Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,512,276	C→T	14.8%	R301C (CGC→TGC)	PP_3108 →	rhs family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,512,276	0	C	T	14.8%	57.4 / 4.2	27	R301C (CGC→TGC)	PP_3108	rhs family protein
Reads supporting (aligned to +/- strand):  ref base C (10/13);  new base T (2/2);  total (12/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.91e-01

CCTGCCGGGCCTGATGCCGATCGAGTGGTCGCGCTTCTACGCCAGCGACCTGACGGTCGACAGCGTACTCGGCCGCGGCTGGGTGCTGCCCTGGGAGCAGAGCCTGCGCCGCCAGGGGGCATTCATCTACCTCACCGACAACCAGGGCCGCGAAGTCCCGTTCGTGACCCTGCAACCGGGGCAGCGCATCTACAACCCGCACGAGCAGGTGTACCTGGTGTGCACCGAGGGCGGTCACTACATCCTGCAGACCCTCGACAACCTGTTCTT  >  NC_002947/3512128‑3512397                                                                                                                                                     |                                                                                                                          ccTGCCGGGCCTGATGCCGATCGAGTGGTCGCGCTTCTACGCCAGCGACCTGACGGTCGACAGCGTACTCGGCCGCGGCTGGGTGCTGCCCTGGGAGCAGAGCCTGCGCCGCCAGGGGGCATTCATCTACCTCACCGACAACCAGGGCcg                                                                                                                          <  2:404374/150‑1 (MQ=255)   tGCCGGGCCTGATGCCGATCGAGTGGTCGCGCTTCTACGCCAGCGACCTGACGGTCGACAGCGTACTCGGCCGCGGCTGGGTGCTGCCCTGGGAGCAGAGCCTGCGCCGCCAGGGGGCATTCATCTACCTCACCGACAACCAGGGCcgcg                                                                                                                        >  1:785474/1‑150 (MQ=255)        ggCCTGATGCCGATCGAGTGGTCGCGCTTCTACGCCAGCGACCTGACGGTCGACAGCGTACTCGGCCGCGGCTGGGTGCTGCCCTGGGAGCAGAGCCTGCGCCGCCAGGGGGCATTCATCTACCTCACCGACAACCAGGGCCGCGAAGTc                                                                                                                   >  2:640804/1‑150 (MQ=255)          ccTGATGCCGATCGAGTGGTCGCGCTTCTACGCCAGCGACCTGACGGTCGACAGCGTACTCGGCCGCGGCTGGGTGCTGCCCTGGGAGCAGAGCCTGCGCCGCCAGGGGGCATTCATCTACCTCACCGACAACCAGGGCCGCGAAGTccc                                                                                                                 <  1:545955/150‑1 (MQ=255)          ccTGATGCCGATCGAGTGGTCGCGCTTCTACGCCAGCGACCTGACGGTCGACAGCGTACTCGGCCGCGGCTGGGTGCTGCCCTGGGAGCAGAGCCTGCGCCGCCAGGGGGCATTCATCTACCTCACCGACAACCAGGGCCGCGAAGTccc                                                                                                                 <  1:517850/150‑1 (MQ=255)           cTGATGCCGATCGAGTGGTCGCGCTTCTACGCCAGCGACCTGACGGTCGACAGCGTACTCGGCCGCGGCTGGGTGCTGCCCTGGGAGCAGAGCCTGCGCCGCCAGGGGGCATTCATCTACCTCACCGACAACCAGGGCCGCGAAGTCCCg                                                                                                                <  1:264414/150‑1 (MQ=255)             gATGCCGATCGAGTGGTCGCGCTTCTACGCCAGCGACCTGACGGTCGCCAGCGTACTCGGCCGCGGCTGGGTGCTGCCCTGGGAGCAGAGCCTGCGCCGCCAGGGGGCATTCATCTACCTCACCGACAACCAGGGCCGCGAAGTCCCGtt                                                                                                              >  1:742820/1‑150 (MQ=255)                     tCGAGTGGTCGCGCTTCTACGCCAGCGACCTGACGGTCGACAGCGTACTCGGCCGCGGCTGGGTGCTGCCCTGGGAGCAGAGCCTGCGCCGCCAGGGGGCATTCATCTACCTCACCGACAACCAGGGCCGCGAAGTCCCGTTc                                                                                                             >  1:480980/1‑143 (MQ=255)                     tCGAGTGGTCGCGCTTCTACGCCAGCGACCTGACGGTCGACAGCGTACTCGGCCGCGGCTGGGTGCTGCCCTGGGAGCAGAGCCTGCGCCGCCAGGGGGCATTCATCTACCTCACCGACAACCAGGGCCGCGAAGTCCCGTTc                                                                                                             <  2:480980/143‑1 (MQ=255)                            gTCGCGCTTCTACGCCAGCGACCTGACGGTCGACAGCGTACTCGGCCGCGGCGGGGTGCTGCCCTGGGAGCAGAGCCTGCGCCGCCAGGGGGCATTCATCTACCTCACCGACAACCAGGGCCGCGAAGTCCCGTTCGTGACCCTGCAAcc                                                                                               >  2:111216/1‑150 (MQ=255)                               gcgcTTCTACGCCAGCGACCTGACGGTNGACAGCGTACTCGGCCGCGNCTGGGTGCTGCCCTGGGAGCAGAGCCTGCGCCGCCAGGGGGCATTCATCTACCTCACCGACAACCAGGGCTGCGAAGTCCCGTTCGTGACCCTGCAACCggg                                                                                            >  1:763250/1‑150 (MQ=255)                               gcgcTTCTACGCCAGCGACCTGACGGTCGACAGCGTACTCGGCCGCGGCTGGGTGCTGCCCTGGGAGCAGAGCCTGCGCCGCCAGGGGGCATTCATCTACCTCACCGACAACCAGGGCTGCGAAGTCCCGTTCGTGACCCTGCAACCggg                                                                                            >  1:562191/1‑150 (MQ=255)                                cgcTTCTACGCCAGCGACCTGACGGTCGACAGCGTACTCGGCCGCGGCTGGGTGCTGCCCTGGGAGCAGAGCCTGCGCCGCCAGGGGGCATTCATCTACCTCACCGACAACCAGGGCCGCGAAGTCCAGTTCGTGACCCTGCAACCgggg                                                                                           <  2:670222/150‑1 (MQ=255)                                   ttCTACGCCAGCGACCTGACGGTCGACAGCGTACTCGGCCGCGGCTGGGTGCTGCCCTGGGAGCAGAGCCTGCGCCGCCAGGGGGCATTCATCTACCTCACCGACAACCATGGCCGCGAAGTCCCGTTCGTGACCCTGCAACCGGGGCAg                                                                                        <  2:730721/150‑1 (MQ=255)                                        cGCCAGCGACCTGACGGTCGACAGCGTACTCGGCCGCGGCTGGGTGCTGCCCTGGGAGCAGAGCCTGCGCCGCCAGGGGGCATTCATCTACCTCACCGACAACCAGGGCCGCGAAGTCCCGTTCGTGACCCTGCAACCGGGGCAGCGCAt                                                                                   <  2:785474/150‑1 (MQ=255)                                                           gACAGCGTACTCGGCCGCGGCTGGGTGCTGCCCTGGGAGCAGAGCCTGCGCCGCCAGGGGGCATTCATCTACCTCACCGACAACCAGGGCTGCGAAGTCCCGTTCGTGACCCTGCAACCGGGGCAGCGCATCTACAACCCGCACGAGCAg                                                                <  2:562191/150‑1 (MQ=255)                                                           gACAGCGTACTCGGCCGCGGCTGGGTGCTGCCCTGGGAGCAGAGCCTGCGCCGCCAGGGGGCATTCATCTACCTCACCGACAACCAGGGCTGCGAAGTCCCGTTCGTGACCCTGCAACCGGGGCAGCGCATCTACAACCCGCACGAGCAg                                                                <  2:763250/150‑1 (MQ=255)                                                                  tACTCGGCCGCGGCTGGGTGCTGCCCTGGGAGCAGAGCCTGCGCCGCCAGGGGGCATTCATCTAGCTCACCGACAACCAGGGCCGCGAAGTCCCGTTCGAGACCCTGCAACCGGGGCAGCGCATCTACAACCCGCACGAAAAGGtatagc                                                         >  2:205699/1‑148 (MQ=255)                                                                     tCGGCCGCGGCTGGGTGCTGCCCTGGGAGCAGAGCCTGCGCCGCCAGGGGGCATTCATCTACCTCACCGACAACCAGGGCCGCGAAGTCCCGTTCGTGACCCTGCAACCGGGGCAGCGCATCTACAACCCGCACGAGCAGGTGTACCTgg                                                      >  2:673049/1‑150 (MQ=255)                                                                      cgcccGCGGCTGGGTGCTCCCCTGGGAGCAGAGCCTGCTCCGCGAGGGGGCATTCATCTACCTCACCCACACCCAGGGCCGCGAAGTCCCGTTCGTGACCCTGCAACCGGGGCAGCGCATCTAGAACCCGCACGAGCAGGTGTACCTGgt                                                     <  1:315655/147‑1 (MQ=255)                                                                      cGGCCGCGGCTGGGTGCTGCCCTGGGAGCAGAGCCTGCGCCGCCAGGGGGCATTCATCTACCTCACCGACAACCAGGGCCGCGAAGTCCCGTTCGTGACCCTGCAACCGGGGCAGCGCATCTACAACCCGCACGAGCAGGTGTACCTGgt                                                     <  1:640804/150‑1 (MQ=255)                                                                       ggCCGCGGCTGGGTGCTGCCCTGGGAGCAGAGCCTGCGCCGCCAGGGGGCATTCATCTACCTCACCGACAACCAGGGCCGCGAAGTCCCGTTCGTGACCCTGCAACCGGGGCAGCGCATCTACAACCCGCACGAGCAGGTGTACCTGgtg                                                    >  1:430590/1‑150 (MQ=255)                                                                       ggCCGCGGCTGGGTGCTGCCCTGGGAGCAGAGCCTGCGCCGCCAGGGGGCATTCATCTACCTCACCGACAACCAGGGCCGCGAAGTCCCGTTCGTGACCCTGCAACCGGGGCAGCGCATCTACAACCCGCACGAGCAGGTGTACCTGgtg                                                    <  2:430590/150‑1 (MQ=255)                                                                        gCCGCGGCTGGGTGCTGCCCTGGGAGCAGAGCCTGCGCCGCCAGGGGGCATTCATCTACCTCACCGACAACCAGGGCCGCGAAGTCCCGTTCGTGACCCTGCAACCGGGGCAGCGCATCTACAACCCGCACGAGCAGGTGTACCTGgtgt                                                   <  1:111216/150‑1 (MQ=255)                                                                                                                         aTTCATCTACCTCACCGACAACCAGGGCCGCGAAGTCCCGTTCGTGACCCTGCAACCGGGGCAGCGCATCTACAACCCGCACGAGCAGGTGTACCTGGTGTGCACCGAGGGCGGTCACTACATCCTGCAGACCCTCGACAACCTGttctt  >  1:709907/1‑150 (MQ=255)                                                                                                                                        cGACAACCAGGGCCGCGAAGTCCCGTTCGTGACCCTGCAACCGGGGCAGCGCATCTACAACCCGCACGAGCAGGTGTACCTGGTGTGCACCGAGGGCGGTCACTACATCCTGCAGACCCTCGACAACCTGttctt  <  1:686234/135‑1 (MQ=255)                                                                                                                                        cGACAACCAGGGCCGCGAAGTCCCGTTCGTGACCCTGCAACCGGGGCAGCGCATCTACAACCCGCACGAGCAGGTGTACCTGGTGTGCACCGAGGGCGGTCACTACATCCTGCAGACCCTCGACAACCTGttctt  >  2:686234/1‑135 (MQ=255)                                                                                                                                           cAACCAGGGCCGCGAAGTCCCGTTCGTGACCCTGCAACCGGGGCAGCGCATCTACAACCCGCACGAGCAGGTGTACCTGGTGTGCACCGAGGGCGGTCACTACATCCTGCAGAccc                  >  2:682600/1‑116 (MQ=255)                                                                                                                                           cAACCAGGGCCGCGAAGTCCCGTTCGTGACCCTGCAACCGGGGCAGCGCATCTACAACCCGCACGAGCAGGTGTACCTGGTGTGCACCGAGGGCGGTCACTACATCCTGCAGAccc                  <  1:682600/116‑1 (MQ=255)                                                                                                                                                     |                                                                                                                          CCTGCCGGGCCTGATGCCGATCGAGTGGTCGCGCTTCTACGCCAGCGACCTGACGGTCGACAGCGTACTCGGCCGCGGCTGGGTGCTGCCCTGGGAGCAGAGCCTGCGCCGCCAGGGGGCATTCATCTACCTCACCGACAACCAGGGCCGCGAAGTCCCGTTCGTGACCCTGCAACCGGGGCAGCGCATCTACAACCCGCACGAGCAGGTGTACCTGGTGTGCACCGAGGGCGGTCACTACATCCTGCAGACCCTCGACAACCTGTTCTT  >  NC_002947/3512128‑3512397

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑