACGCCTCAAGGAAGGCATCGACGCGCTCGGCATTGTAGTTTGCCCCCAGCTCATGGCGCAGATAAGTCCGCGGCTGTTCGAT  >  NC_002947/2975369‑2975625                                                                                                                                |                                                                                                                                  gTCTTGCGCAAGCGTGGCAGCAGGGCGCCAACCTCGCGGGCATCGTAGGGCGCGGCGATCACCTGGTGGCCGCCAAGGGCTGCGCCTGGCGTATCGCCATGCATGTCCGGGATGCCGTTGCCGTCGGCAAACTGCa                                                                                                                           <  1:182698/136‑1 (MQ=255)      gcgcAAGCGTGGCAGCAGGGCGCCAACCTCGCGGGCATCGTAGGGCGCGGCGATCACCTGGTGGCCGCCAAGGGCTGCGCCTGGCGTATCGCCATGCATGTCCGGGATGCCGTTGCCGTCGGCAAACTGCAACGcc                                                                                                                      <  2:339608/136‑1 (MQ=255)               tGGCAGCAGGGCGCCAACCTCGCGGGCATCGTAGGGCGCGGCGATCACCTGGTGGCTGCCAAGGGCTGCGCCTGGCGTATCGCCATGCATGTCCGGGATGCCGTTGCCGTCGGCAAACTGCAACGCCGTGTACTtc                                                                                                             >  2:358818/1‑136 (MQ=255)               tGGCAGCAGGGCGCCAACCTCGCGGGCATCGTAGGGCGCGGCGATCACCTGGTGGCCGCCAAGGGCTGCGCCTGGCGTATCGCCATGCATGTCCGGGATGCCGTTGCCGTCGGCAAACTGCAACGCCGTGTACTtc                                                                                                             >  1:229641/1‑136 (MQ=255)               tGGCAGCAGGGCGCCAACCTCGCGGGCATCGTAGGGCGCGGCGATCACCTGGTGGCCGCCAAGGGCTGCGCCTGGCGTATCGCCATGCATGTCCGGGATGCCGTTGCCGTCGGCAAACTGCAACGCCGTGTACTtc                                                                                                             >  1:312159/1‑136 (MQ=255)               tGGCAGCAGGGCGCCAACCTCGCGGGCATCGTAGGGCGCGGCGATCACCTGGTGGCCGCCAAGGGCTGCGCCTGGCGTATCGCCATGCATGTCCGGGATGCCGTTGCCGTCGGCAAACTGCAACGCCGTGTACTtc                                                                                                             >  2:23641/1‑136 (MQ=255)                    gcagGGCGCCAACCTCGCGGGCATCGTAGGGCGCGGCGATCACCTGGTGGCCGCCAAGGGCTGCGCCTGGCGTATCGCCATGCATGTCCGGGATGCCGTTGCCGTCGGCAAACTGCAACGCCGTGTACTTCTCGaa                                                                                                        >  1:84743/1‑136 (MQ=255)                       gggCGCCAACCTCGCGGGCATCGTAGGGCGCGGCGATCACCTGGTGGCCGCCAAGGGCTGCGCCTGGCGTATCGCCATGCATGTCCGGGATGCCGTTGCCGTCGGCAAACTGCAACGCCGTGTACTTCTCGaaaaa                                                                                                     <  2:373700/136‑1 (MQ=255)                                      gggCATCGTAGGGCGCGGCGATCACCTGGTGGCCGCCAAGGGCTGCGCCTGGCGTATCGCCATGCATGTCCGGGATGCCGTTGCCGTCGGCAAACTGCAACGCCGTTTACTTCTCGAAAAACGCCACCATATGCgg                                                                                      <  2:49624/136‑1 (MQ=255)                                              tAGGGCGCGGCGATCACCTGGTGGCCGCCAAGGGCTGCGCCTGGCGTATCGCCATGCATGTCCGGGATGCCGTTGCCGTCGGCAAACTGCAACGCCGTGTACTTCTCGAAAAACGCCACCATATGCGGGCACGccg                                                                              >  2:453346/1‑135 (MQ=255)                                                        cgATCACCTGGTGGCCGCCAAGGGCTGCGCCTGGCGTATCGCCATGCATGTCCGGGATGCCGTTGCCGTCGGCAAACTGCAACGCCGTGTACTTCTCGAAAAACGCCACCATATGCGGGCACGCCTCAAGGAAGGc                                                                    >  2:199518/1‑136 (MQ=255)                                                         gATCACCTGGTGGCCGCCAAGGGCTGCGCCTGGCGTATCGCCATGCATGTCCGGGATGCCGTTGCCGTCGGCAAACTGCAACGCCGTGTACTTCTCGAAAAACGCCACCATATGCGGGCACGCCTCAAGGAAGGCa                                                                   >  1:191166/1‑136 (MQ=255)                                                         gATCACCTGGTGGCCGCCAAGGGCTGCGCCTGGCGTATCGCCATGCATGTCCGGGATGCCGTTGCCGTCGGCAAACTGCAACGCCGTGTACTTCTCGAAAAACGCCACCATATGCGGGCACGCCTCAAGGAAGGCa                                                                   <  1:315299/136‑1 (MQ=255)                                                         gATCACCTGGTGGCCGCCAAGGGCTGCGCCTGGCGTATCGCCATGCATGTCCGGGATGCCGTTGCCGTCGGCAAACTGCAACGCCGTGTACTTCTCGAAAAACGCCACCATATGCGGGCACGCCTCAAGGAAGGCa                                                                   >  1:315050/1‑136 (MQ=255)                                                              ccTGGGGGCCGCCAAGGGCTGCGCCTGGCGTATCGCCATGCATGTCCGGGATGCCGTTGCCGTCGGCAAACTGCAACGCCGTGTACTTCTCGAAAAACGCCACCATATGCGGGCACGCCTCAAGGAAGGCATCGAc                                                              <  1:557600/136‑1 (MQ=255)                                                                     gccgccAAGGGCTGCGCCTGGCGTATCGCCATGCATGTCCGGGATGCCGTTGCCGTCGGCAAACTGCAACGCCGTGTAGTTCTCGAAAAACGCCACCATATGCGGGCACGCCTCAAGGAAGGCCTCGACGCGCTCg                                                       >  2:286657/1‑136 (MQ=255)                                                                        gccAAGGGCTGCGCCTGGCGTATCGCCATGCATGTCCGGGATGCCGTTGCCGTCGGCAAACTGCAACGCCGTGTACTTCTCGAAAAACGCCACCATATGCGGGCACGCCTCAAGGAAGGCATCGACGCGCTCGGCa                                                    >  2:555334/1‑136 (MQ=255)                                                                          cAAGGGCTGCGCCTGGCGTATCGCCATGCATGTCCGGGATGCCGTTGCCGTCGGTAAACTGCAACGCCGTGTACTTCTCGAAAAACGCCACCATATGCGGGCACGCCTCAAGGAAGGCATCGAcgc                                                            <  1:331483/126‑1 (MQ=255)                                                                          cAAGGGCTGCGCCTGGCGTATCGCCATGCATGTCCGGGATGCCGTTGCCGTCGGTAAACTGCAACGCCGTGTACTTCTCGAAAAACGCCACCATATGCGGGCACGCCTCAAGGAAGGCATCGAcgc                                                            <  1:329763/126‑1 (MQ=255)                                                                          cAAGGGCTGCGCCTGGCGTATCGCCATGCATGTCCGGGATGCCGTTGCCGTCGGTAAACTGCAACGCCGTGTACTTCTCGAAAAACGCCACCATATGCGGGCACGCCTCAAGGAAGGCATCGAcgc                                                            >  2:329763/1‑126 (MQ=255)                                                                          cAAGGGCTGCGCCTGGCGTATCGCCATGCATGTCCGGGATGCCGTTGCCGTCGGTAAACTGCAACGCCGTGTACTTCTCGAAAAACGCCACCATATGCGGGCACGCCTCAAGGAAGGCATCGAcgc                                                            >  2:331483/1‑126 (MQ=255)                                                                              ggCTGCGCCTGGCGTATCGCCATGCATGTCCGGGATGCCGTTGCCGTCGGCAAACTGCAACGCCGTGTACTTCTCGAAAAACGCCACCATATGCGGGCACGCCTCAAGGAAGGCATCGACGCGCTCGGCATTGTAg                                              <  2:138753/136‑1 (MQ=255)                                                                                               cGCCATGCATGTCCGGGATGCCGTTGCCGTCGGCAAACTGCAACGCCGTGTACTTCTCGAAAAACGCCACCATATGCGGGCACGCCTCAAGGAAGGCATCGACGCGCTCGGCATTGTAGTTTGCCCCCAGCTCATg                             <  2:389199/136‑1 (MQ=255)                                                                                                    tgcatgCCCGGGATGCCGTTGCCGTCGGCAAACTGCAACGCCGTGTACTTCTCGAAAAACGCCACCATATGCGGGCACGCCTCAAGGAAGGCATCGACGCGCTCGGCATTGTAGTTTGCCCCCAGCTCATGGCGCa                        <  1:374722/136‑1 (MQ=255)                                                                                                      catgTCCGGGATGCCGTTGCCGTCGGCAAACTGCAACGCCGTGTACTTCTCGAAAAACGCCACCATATGCGGGCACGCCTCAACGAAGGCATCGACGCGCACGGCATTGTAGTTTGCCCCCAGCTCAAGGCGCAGa                      >  2:189455/1‑136 (MQ=255)                                                                                                              ggATGCCGTTGCCGTCGGCAAACTGCAACGCCGTGTACTTCTCGAAAAACGCCACCATATGCGGGCACGCCTCaa                                                                           <  1:86381/75‑1 (MQ=255)                                                                                                              ggATGCCGTTGCCGTCGGCAAACTGCAACGCCGTGTACTTCTCGAAAAACGCCACCATATGCGGGCACGCCTCaa                                                                           >  2:86381/1‑75 (MQ=255)                                                                                                                       tgccgtCGGCAAACTGCAACGCCGTGTACTTCTCGAAAAACGCCACCATATGCGGGCACGCCTCAAGGAAGGCATCGACGCGCTCGGCATTGTAGTTTGCCCCCAGCTCATGGCGCAGATAAGTCCGCGGCTGTTc     >  2:325036/1‑136 (MQ=255)                                                                                                                          cgtCGGCAAACTGCAACGCCGTGTACTTCTCGAAAAACGCCACCATATGCGGGCACGCCTCAAGGAAGGCATCGACGCGCTCGGCATTGTAGTTTGCCCCCAGCTCATGGCGCAGATAAGTCCGCGGCTGTTCGAt  <  1:306809/136‑1 (MQ=255)                                                                                                                                |                                                                                                                                  GTCTTGCGCAAGCGTGGCAGCAGGGCGCCAACCTCGCGGGCATCGTAGGGCGCGGCGATCACCTGGTGGCCGCCAAGGGCTGCGCCTGGCGTATCGCCATGCATGTCCGGGATGCCGTTGCCGTCGGCAAACTGCAACGCCGTGTACTTCTCGAAAAACGCCACCATATGCGGGCACGCCTCAAGGAAGGCATCGACGCGCTCGGCATTGTAGTTTGCCCCCAGCTCATGGCGCAGATAAGTCCGCGGCTGTTCGAT  >  NC_002947/2975369‑2975625

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑