Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,030,799	C→T	18.4%	intergenic (+37/‑458)	PP_4433 → / → dadA‑I	amino acid MFS transporter/D‑amino acid dehydrogenase small subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,030,799	0	C	T	18.4%	97.8 / 16.3	49	intergenic (+37/‑458)	PP_4433/dadA‑I	amino acid MFS transporter/D‑amino acid dehydrogenase small subunit
Reads supporting (aligned to +/- strand):  ref base C (19/21);  new base T (5/4);  total (24/25)
Fisher's exact test for biased strand distribution p-value = 7.25e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.63e-01

ACCTGCCTACTACATCATGGTTGCATCAGCACTTGGGATTATTGCGTTGTTCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTTATCTCACCTCTTGGCATCTGGCCCTGATAACAGTGTCTTCGCTATCTCTTGCCC  >  NC_002947/5030651‑5030947                                                                                                                                                     |                                                                                                                                                     aCCTGCCTACTACATCATGGTTGCATCAGCACTTGGGATTATTGCGTTGTTCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGTGCTAGTCa                                                                                                                                                     >  2:141960/1‑150 (MQ=255) aCCTGCCTACTACATCATGGTTGCATCAGCACTTGGGATTATTGCGTTGTTCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGTGCTAATCa                                                                                                                                                     >  1:1398384/1‑150 (MQ=255)     gCCTACTACATCATGGTTGCATCAGCACTTGGGATTATTGCGTTGTTCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGTGCTAGTCAGCAc                                                                                                                                                 <  1:141960/150‑1 (MQ=255)         actacATCATGGTTGCATCAGCACTTGGGATTATTGCGTTGTTCTTTGTGATCGCGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGTGCTAATCAGCACCCAg                                                                                                                                             <  1:791414/150‑1 (MQ=255)         actacATCATGGTTGCATCAGCACTTGGGATTATTGCGTTGTTCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGTGCTAATCAGCACCCAg                                                                                                                                             >  2:737142/1‑150 (MQ=255)         actacATCATGGTTGCATCAGCACTTGGGATTATTGCGTTGTTCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGTGCTAATCAGCACCCAg                                                                                                                                             <  1:210548/150‑1 (MQ=255)         actacATCATGGTTGCATCAGCACTTGGGATTATTGCGTTGTTCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGTGCTAATCAGCACCCAg                                                                                                                                             <  1:793402/150‑1 (MQ=255)                          tCAGCACTTGGGATTATTGCGTTGTTCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGTAGATGGTATACAGTCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCa                                                                                                                            >  2:447570/1‑150 (MQ=255)                                  tGGGATTATTGCGTTGTTCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCg                                                                                                                    <  2:624091/150‑1 (MQ=255)                                      attattGCGTTGTTCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGTGCTGATTAGCACCCAGGCtctat                                                                                                                                      <  2:350338/128‑5 (MQ=255)                                      attattGCGTTGTTCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGTGCTGATTAGCACCCAGGCtctat                                                                                                                                      >  1:350338/1‑124 (MQ=255)                                         attGCGTTGTTCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCTGGCAAGc                                                                                                             <  2:769883/150‑1 (MQ=255)                                              gttgttCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGAcc                                                                                                        >  2:803456/1‑150 (MQ=255)                                                tgttCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGAcc                                                                                                        >  1:48645/1‑148 (MQ=255)                                                tgttCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGAcc                                                                                                        <  2:48645/148‑1 (MQ=255)                                                         tgATCGAGACTACTGTTTCCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGa                                                                                             <  2:969743/150‑1 (MQ=255)                                                         tgATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGa                                                                                             <  1:737142/150‑1 (MQ=255)                                                            tCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGatat                                                                                          >  2:1367435/1‑150 (MQ=255)                                                            tCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGTGCCGATTAGCACCCAGGCtct                                                                                                                                        >  2:812081/1‑102 (MQ=255)                                                            tCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGTGCCGATTAGCACCCAGGCtct                                                                                                                                        <  1:812081/104‑3 (MQ=39)                                                                   tAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGTGCTAATCAGCACCCAGGCTGtt                                                                                                                                       <  2:495302/98‑1 (MQ=255)                                                                   tAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGTGCTAATCAGCACCCAGGCTGtt                                                                                                                                       >  1:495302/1‑98 (MQ=255)                                                                    aaaGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAagcagca                                                                                  <  1:803456/150‑1 (MQ=255)                                                                       ggTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAagc                                                                                      >  1:1030622/1‑143 (MQ=255)                                                                       ggTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAagc                                                                                      <  2:1030622/143‑1 (MQ=255)                                                                            cTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAag                                                                                       <  1:428465/137‑1 (MQ=255)                                                                            cTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAag                                                                                       >  2:428465/1‑137 (MQ=255)                                                                            cTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCa                                                                          >  1:922232/1‑150 (MQ=255)                                                                                    gcgGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCGTGCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACccttcct                                                                  >  1:728979/1‑150 (MQ=255)                                                                                       gggATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGTGCTGATTAGCAcc                                                                                                                                                <  1:427717/69‑1 (MQ=38)                                                                                       gggATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGTGCTGATTAGCAcc                                                                                                                                                >  2:427717/1‑69 (MQ=255)                                                                                       gggATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGCTATAGAGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCttta                                                               <  2:973488/150‑2 (MQ=255)                                                                                               aTACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTTa                                                       >  1:723204/1‑150 (MQ=255)                                                                                                   cTGGGGCAAAATAACCTAATAGGCAGATGGTATAATGCCGTTGATCTAATCAGCACCCAGGCTGTTGGTTGGCGCCATTCTTCCTGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTCCCTTTTGATTCGTAtctc                                                   >  1:811808/1‑150 (MQ=255)                                                                                                    tGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCa                                                                                                                            >  2:297761/1‑76 (MQ=255)                                                                                                    tGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCa                                                                                                                            <  1:297761/76‑1 (MQ=255)                                                                                                         cAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTTATCTCACctct                                             <  1:1291230/150‑1 (MQ=255)                                                                                                                  cTAATAGGCAGATGGTATAGAGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTTATCTCACCTCTTGGCATCTg                                    >  1:1335883/1‑150 (MQ=255)                                                                                                                       aGGCAGATGGTATAGAGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTTATCTCACCTCTTGGCATCTGGCCCt                               <  2:723204/150‑1 (MQ=255)                                                                                                                                gTATAGAGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCAt                                                                                                                           <  1:916436/49‑1 (MQ=255)                                                                                                                                gTATAGAGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCAt                                                                                                                           >  2:916436/1‑49 (MQ=255)                                                                                                                                gTATAGAGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTTATCTCACCTCTTGGCATCTGGCCCTGATaccaat                      <  2:1398384/150‑6 (MQ=255)                                                                                                                                     gagCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGc                                                                                                     >  2:483585/1‑66 (MQ=255)                                                                                                                                     gagCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGc                                                                                                     <  1:483585/66‑1 (MQ=255)                                                                                                                                         cTGGGTGCTGATTAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATCATTATCTCACCTCTTGGCATCTGGCCCTGATAACAGTGTCTTCGCt             >  1:81512/1‑150 (MQ=255)                                                                                                                                          tGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTTATCTCACCTCTTGGCATCTGGCCCTGATAACAGTGTCTTCGCTa            >  1:1228588/1‑150 (MQ=255)                                                                                                                                             gTGCTGATTAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCgg                                                                                                                   >  2:472065/1‑44 (MQ=25)                                                                                                                                             gTGCTGATTAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCgg                                                                                                                   <  1:472065/44‑1 (MQ=25)                                                                                                                                                    tCAGCACCCAGGCTGTTGCGAAGCTCCCTTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTTATCTCACCTCTTGGCATCTGGCCCTGATAACAGTGTCTTCGCTATCTCTTGccc  <  1:1073903/150‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                     ACCTGCCTACTACATCATGGTTGCATCAGCACTTGGGATTATTGCGTTGTTCTTTGTGATCGAGACTAAAGGTTGCTCGATTCGCGGGGATGGAATACCTGGGGCAAAATAACCTAATAGGCAGATGGTATAGAGCCTGGGTGCTAATCAGCACCCAGGCTGTTGCGAAGCTCCATTCCTCCGGGCAAGCCGACCGGCTACGTCGATATAAGCAGCAGCGCTCCACCCTTCCTTTTTATTCTTATCTCACCTCTTGGCATCTGGCCCTGATAACAGTGTCTTCGCTATCTCTTGCCC  >  NC_002947/5030651‑5030947

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: ‑