Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,612,184	T→A	11.8%	S375T (TCC→ACC)	PP_2287 →	internal core protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,612,184	0	T	A	11.8%	79.3 / 4.0	34	S375T (TCC→ACC)	PP_2287	internal core protein
Reads supporting (aligned to +/- strand):  ref base T (15/15);  new base A (2/2);  total (17/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.05e-01

CCGATACAACCCGCTCCGCACGGATGACGACCTGTACATCTCCGCTGCGATGGGCCTGGGCCTCGGGGCCATTGGCGGTAGCCTCGCTCACGTAGAGGGGCCGCTGGCTGAGGAAAACGCCCGCCTGGCCCAGTGGGGCCGCCAGGAGTCCAGCGGGGCGCAAATCAAGGAGCTTACCGATTCGGGCCTCATGCGCCCCGGTGAAGGCGCGCTGAGCCAGCCTGAGTTTCTCCGCAGGTTCGGCCAGGACGTGGACACGAAGAACACCCCTGGCAACGCCATTATCTG  >  NC_002947/2612036‑2612323                                                                                                                                                     |                                                                                                                                            ccGATACAACCCGCTCCGCACGGATGACGACCTGTACATCTCCGCTGCGATGGGCCTGGGCCTCGGGGCCATTGGCGGTAGCCTCGCTCACGTAGAGGGGCCGCTGGCTGAGGAAAACGCCCGCCTGGCCCAGTGGGGCCGCCAGGAGt                                                                                                                                             >  1:171707/1‑149 (MQ=255)    aTACAACCCGCTCCGCACGGATGACGACCTGTACATCTCCGCTGCGATGGGCCTGGGCCTCGGGGCCATTGGCGGTAGCCTCGCTCACGTAGAGGGGCCGCTGGCTGAGGAAAACGCCCGCCTGGCCCAGTGGGGCCGCCAGGAGTc                                                                                                                                            >  6:45840/1‑147 (MQ=255)          cccGCTCCGCACGGATGACGACCTGTACATCTCCGCTGCGATGGGCCTGGGCCTCGGGGCCATTGGCGGTAGCCTCGCTCACGTAGAGGGGCCGCTGGCTGAGGAAAACGCCCGCCTGGCCCAGTGGGGCCGCCAGGAGTCCAGCgggg                                                                                                                                    >  1:117753/1‑149 (MQ=255)                     cGGATGACGACCTGTCCATCTCCGCTGCGAGGGGCCTGGGCCTCGGGGCCATTGGCGGTAGCCTCGCTCACGTAGAGGGGCCGCTGGCTGAGGAAAACGCCCGCCTGGCCCAGTGGGGCCGCCAGGAGTCCAGCGGGGCGCAAATCAAg                                                                                                                         <  1:96503/149‑1 (MQ=255)                       gATGACGACCTGTACATCTCCGCTGCGATGGGCCTGGGCCTCGGGGCCATTGGCGGTAGCCTCGCTCACGTAGAGGGGCCGCTGGCTGAGGAAAACGCCCGCCTGGCCCAGTGGGGCCGCCAGGAGTCCAGCGGGGCGCAAATCAAGGa                                                                                                                       <  8:79450/149‑1 (MQ=255)                         tGACGACCTGTACATCTCCGCTGCGATGGGCCTGGGCCTCGGGGCCATTGGCGGTAGCCTCGCTCACGTAGAGGGGCCGCTTGATGAGGAAAACGCCCGCCTGGCCAACTGGGGACGCCAGGAGTCCAGCGGGGCGCAAATCAAGGAGc                                                                                                                     >  5:3371/1‑149 (MQ=255)                            cgacCTGTACATCTCCGCTGCGATGGGCCTGGGCCTCGGGGCCATTGGCGGTAGCCTCGCTCACGTAGAGGGGCCGCTGGCTGAGGAAAACGCCCGCCTGGCCCAGTGGGGCCGCCAGGAGTCCAGCGGGGCGCAAATCAAGGAGCTTa                                                                                                                  >  4:78168/1‑149 (MQ=255)                                  gTACATCTCCGCTGCGATGGGCCTGGGCCTCGGGGCCATTGGCGGTAGCCTCGCTCACGTAGAGGGGCCGCTGGCTGAGGAAAACGCCCGCCTGGCCCAGTGGGGCCGCCAGGAGTCCAGCGGGGCGCAAATCAAGGAGCTTAc                                                                                                                 >  4:193878/1‑144 (MQ=255)                                  gTACATCTCCGCTGCGATGGGCCTGGGCCTCGGGGCCATTGGCGGTAGCCTCGCTCACGTAGAGGGGCCGCTGGCTGAGGAAAACGCCCGCCTGGCCCAGTGGGGCCGCCAGGAGTCCAGCGGGGCGCAAATCAAGGAGCTTAc                                                                                                                 <  3:193878/144‑1 (MQ=255)                                          ccGCTGCGATGGGCCTGGGCCTCGGGGCCATTGGCGGTAGCCTCGCTCACGTAGAGGGGCCGCTGGCTGAGGAAAACGCCCGCCTGGCCCAGTGGGGCCGCCAGGAGTCCAGCGGGGCGCAAATCAAGGAGCTTACCGATTCGGGCCt                                                                                                     >  2:134740/1‑148 (MQ=255)                                                  aTGGGCCTGGGCCTCGGGGCCATTGGCGGTAGCCTCGCTCACGTAGAGGGGCCGCTGGCTGAGGAAAACGCCCGCCTGGCCCAGTGGGGCCGCCAGGAGACCAGCGGGGCGCAAATCAAGGAGCTTACCGATTCGGGCCTCATGCGccc                                                                                            >  6:165275/1‑149 (MQ=255)                                                  aTGGGCCTGGGCCTCGGGGCCATTGGCGGTAGCCTCGCTCACGTAGAGGGGCCGCTGGCTGAGGAAAACGCCCGCCTGGCCCAGTGGGGCCGCCAGGAGACCAGCGGGGCGCAAATCAAGGAGCTTACCGATTCGGGCCTCATGCGcca                                                                                            >  6:161509/1‑148 (MQ=255)                                                    gggcctgtgcctGGGGGCCATTGGCGGTAGCCTCGCTCACGTAGAGGGGCCGCTGGCTGAGGAAAACGCCCGCCTGGCCCAGTGGGGCCGCCAGGAGTCCAGCGGGGCGCAAATCAAGCAGCTTACCGATTCGGGCCTCATGCGcccc                                                                                           <  8:72509/148‑1 (MQ=255)                                                             cctCGGGGCCATTGGCGGTAGCCTCGCTCACGTAGAGGGGCCGCTGGCTGAGGAAAACGCCCGCCTGGCCCAGTGGGGCCGCCAGGAGTCCAGCGGGGCGCAAATCAAGGAGCTTACCGATTCGGGCCTCATGCGCCCCGGTGAAGgcg                                                                                 <  5:45840/149‑1 (MQ=255)                                                             cctCGGGGCCATTGGCGGTAGACTCGCTCACGTAGAGGGGCCGCTGGCTGAGGAAAACGCCCGCCTGGCCCAGTGGGGCCGCCAGGAGTCCAGCGGGGCGCAAATCAAGGAGCTTACCGATTCGGGCCTCATGCGCCCCGGTGAAGgcg                                                                                 >  1:194643/1‑149 (MQ=255)                                                                   ggCCATTGGCGGTAGCCTCGCTCACGTAGAGGGGCCGCTGGCTGAGGAAAACGCCCGCCTGGCCCAGTGGGGCCGCCAGGAGTCCAGCGGGGCGCAAATCAAGGAGCTTACCGATTCGGGCCTCATGCGCCCCGGTGAAGGCGCGCTGa                                                                           <  3:78168/149‑1 (MQ=255)                                                                             ggTAGCCTCGCTCACGTAGAGGGGCCGCTGGCTGAGGAAAACGCCCGCCTGGCCCAGTGGGGCCGCCAGGAGTCCAGCGGGGCGCAAATCAAGGAGCTTACCGATTCGGGCCTCATGCGCCCCGGTGAAGGCGCGCTGAGCCAGCCTGa                                                                 <  2:117753/149‑1 (MQ=255)                                                                                    tCGCTCACGTAGAGGGGCCGCTGGCTGAGGAAAACGCCCGCCTGGCCCAGTGGGGCCGCCAGGAGTCCAGCGGGGCGCAAATCAAGGAGCTTACCGATTCGGGCCTCATGCGCCCCGGTGAAGGCGCGCTGAGCCAGCCTGAGTTtctc                                                          >  1:137270/1‑149 (MQ=255)                                                                                           cGTAGAGGGGCCGCTGGCTGAGGAAAACGCCCGCCTGGCCCAGTGGGGCCGCCAGGAGTCCAGCGGGGCGCAAATCAAGGAGCTTACCGATTCGGGCCTCATGCGCCCCGGTGAAGGCGCGCTGAGCCAGCCTGAGTTTCTCCGCAGGt                                                   <  2:171707/149‑1 (MQ=255)                                                                                            gTAGAGGGGCCGCTGGCTGAGGAAAACGCCCGCCTGGCCCAGTGGGGCCGCCAGGAGTCCAGCGGGGCGCAAATCAAGGAGCTTACCGATTCGGGCCTCATGCGCCCCGGTGAAGGCGCGCTGAGCCAGCCTGAGTTTCTCCGCAGGtt                                                  >  2:178437/1‑149 (MQ=255)                                                                                                agGGGCCGCTGGCTGAGGAAAAGGCCCGCCTGGCCCAGTGGGGCCGCCAGGAGACCAGCGGGGCGCAAATCAAGGAGCTTACCGATTCGGGCCTCATGCGCCCCGGTGAAGGCGCGCTGAGCCAGCCTGAGTTTCTCCGCAGGTTCGGc                                              <  5:161509/149‑1 (MQ=255)                                                                                                agGGGCCGCTGGCTGAGGAAAACGCCCGCCTGGCCCAGTGGGGCCGCCAGGAGACCAGCGGGGCGCAAATCAAGGAGCTTACCGATTCGGGCCTCATGCGCCCCGGTGAAGGCGCGCTGAGCCAGCCTGAGTTTCTCCGCAGGTTCGGc                                              <  5:165275/149‑1 (MQ=255)                                                                                                agGGGCCGCTGGCTGAGGAAAACGCCCGCCTGGCCATGTGGGGCCGCCAGGAGTCCAGCGTGGCGCAAATAAAGGAGCTTACCGATTCGGGCCTAATGCGCCCCGGTGAAGGAGCGCTGAGCCAGCCTTATTTTCTCCGCAGGTTCGGc                                              <  6:3371/149‑1 (MQ=255)                                                                                                    gCCGCTGGCTGAGGAAAACGCCCGCCTGGCCCAGTGGGGCCGCCAGGAGTCCAGCGGGGCGCAAATCAAGGAGCTTACCGATTCGGGCCTCATGCGCCCCGGTGAAGGCGCGCTGAGCCAGCCTGAGTTTCTCCGCAGGTTCGGCCAgg                                          <  4:74975/149‑1 (MQ=255)                                                                                                                 gAAAACGCCCGCCTGGCCCAGTGGGGCCGCCAGGAGTCCAGCGGGGCGCAAATCAAGGAGCTTACCGATTCGGGCCTCATGCGCCCCGGTGAAGGCGCGCTGAGCCAGCCTGAGTTTCTCCGCAGGTTCGGCCAGGACGTgg                                    >  5:253400/1‑142 (MQ=255)                                                                                                                 gAAAACGCCCGCCTGGCCCAGTGGGGCCGCCAGGAGTCCAGCGGGGCGCAAATCAAGGAGCTTACCGATTCGGGCCTCATGCGCCCCGGTGAAGGCGCGCTGAGCCAGCCTGAGTTTCTCCGCAGGTTCGGCCAGGACGTgg                                    <  6:253400/142‑1 (MQ=255)                                                                                                                 gAAAACGCCCGCCTGGCCCAGTGGGGCCGCCAGGAGTCCAGCGGGGCGCAAATCAAGGAGCTTACCGATTCGGGCCTCATGCGCCCCGGTGAAGGCGCGCTGAGCCAGCCTGAGTTTCTCCGCAGGTTCGGCCAGGACGTGGACACgaa                             <  1:134740/149‑1 (MQ=255)                                                                                                                                   cAGTGGGGCCGCCAGGAGTCCAGCGGGGCGCAAATCAAGGAGCTTACCGATTCGGGCCTCATGCGCCCCGGTGAAGGCGCGCTGAGCCAGCCTGAGTTTCTCCGCAGGTTCGGCCAGGACGTGGACACGAAGAACACCCCTGGCAACGc           >  7:156152/1‑149 (MQ=255)                                                                                                                                      tGGGGCCGCCAGGAGTCCAGCGGGGCGCAAATCAAGGAGCTTACCGATTCGGGCCTCATGCGCCCCGGTGAAGGCGCGCTGAGCCAGCCTGAGTTTCTCCGCAGGTTCGGCCAGGACGTGGACACGAAGAACACCCCTGGCAACGCCAt        <  8:156152/149‑1 (MQ=255)                                                                                                                                        gggCCGCCAGGAGTCCAGCGGGGCGCAAATCAAGGAGCTTACCGATTCGGGCCTCATGCGCCCCGGTGAAGGCGCGCTGAGCCAGCCTGAGTTTCTCCGCAGGTTCGGCCAGGACGTGGACACGAAGCACAGCCCTGGCAACGCCATTa      >  8:93477/1‑149 (MQ=255)                                                                                                                                            cgccAGGAGTCCAGCGGGGCGCAAATCAAGGAGCTTACCGATTCGGGCCTCATGCGCCCCGGTGAAGGCGCGCTGAGCCAGCCTGAGTTTCTCCGCAGGTTCGGCCAGGACGTGGACACGAAGAACACCCCTGGCAACGCCATTATCTg  >  6:162398/1‑149 (MQ=255)                                                                                                                                             gccAGGAGTCCAGCGGGGCGCAAATCAAGGAGCTTACCGATTCGGGCCTCATGCGCCCCGGTGAAGGCGCGCTGAGCCAGCCTGAGTTTCTCCGCAGGTTCGGCCAGGACGTGGACACGAAGAac                         <  4:196311/125‑1 (MQ=255)                                                                                                                                             gccAGGAGTCCAGCGGGGCGCAAATCAAGGAGCTTACCGATTCGGGCCTCATGCGCCCCGGTGAAGGCGCGCTGAGCCAGCCTGAGTTTCTCCGCAGGTTCGGCCAGGACGTGGACACGAAGAac                         >  3:196311/1‑125 (MQ=255)                                                                                                                                                aGGAGTCCAGCGGGGCGCAAATCAAGGAGCTTACCGATTCGGGCCTCATGCGCCCCGGTGAAGGCGCGCTGAGCCAGCCTGAGTTTCTCCGCAGGTTCGGCCAGGACGTGGACACGAAGAACACCCCTg                  <  6:181768/129‑1 (MQ=255)                                                                                                                                                aGGAGTCCAGCGGGGCGCAAATCAAGGAGCTTACCGATTCGGGCCTCATGCGCCCCGGTGAAGGCGCGCTGAGCCAGCCTGAGTTTCTCCGCAGGTTCGGCCAGGACGTGGACACGAAGAACACCCCTg                  >  5:181768/1‑129 (MQ=255)                                                                                                                                                     |                                                                                                                                            CCGATACAACCCGCTCCGCACGGATGACGACCTGTACATCTCCGCTGCGATGGGCCTGGGCCTCGGGGCCATTGGCGGTAGCCTCGCTCACGTAGAGGGGCCGCTGGCTGAGGAAAACGCCCGCCTGGCCCAGTGGGGCCGCCAGGAGTCCAGCGGGGCGCAAATCAAGGAGCTTACCGATTCGGGCCTCATGCGCCCCGGTGAAGGCGCGCTGAGCCAGCCTGAGTTTCTCCGCAGGTTCGGCCAGGACGTGGACACGAAGAACACCCCTGGCAACGCCATTATCTG  >  NC_002947/2612036‑2612323

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: ‑