Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,731,889	A→G	13.8%	R465R (CGT→CGC)	PP_3299 ←	lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,731,889	0	A	G	13.8%	105.7 / 7.2	43	R465R (CGT→CGC)	PP_3299	lipoprotein
Reads supporting (aligned to +/- strand):  ref base A (17/20);  new base G (4/2);  total (21/22)
Fisher's exact test for biased strand distribution p-value = 4.12e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.95e-01

TACGCGGTATGAGCCCAATCCTCAACGAAGGTGAGTACGTCTTCTGCACCAAGGCATTTACGCAGTCCCATCATCGCTGTGCCACATCTGAGTCAGTTGACCACCCGCCACCCAGGGCGAGGTAGGCAGCAATAGCAGCACGCGCTGCTTCAGTTTGCGCAACTGCTCGGA‑AATCCGATGTCCTGAGAAGCTGCTGATCTGCGTTCAGAACGTCTATCAAACTGGCTACACCGTTCTGGAATGCTACGAAGGACGAACGTCGTGCTCGCTCCAGGGATAC  >  NC_002947/3731750‑3732029                                                                                                                                            |                                                                                                                                              tACGCGGTATGAGCCCAATCCTCAACGAAGGTGAGTACGTCTTCTGCACCAAGGCATTTACGCAGTCCCATCATCGCTGTGCCACATCTGAGTCAGTTGACCACCCGCCACCCAGGGCGAGGTAGGCAGCAATAGCAGCGCGTgctgcta                                                                                                                                     <  1:347560/150‑2 (MQ=255)     cgGTATGAGCCCAATCCTCAACGAAGGTGAGTACGTCTTCTGCACCAAGGCATTTACGCAGTCCCATCATCGCTGTGCCACATCTGAGTCAGTTGACCACCCGCCACCCAGGGCGAGGTAGGCAGCAATAGCAGCACGCGCTGCTTCAGt                                                                                                                                 <  2:664385/150‑1 (MQ=255)                   tCCTCAACGAAGGTGAGTACGTCTTCTGCACCAAGGCATTTACGCAGTCCCATCATCGCTGTGCCACATCTGAGTCAGTTGACCACCCGCCACCCAGGGCGAGGTAGGCAGCAATAGCAGCACGCGCTGCTTCAGTTTGCGCAACTGCTc                                                                                                                   <  1:422917/150‑1 (MQ=255)                      tCAACGAAGGTGAGTACGTCTTCTGCACCAAGGCATTTACGCAGTCCCATCATCGCTGTGCCACATCTGAGTCAGTTGACCACCCGCCACCCAGGGCGAGGTAGGCAGCAATAGCAGCACGCGCTGCTTCAGTTTGCGCAACTGCTCGGa                                                                                                                >  2:542939/1‑150 (MQ=255)                        aaCGAAGGTGAGTACGTCTTCTGCACCAAGGCATTTACGCAGTCCCATCATCGCTGTGCCACATCTGAGTCAGTTGACCACCCGCCACCCAGGGCGAGGTAGGCAGCAATAGCAGCACGCGCTGCTTCAGTTTGCGCAACTGCTCGGa‑aa                                                                                                             >  1:38010/1‑150 (MQ=255)                           gAAGGTGAGTACGTCTTCTGCACCAAGGCATTTACGCAGTCCCATCATCGCTGTGCCACATCTGAGTCAGTTGACCACCCGCCACCCAGGGCGAGGTAGGCAGCAATAGCAGCACgcgc                                                                                                                                          <  1:705912/119‑1 (MQ=255)                           gAAGGTGAGTACGTCTTCTGCACCAAGGCATTTACGCAGTCCCATCATCGCTGTGCCACATCTGAGTCAGTTGACCACCCGCCACCCAGGGCGAGGTAGGCAGCAATAGCAGCACgcgc                                                                                                                                          >  2:705912/1‑119 (MQ=255)                              ggTGAGTACGTCTTCTGCACCAAGGCATTTACGCAGTCCCATCATCGCTGTGCCACATCTGAGTCAGTTGACCACCCGCCACCCAGGGCGAGGTAGGCAGCAATAGCAGCACGCGCTGCTTCAGTTTGCGCAACTGCTc                                                                                                                   >  2:501660/1‑139 (MQ=255)                              ggTGAGTACGTCTTCTGCACCAAGGCATTTACGCAGTCCCATCATCGCTGTGCCACATCTGAGTCAGTTGACCACCCGCCACCCAGGGCGAGGTAGGCAGCAATAGCAGCACGCGCTGCTTCAGTTTGCGCAACTGCTc                                                                                                                   <  1:501660/139‑1 (MQ=255)                                       gTCTTCTGCACCAAGGCATTTACGCAGTCCCATCATCGCTGTGCCACATCTGAGTCAGTTGACCACCCGCCACCCAGGGCGAGGTAGGCAGCAATAGCAGCACGCGCTGCTTCAGTTTGCGCAACTGCTCGGA‑AATCCGATGTCCTgaga                                                                                              >  2:525706/1‑150 (MQ=255)                                        tcttctGCACCAAGGCATTTACGCAGTCCCATCATCGCTGTGCCACATCTGAGTCAGTTGACCACCCGCCACCCAGGGCGAGGTAGGCAGCAATAGCAGCACGCGCTGCTTCAGTTTGCGCAACTGCTCGGA‑AATCCGATGTCCTGAGaa                                                                                             <  1:525706/150‑1 (MQ=255)                                                  cAAGGCATTTACGCAGTCCCATCATCGCTGTGCCACATCTGAGTCAGTTGACCACCCGCCACCCAGGGCGAGGTAGGCAGCAATAGCAGCACGCGCTGCTTCAGTTTGCGCAACTGCTCGGA‑AATCCGAt                                                                                                       >  1:824330/1‑130 (MQ=255)                                                  cAAGGCATTTACGCAGTCCCATCATCGCTGTGCCACATCTGAGTCAGTTGACCACCCGCCACCCAGGGCGAGGTAGGCAGCAATAGCAGCACGCGCTGCTTCAGTTTGCGCAACTGCTCGGA‑AATCCGAt                                                                                                       <  2:824330/130‑1 (MQ=255)                                                   aaGGCATAAACGCAGTCCCACCATCGATATTCAAAATCTGAGTCAGTTGACCACCCGACACCCAGGGCGAGGTAGTCAGCAATAGCAGCACGCGCTGCTTCAGTTTGAGCAACTGCTCGGA‑AATCCGATGTCCTGAGAAGCTGCTGATCt                                                                                  <  2:158919/150‑1 (MQ=255)                                                     ggCATTTACGCAGTCCCATCATCGCTGTGCCACATCCGAGTCAGTTGACCACCCGCCACCCAGGGCGAGGTAGGCAGCAATAGCAGCACGCGCTGCGTCAGTTTGCGCAACTGCTCGGA‑AATCCGATGTCCTGAGAAGCTGCTGATCTGc                                                                                <  1:107503/150‑1 (MQ=255)                                                              gCAGTCCCATCATCGCTGTGCCACATCTGAGTCAGTTGACCACCCGCCACCCAGGGCGAGGTAGGCAGCAATAGCAGCACGCGCTGCTTCAGTTTGCGCAACTGCTCGGA‑AATCCGATGTCCTGGGTAGCTGCTGATCTGCGTTCAGAAc                                                                       <  1:542939/150‑1 (MQ=255)                                                                 gTCCCATCATCGCTGTGCCACATCTGAGTCAGTTGACCACCCGCCACCCAGGGCGAGGTAGGCAGCAATAGCAGCACGCGCTGCTTCAGTTTGCGCAACTGCTAGGA‑AATCCGATGTCCTGAGAAGCTGCTGATCTGCGTTCAGAACGTc                                                                    <  1:452962/150‑1 (MQ=255)                                                                   cccATCATCGCTGTGCCACATCTGAGTCAGTTGACCACCCGCCACCCAGGGCGAGGTAGGCAGCCATAGCAGCACGCGCTGCTTCCGTTTGCGCAACTGCTCGGA‑AATCCGATGTCCTGAGAAGCTGCTGATCTGCGTTCAGAACGTCTa                                                                  >  1:841697/1‑150 (MQ=255)                                                                         atcGCTGTGCCACATCTGAGTCAGTTGACCACCCGCCACCCAGGGCGAGGTAGGCAGCAATAGCAGCACGCGCTGCTTCAGTTTGCGCAACTGCTCGGA‑AATCCGATGTCCt                                                                                                  >  1:87260/1‑112 (MQ=255)                                                                         atcGCTGTGCCACATCTGAGTCAGTTGACCACCCGCCACCCAGGGCGAGGTAGGCAGCAATAGCAGCACGCGCTGCTTCAGTTTGCGCAACTGCTCGGA‑AATCCGATGTCCt                                                                                                  <  2:87260/112‑1 (MQ=255)                                                                         atcGCTGTGCCACATCTGAGTCAGTTGACCACCCGCCACCCAGGGCGAGGTAGGCAGCAATAGCAGCACGCGCTGCTTCAGTTTGCGCAACTGCTCGGA‑AATCCGATGTCCTGAGAAGCTGCTGATCTGCGTTCAGAACGTCTATCAAAc                                                            >  1:848763/1‑150 (MQ=255)                                                                          tcGCTGTGCCACATCTGAGTCAGTTGACCACCCGCCACCCAGGGCGAGGTAGGCAGCAATAGCAGCACGCGCTGCTTCAGTTTGCGCAACTGCTCGGA‑AATCCGATGTCCTGAGAAGCTGCTGATCTGCGTTCAGAACGTCTATCAAACt                                                           <  2:38010/150‑1 (MQ=255)                                                                                  ccACATCTGAGTCAGTTGACCACCCGCCACCCAGGGCGAGGTAGGCAGCAATAGCAGCACGCGCTGCTTCAGTTTGCGCAACTGCTCGGA‑AATCCGATGTCCTGAGAAGCTGCTGATCTGCGTTCAGAACGTCTATCAAACTGGCTacac                                                   >  2:648958/1‑150 (MQ=255)                                                                                  ccACATCTGAGTCAGTTGACCACCCGCCACCCAGGGCGAGGTAGGCAGCAATAGCAGCACGCGCTGCTTCAGTTTGCGCAACTGCTAGCACCAACGGCCTTTCAG‑GAATGTGCTGATCTGGGTTCAGAACGTCTATCAAACTGGCTacac                                                   >  2:239850/1‑150 (MQ=255)                                                                                   cacaTCTGAGTCAGTTGACCACCCGCCACCCAGGGCGAGGTAGGCAGCAATAGCAGCACGCGCTGCTTCAGTTTGCGCAACTGCTCGGA‑AATCCGATGTCCTGAGAAGCTGCTGATCTGCGTTCAGAACGt                                                                     <  2:516369/131‑1 (MQ=255)                                                                                   cacaTCTGAGTCAGTTGACCACCCGCCACCCAGGGCGAGGTAGGCAGCAATAGCAGCACGCGCTGCTTCAGTTTGCGCAACTGCTCGGA‑AATCCGATGTCCTGAGAAGCTGCTGATCTGCGTTCAGAACGt                                                                     >  1:516369/1‑131 (MQ=255)                                                                                      aTCTGAGTCAGTTGACCACCCGCCACCCAGGGCGAGGTAGGCAGCAATAGCAGCACGCGCTGCTTCAGTTTGCGCAACTGCTCGGA‑AATCCGATGTCCTGAGAAGCTGCTGATCTGCGTTCAGAACGTCTATCAAACTGTCTACACCGtt                                               >  1:498151/1‑150 (MQ=255)                                                                                        cTGAGTCAGTTGACCACCCGCCAGCCAGGGCGAGGTAGGCAGCAATAGCAGCACGCGCTGCTTCAGTTTGCGCAACTGCTCGGA‑AATCCGATATCCTAAGAAGCTGCGGATCTGCGTTCAGAACGTCTATCAAACTGGCTACACCGTTCt                                             <  2:292395/150‑1 (MQ=255)                                                                                        cTGAGTCAGTTGACCACCCGCCACCCAGGGCGAGGTAGGCAGCAATAGCAGCACGCGCTGCTTCAGTTTGCGCAACTGCTCGGA‑AATCCGATGTCCTGAGAAGCTGCTGATCTGCGTTCAGAACGTCTATCAAACTGGCTACACCGTTCt                                             <  2:51075/150‑1 (MQ=255)                                                                                                     ccaccCGCCACCCAGGGCGACGTAGGCAGCAATAGCAGCACGCGCTGCTTCAGTTTGCGCAACTGCTCGGA‑AATCCGATGTCCTGAGAAGCTGCTGATCTGCGTTCAGAACGTCTATCAAACTGGCTACACCGTTCTGGAATGCTACGaa                                <  1:648958/150‑1 (MQ=255)                                                                                                         ccGCCACCCAGGGCGAGGTAGGCAGCAATAGCAGCACGCGCTGCTTCAGTTTGCGCAACTGCTCGGA‑AATCCGATGTCCTGAGAAGCTGCTGATCTGCGTTCAGAACGTCTATCAAACTGGCTACACCGTTCTGGAATGCTACGAAGGAc                            >  2:829157/1‑150 (MQ=255)                                                                                                             cACCCAGGGCGAGGTAGGCAGCAATAGCAGCACGCGCTGCTTCAGTTTGCGCAACTGCTCGGA‑AATCCGATGTCCTGAGAAGCTGCTGATCTGCGTTCAGAACGTCTATCAAACTGGCTACACCGTTCTGGAATGCTACGAAGGACGAAc                        <  1:725156/150‑1 (MQ=255)                                                                                                              aCCCAGGGCGAGGTAGGCAGCAATAGCAGCACGCGCTGCTTCAGTTTGCGCAACTGCTCGGA‑AATCCGATGTCCTGAGAAGCTGCTGATCTGCGTTCAGAACGTCTATCAAACTGGCTACACCGTTCTGGAATGCTACGAAGGACGAAcg                       >  2:811089/1‑150 (MQ=255)                                                                                                               cccAGGGCGAGGTAGGCAGCAATAGGCATGTTCGCTGCTTCAGTTTGCGCAACTGCTCGGA‑AATCCGATGTCCTGAGAAGCTGCTGATCTGCGTTCAGAACGTCTATCAAACTGGCTACACCGTTCTGGAATGCTACGAAGGACGAAcgt                      >  1:663291/1‑150 (MQ=255)                                                                                                                       gAGGTAGGCAGCAATAGCAGCACGCGCTGCTTCAGTTTGCGCAACTGCTCGGA‑AATCCGATGTCCTGAGAAGCTGCTGATCTGCGTTCAGAACGTCTATCAAACTGGCTACACCGTTCTGGAATg                                       <  2:15075/125‑1 (MQ=255)                                                                                                                       gAGGTAGGCAGCAATAGCAGCACGCGCTGCTTCAGTTTGCGCAACTGCTCGGA‑AATCCGATGTCCTGAGAAGCTGCTGATCTGCGTTCAGAACGTCTATCAAACTGGCTACACCGTTCTGGAATg                                       >  1:15075/1‑125 (MQ=255)                                                                                                                             ggCAGCAATAGCAGCACGCGCTGCTTCAGTTTGCGCAACTGCTCGGA‑AATCCGATGTCCTGAGAAGCTGCTGATCTGCGTTCAGAACGTCTATCAAACTGGCTACACCGTTCTGGAATGCTACGAAGGACGAACGTCGTGCTCGCTCCAg        >  1:528174/1‑150 (MQ=255)                                                                                                                                 actgaagcagcGCGTGCTGCTTCAGTTTGCGCAACTGCTCGGA‑AATCCGATGTCCTGAGAAGCTGCTGATCTGCGTTCAGAACGTCTATCAAACTGGCTACACCGTTCTGGAATGCTACGAAGGACGAACGTCGTGCTCGCTCCAGGGAt    >  1:412854/6‑150 (MQ=255)                                                                                                                                  ctgaagcagcGCGTGCTGCTTCAGTTTGCGCAACTGCTCGGA‑AATCCGATGTCCTGAGAAGCTGCTGATCTGCGTTCAGAACGTCTATCAAACTGGCTaca                                                    >  2:313412/5‑101 (MQ=255)                                                                                                                                  ctgaagcagcGCGTGCTGCTTCAGTTTGCGCAACTGCTCGGA‑AATCCGATGTCCTGAGAAGCTGCTGATCTGCGTTCAGAACGTCTATCAAACTGGCTaca                                                    <  1:313412/97‑1 (MQ=255)                                                                                                                                  ctgaagcagcGCGTGCTGCTTCAGTTTGCGCAACTGCTCGGA‑AATCCGATGTCCTGAGAAGCTGCTGATCTGCGTTCAGAACGTCTATCAAACTGGCTACACCGTTCTGGAATGCTACGAAGGACGAACGTCGTGCTCGCTCCAGGGATa   >  1:197762/5‑150 (MQ=255)                                                                                                                                  caATAGCAGCACGCGCTGCTTCAGTTTGCGCAACTGCTCGGA‑AATCCGATGTCCTGAGAAGCTGCTGATCTGCGTTCAGAACGTCTATCAAACTGGCTACACCGTTCTGGAATGCTACGAAGGACGAACGTCGTGCTCGCTCCAGGGATa   <  2:528174/150‑1 (MQ=255)                                                                                                                                   aaTAGCAGCACGCGCTGCTTCAGTTTGCGCAACTGCTCGGA‑AATCCGATGTCCTGAGAAGCTGCTGATCTGCGTTCAGAACGTCTATCAAACTGTCTACACCGTTCTGGAATGCTACGAAGGACGAACGTCGTGCTCGCTCCAGGGATAc  <  2:498151/150‑1 (MQ=255)                                                                                                                                            aCGCGCTGCTTCAGTTTGCGCAACTGCTCGGA‑AATCCGATGTCCTGAGAAGCTGCTGATCTGCGTTCAGAACGTCTATCAAACTGGCTACACCGTTCTGGAATGCTACGAAGGACGAACGTCGTGCTCGCTCCAGGGATAc  >  2:319207/1‑141 (MQ=255)                                                                                                                                            aCGCGCTGCTTCAGTTTGCGCAACTGCTCGGA‑AATCCGATGTCCTGAGAAGCTGCTGATCTGCGTTCAGAACGTCTATCAAACTGGCTACACCGTTCTGGAATGCTACGAAGGACGAACGTCGTGCTCGCTCCAGGGATAc  <  1:319207/141‑1 (MQ=255)                                                                                                                                            |                                                                                                                                              TACGCGGTATGAGCCCAATCCTCAACGAAGGTGAGTACGTCTTCTGCACCAAGGCATTTACGCAGTCCCATCATCGCTGTGCCACATCTGAGTCAGTTGACCACCCGCCACCCAGGGCGAGGTAGGCAGCAATAGCAGCACGCGCTGCTTCAGTTTGCGCAACTGCTCGGA‑AATCCGATGTCCTGAGAAGCTGCTGATCTGCGTTCAGAACGTCTATCAAACTGGCTACACCGTTCTGGAATGCTACGAAGGACGAACGTCGTGCTCGCTCCAGGGATAC  >  NC_002947/3731750‑3732029

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑