Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,768,275	C→A	13.7%	P97Q (CCG→CAG)	PP_5600 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,768,275	0	C	A	13.7%	96.0 / 5.2	36	P97Q (CCG→CAG)	PP_5600	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (19/12);  new base A (3/2);  total (22/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGGCCGACAGCAGCGGCATGGTCCAAGGTGAGCAAGACTTCAGCGATCCGACCCTGTCTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTCCCGCTTCGCTTCTCGCGTTCTGACATCGCCACGTCCCCGTGCCGCCTGATCGG  >  NC_002947/3768128‑3768405                                                                                                                                                    |                                                                                                                                    cGGCCGACAGCAGCGGCATGGTCCAAGGTGAGCAAGACTTCAGCGATCCGACCCTGTCTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCg                                                                                                                                    <  6:158965/149‑1 (MQ=255)              cGGCATGGTCCAAGGTGAGTAAGACTTCAGCGATCCGACCCTGTCCGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTAc                                                                                                                      <  1:238490/149‑1 (MQ=255)                                  aaGACTTCAGCGATCCGACCCTGTCTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCCCGc                                                                                                  >  6:241179/1‑149 (MQ=255)                                  aaGACTTCAGCGATCCGACCCTGTCTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGc                                                                                                  <  5:61000/149‑1 (MQ=255)                                    gACTTCAGCGATCCGACCCTGTCTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACccaac                                                                                                                 <  3:125842/132‑1 (MQ=255)                                    gACTTCAGCGATCCGACCCTGTCTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACccaac                                                                                                                 >  4:125842/1‑132 (MQ=255)                                     aCTTCAGCGATCCGACCCTGTCTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTg                                                                                               >  5:77240/1‑149 (MQ=255)                                           gCGATCCGACCCTGTCTGCCGGCGGTTACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAag                                                                                         >  1:7976/1‑149 (MQ=255)                                              aTCCGACCCTGTCTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAagcag                                                                                      <  6:77240/149‑1 (MQ=255)                                               tCCGACCCTGTCTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAagcagc                                                                                     >  5:228737/1‑149 (MQ=255)                                                     ccTGTCTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGCGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGc                                                                               >  7:234519/1‑149 (MQ=255)                                                       tGTCTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCCACCAACCTCCGCCCCGCCTGCCCCAGCAGCGCTGGCCa                                                                             >  3:261095/1‑149 (MQ=255)                                                          cTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAgcg                                                                                    >  8:212380/1‑139 (MQ=255)                                                          cTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAgcg                                                                                    <  7:212380/139‑1 (MQ=255)                                                              cggcggTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCAGGG‑CAGCCGCTTACCCAACCAACCTCCGcc                                                                                                      >  1:220570/1‑117 (MQ=255)                                                              cggcggTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCAGGG‑CAGCCCCTTACCCAACCAACCTCCGcc                                                                                                      >  1:217593/1‑117 (MQ=255)                                                              cggcggTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCAGGG‑CAGCCCCTTACCCAACCAACCTCCGcc                                                                                                      <  2:220570/117‑1 (MQ=255)                                                              cggcggTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCAGGG‑CAGCCCCTTACCCAACCAACCTCCGcc                                                                                                      <  2:217593/117‑1 (MQ=255)                                                                    tGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATcccc                                                                <  6:228737/149‑1 (MQ=255)                                                                           gTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCctc                                                         <  2:157867/149‑1 (MQ=255)                                                                                  ccAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTCCcgct                                                  >  4:87/1‑149 (MQ=255)                                                                                   cAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTCCcgctt                                                 >  8:148928/1‑149 (MQ=255)                                                                                     gCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCCATCCCCGCGCCTCTCCcgcttcg                                               >  6:68207/1‑149 (MQ=255)                                                                                     gCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCctc                                                         <  5:71230/139‑1 (MQ=255)                                                                                     gCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCctc                                                         >  6:71230/1‑139 (MQ=255)                                                                                                     acTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTCCCGCTTCGCTTCTCGCGTTCTGa                                >  4:154816/1‑148 (MQ=255)                                                                                                           ggCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTCCCGCTTCGCTTCTCGCGTTCTGACATCGc                          >  7:221328/1‑148 (MQ=255)                                                                                                            gCCGGCTTTTTGGGCCTGCTGAGCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGGTGGCCACTGGTCAATCCCCGCGCCTCTCCCGCTTCGCTTCTCGCGTTCTGACATCGcc                         <  4:23037/148‑1 (MQ=255)                                                                                                                 cTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTCCCGCTTCGCTTCTCGCGTTCTGACATCGCCACGTcc                   >  2:13014/1‑149 (MQ=255)                                                                                                                  tttttCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTCCCGCTTCGCTTCTCGCGTTCTGACATCGCCACGTccc                  >  2:62568/1‑149 (MQ=255)                                                                                                                    tttCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTCCCGCTTCGCTTCTCGCGTTCTGACATCGCCACGTcccc                 <  8:221328/148‑1 (MQ=255)                                                                                                                    tttCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTCCCGCTTCGCTTCTCGCGTTCTGACATCGCCACGTCCCCg                >  2:171893/1‑149 (MQ=255)                                                                                                                           ctgctgACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTCCCGCTTCGCTTCTCGCCTTCTGACATCGCCACGTCCCCGTgccgc          >  6:26449/1‑148 (MQ=255)                                                                                                                               ctgcccGGCTCGCCGGCGAGCAGGGTCAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTCCCGCTTCGCTTCTCGCGTTCTGACATCGCCACGTCCCCGTGCCGCCTGa      >  5:186612/4‑149 (MQ=255)                                                                                                                                 aCCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTCCCGCTTCGCTTCTCGCGTTCTGACATCGCCACGTCCCCGTGCCGCCTGATc    <  3:154816/148‑1 (MQ=255)                                                                                                                                   ccTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTCCCGCTTCGCTTCTCGCGTTCTGACATCGCCACGTCCCCGTGCCGCCTGATCgg  >  6:7491/1‑148 (MQ=255)                                                                                                                                                    |                                                                                                                                    CGGCCGACAGCAGCGGCATGGTCCAAGGTGAGCAAGACTTCAGCGATCCGACCCTGTCTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTCCCGCTTCGCTTCTCGCGTTCTGACATCGCCACGTCCCCGTGCCGCCTGATCGG  >  NC_002947/3768128‑3768405

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: ‑