Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,542,851	G→C	14.8%	S104T (AGC→ACC)	PP_2235 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,542,851	0	G	C	14.8%	62.0 / 5.8	27	S104T (AGC→ACC)	PP_2235	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (11/12);  new base C (2/2);  total (13/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.38e-01

GCTGCCGGGTGTTGCAGTACCTGCAATGGCAGTCACGCCAGGCCTGGGCTGCGGCGGCCGTGCACTTCGTCGAGGAATCGTTTCTTGACCTGCTGGGCCAGCATCAGGCACGCGGTGTCAACTTCGCCGCCTACCAGGCCCTGCGCAGCCTGGTGCGCGGGGACGATGGCGTGCTGCATTGCCAGATGGGCGGTCCTCAGGCATACCAAGGTGCGTAGTGCGGGTAGCGATCCAGGCGGGCACCGATGACCATTTCGCTGATCCATGCCGCCAGGAGCGAGCTATACGCTTTCTGG  >  NC_002947/2542704‑2542999                                                                                                                                                    |                                                                                                                                                     gCTGCCGGGTGTTGCAGTACCTGCAATGGCAGTCACGCCAGGCCTGGGCTGCGGCGGCCGTGCACTTCGTCGAGGAATCGTTTCTTGACCTGCTGGGCCAGCATCAGGCACGCGGTGTCAACTTCGCCGCCTACCAGGCCCTGCGCAGc                                                                                                                                                     <  8:104166/149‑1 (MQ=255)            ttGCAGTACCTGCAATGGCAGTCACGCCAGGCCTGGGCTGCGGCGGCCGTGCACTTCGTCGAGGAATCGTTTCTTGACCTGCTGGGCCAGCATCAGGCACGCGGTGTCAACTTCGCCGCCTACCAGGCCCTGCGCAGCCTGGTGCGCgg                                                                                                                                          <  3:106628/149‑1 (MQ=255)                           tGGCAGTCACGCCAGGCCTGGGCTGCGGCGGCCGTGCACTTCGTCGAGGAATCGTTTCTTGACCTGCTGGGCCAGCATCAGGCACGCGGTGTCAACTTCGCCGCCTACCAGGCCCTGCGCAGCCTGGTGCGCGGGGACGATGGCGtgct                                                                                                                           >  7:154692/1‑149 (MQ=255)                                      ccAGGCCTGGGCTGCGGCGGCCGTGCACTTCGTCGAGGAATCGTTTCTTGACCTGCTGGGCCAGCATCAGGCACGCGGTGTCAACTTCGCCGCCTACCAGGCCCTGCGCAGCCTGGTGCGCGGGGACGATGGCGTGCTGCATTGCCAGa                                                                                                                <  3:2304/149‑1 (MQ=255)                                                  tGCGGCGGCCGTGCACTTCGTCGAGGAATCGTTTCTTGACCTGCTGGGCCAGCATCAGGCACGCGGTGTCAACTTCGCCGCCTACCAGGCCCCGCGCACCAGGCTGCGCagggc                                                                                                                                       <  4:39722/114‑2 (MQ=255)                                                  tGCGGCGGCCGTGCACTTCGTCGAGGAATCGTTTCTTGACCTGCTGGGCCAGCATCAGGCACGCGGTGTCAACTTCGCCGCCTACCAGGCCCCGCGCACCAGGCTGCGCagggc                                                                                                                                       >  3:39722/1‑113 (MQ=255)                                                     ggcggcCGTGCACTTCGTCGAGGAATCGTTTCTTGACCTGCTGGGCCAGCATCAGGCACGCGGTGTCAACTTCGCCGCCTACCAGGCCCTGCGCAGCCTGGTGCGCGGGGACGATGGCGTGCTGCAtt                                                                                                                      >  4:20624/1‑128 (MQ=255)                                                     ggcggcCGTGCACTTCGTCGAGGAATCGTTTCTTGACCTGCTGGGCCAGCATCAGGCACGCGGTGTCAACTTCGCCGCCTACCAGGCCCTGCGCAGCCTGGTGCGCGGGGACGATGGCGTGCTGCAtt                                                                                                                      <  3:20624/128‑1 (MQ=255)                                                      gcggcCGTGCACTTCGTCGAGGAATCGTTTCTTGACCTGCTGTGCCAGCATCAGGCACGCGGTGTCAACTTCGCCGCCTACCAGGCCCTGCGCAGCCTGGTGCGCGGGGACGATGGCGTGCTGCATTGCCAGATGGGCGGTCCTCAgg                                                                                                 >  4:102253/1‑148 (MQ=255)                                                        ggcCGTGCACTTCGTCGAGGAATCGTTTCTTGACCTGCTGGGCCAGCATCAGGCACGCGGTGTCAACTTCGCCGCCTACCAGGCCCTGCGCAGCCTGGTGCGCGGGGACGATGGCGTGCTGCATTGCCAGATGGGCGGTCCTCAGGCAt                                                                                              <  8:154692/149‑1 (MQ=255)                                                                  ttCGTCGAGGAATCGTTTCTTGACCTGCTGGGCCAGCATCAGGCACGCGGTGTCAACTTCGCCGCCTACCAGGCCCTGCGCAGCCTGGTGCGCGGGGACGATGGCGTGCTGCATTGCCAGATGGGCGGTCCTCAGGCATACCAAGGTGc                                                                                    >  1:305210/1‑149 (MQ=255)                                                                                gTTTCTTGACCTGCTGGGCCAGCATCAGGCACGCGGTGTCAACTTCGCCGCCTACCAGGCCCTGCGCAGCCTGGTGCGCGGGGACGATGGCGTGCTGCATTGCCAGATGGGCGGTCCTCAGGCATACCAAGGTGCGTAGTGCGGGTAg                                                                       <  2:305210/148‑1 (MQ=255)                                                                                 tttCTTGACCTGCTGGGCCAGCATCAGGCACGCGGTGTCAACTTCGCCGCCTACCAGGCCCTGCGCAGCCTGGTGCGCGGGGACGATGGCGTGCTGCATTGCCAGAt                                                                                                               >  1:79916/1‑107 (MQ=255)                                                                                 tttCTTGACCTGCTGGGCCAGCATCAGGCACGCGGTGTCAACTTCGCCGCCTACCAGGCCCTGCGCAGCCTGGTGCGCGGGGACGATGGCGTGCTGCATTGCCAGAt                                                                                                               <  2:79916/107‑1 (MQ=255)                                                                                 tttCTTGACCTGCTGGGCCAGCATCAGGCACGCGGTGTCAACTTCGCCGCCTACCAGGCCCCGCGCACCAGGCTGCGCaggg                                                                                                                                        >  6:315719/1‑82 (MQ=37)                                                                                 tttCTTGACCTGCTGGGCCAGCATCAGGCACGCGGTGTCAACTTCGCCGCCTACCAGGCCCCGCGCACCAGGCTGCGCaggg                                                                                                                                        <  5:315719/82‑1 (MQ=37)                                                                                       gACCTGCTGGGCCAGCATCAGGCAGGCGGTGTCAACTTCGCCGCCTACCAGGCCCTGCGCAGCCTGGTGCGCGGGGACGATGGCGTGCTGCATTGCCAGATGGGCGGTCCTCAGGCATACCAAGGTGCGTAGTGCGGGTAGCGATCCAg                                                               >  5:98729/1‑149 (MQ=255)                                                                                          ctgctgGGCCAGCATCAGGCACGCGGTGTCAACTTCGCCGCCTACCAGGCCCTGCGCAGCCTGGTGCGCGGGGACGATGGCGTGCTGCATTGCCAGATGGGCGGTCCTCAGGCATACCAAGGTGCGTAGTGCGGGTAGCGATCCAGGCg                                                            >  6:118534/1‑149 (MQ=255)                                                                                                              aCGCGGTGTCAACTTCGCCGCCTACCAGGCCCTGCGCAGCCTGGTGCGCGGGGACGATGGCGTGCTGCATTGCCAGATGGGCGGTCCTCAGGCATACCAAGGTGCGTAGTGCGGGTAGCGATCCAGGCGGGCACCGATGACCATTTCGc                                        <  3:102253/149‑1 (MQ=255)                                                                                                                         aCTTCGCCGCCTACCAGGCCCTGCGCAGCCTGGTGCGCGGGGACGATGGCGTGCTGCATTGCCAGATGGGCGGTCCTCAGGCATACCAAGGTGCGTAGTGCGGGTAGCGATCCAGGCGGGCACCGATGACCATTTCGCTGATCCATgcc                             >  4:89283/1‑149 (MQ=255)                                                                                                                          cTTCGCCGCCTACCAGGCCCTGCGCAGCCTGGTGCGCGGGGACGATGGCGTGCTGCATTGCCAGATGGGCGGTCCTCAGGCATACCAAGGTGCGTAGTGCGGGTAGCGATCCAGGCGGGCACCGATGACCATTTCGCTGATCCATgccg                            >  3:139960/1‑149 (MQ=255)                                                                                                                              gccgccTACAAGGCCCTGCGCAGCCTGGAGCGCGGGGACGATCGCGTGCTGCATTGCCAGATGGGCGGTCCTCAGGCATACCAAGGTGCGTAGTGCGGGTAGCGATCCAGGCGGGCACCGATGACCATTTCGCTGATCCATGCCGCCAg                        >  7:230507/1‑149 (MQ=255)                                                                                                                                  ccTACCAGGCCCTGCGCAGCCTGGTGCGCGGGGACGATGGCGTGCTGCATTGCCAGATGGGCGGTCCTCAGGCATACCAAGGTGCGTAGTGCGGGTAGCGATCCAGGCGGGCACCGATGACCATTTCGCTGATCCATGCCGCCAGgagc                    <  4:139960/149‑1 (MQ=255)                                                                                                                                      ccAGGCCCTGCGCAGCCTGGTGCGCGGGGACGATGGCGTGCTGCATTGCCAGATGGGCGGTCCTCAGGCATACCAAGGTGCGTAGTGCGGGTAGCGATCCAGGCGGGCACCGATGACCATTTCGCTGATCCATGCCGCCAGgagcga                  <  8:230507/147‑1 (MQ=255)                                                                                                                                         agCCCTGCGCAGCCTGGTGCGCGGGGACGATGGCGTGCTGCATTGCCAGATGGGCGGTCCTCAGGCATACCAAGGTGCGTAGTGCGGGTAGCGATCCAGGCGGGCACCGATGACCATTTCGCTGATCCATGCCGCCAGGAGCGAGCtat             <  5:18721/148‑1 (MQ=255)                                                                                                                                             cTGCGCAGCCTGGTGCGCGGGGACGATGGCGTGCTGCATTGCCAGATGGGCGGTCCTCAGGCATACCAAGGTGCGTAGTGCGGGTAGCGATCCAGGCGGGCACCGATGACCATTTCGCTGATCCATGCCGCCAGGAGCGAGCTATACGc         >  1:153202/1‑149 (MQ=255)                                                                                                                                                cgcAGCCTGGTGCGCGGGGACGATGGCGTGCTGCATTGCCAGATGGGCGGTCCTCAGGCATACCAAGGTGCGTAGTGCGGGTAGCGATCCAGGCGGGCACCGATGACCATTTCGCTGATCCATGCCGCCAGGAGCGAGCTATACGCt        <  5:118534/147‑1 (MQ=255)                                                                                                                                                    gCCTGGTGCGCGGGGACGATGGCGTGCTGCATTGCCAGATGGGCGGTCCTCAGGCATACCAAGGTGCGTAGTGCGGGTAGCGATCCAGGCGGGCACCGATGACCATTTCGCTGATCCATGCCGCCAGGAGCGAGCTATACGCTTTCTgg  <  3:89283/149‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                     GCTGCCGGGTGTTGCAGTACCTGCAATGGCAGTCACGCCAGGCCTGGGCTGCGGCGGCCGTGCACTTCGTCGAGGAATCGTTTCTTGACCTGCTGGGCCAGCATCAGGCACGCGGTGTCAACTTCGCCGCCTACCAGGCCCTGCGCAGCCTGGTGCGCGGGGACGATGGCGTGCTGCATTGCCAGATGGGCGGTCCTCAGGCATACCAAGGTGCGTAGTGCGGGTAGCGATCCAGGCGGGCACCGATGACCATTTCGCTGATCCATGCCGCCAGGAGCGAGCTATACGCTTTCTGG  >  NC_002947/2542704‑2542999

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: ‑