Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	2,623,603	C→T	41.7%	P187L (CCA→CTA)	ppk →	polyphosphate kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,623,603	0	C	T	41.7%	13.2 / 27.8	31	P187L (CCA→CTA)	ppk	polyphosphate kinase
Reads supporting (aligned to +/- strand):  ref base C (8/10);  new base T (9/4);  total (17/14)
Fisher's exact test for biased strand distribution p-value = 2.75e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCTGACACTGACTTAGTGCAGTTCCTGAAAGATGATTACACCTATCTGGCGGTGGAAATTATCCGTGGCGATACCATCCGTTACGCGCTGCTGGAGATCCCATCAGATAAAGTGCCGCGCTTTGTGAATTTACCGCCAGAAGCGCCGCGTCGACGCAAGCCGATGATTCTTCTGGATAACATTCTGCGTTACTGCCTTGATGATATTTTCAAAGGCTTCTTTGATTATGACGCGCTGAATGCCTATTCAATGAAGATGACCCGCGATGCCGAATACGAT  >  NC_000913/2623467‑2623745                                                                                                                                         |                                                                                                                                               ccTGACAGTGACTTAGTGCAGTTCCTGAAAGATGATTACACCTATCTGGCGGTGTAAATTATCCGTGGCGATACCATCCGTTACGCGCTGCTGGAGATCCCATCAGATAAAGTGCCGCGCTTTGTGAATTTACCGCCAGAAgc                                                                                                                                          <  1:158049/143‑1 (MQ=255)           aCTTAGTGCAGTTCCTGAAAGATGAGTACACCTATCTGGCGGTGGAAATTATCCGTGGCGATACCATCCGTTACGCGCTGCTGGAGAGCCCATCAGATAAAGTGCCGCGCTTGGTGAATTTACCGCCAGAAGCGCCGCGTCGa                                                                                                                                >  1:167056/1‑143 (MQ=255)            cTTAGTGCAGTTCCTGAAAGATGATTACACCTATCTGGCGGTGGAAATTATCCGTGGCGATAGCATCCGTTACCCGCTGCTGGAGATCCCATCAGATAAAGTGCCGCGCTTTGTGAATTTACCGCCAGAAGCGCCGCGTCGAc                                                                                                                               >  1:414060/1‑143 (MQ=255)             ttAGTGCAGTTCCTGAAAGATGATTACACCTAGCTGGCGGTGGAAATTATCCGTGGCGATACCATCCGTTACGCGCTGCTGGAGATCCCATCAGATAAAGTGCCGCGCTTTGTGAATTTACCGCTAGAAGCGCCGCGTCGACg                                                                                                                              <  1:629792/143‑1 (MQ=255)              tAGTGGAGTCCCTGAAAGAGGATTACACCTATCTGGCGGTGGAAATTATCCGTGGCGATACCATCCGTTACGCGCTGCTGGAGATCCCATCAGATAAAGTGCCGCGCTTTGTGAATTTACCGCCAGAAGCGCCGCGTCGACGc                                                                                                                             <  2:36505/143‑1 (MQ=255)              tAGGGCAGTTCCTGAAAGAGGATTACACCGATCTGGCGGTGGAAATGATCCGTGGCGATACCATCCGTTACGCGCTGCTGGAGATCCCATCAGATAAAGTGCCGCGCTTTGTGAATTTACCGCCAGAAGCGCCGCGTCGACGc                                                                                                                             <  2:24779/143‑1 (MQ=255)                   cAGTTCCTGAAAGATGATTACACCTATCTGGCGGTGGAAATTATCCGTGGCGATACCATCCGTTACGCGCTGCTGGAGATCCCATCAGATAAAGTGCCGCGCTTTGTGAATTTACGGCTCGAAGCGCCGCGTCGGCGCAAGca                                                                                                                        >  1:396611/1‑142 (MQ=255)                          tGAAAGATGATTACACCTATCTGGCGGTGGAAATTATCCGTGGCGATACCATCCGTTACGCGCTGCTGGAGATCCCATCAGATAAAGTGCCGCGCTTTGTGAATTTACCGCTAGAAGCGCCGCGTCGACGCAAGCCGATGAtt                                                                                                                 >  1:107827/1‑143 (MQ=255)                           gAAAGATGATTACACCTATCGGGCGGTGGAAATTATCCGTGGCGATACCATCCGTTACGCGCTGCTGGAGATCCCATCAGATAAAGTGCCGCGCTTTGTGAATTTACCGCCAGAAGCGCCGCGTCGACGCAAGCCGATGAttc                                                                                                                <  1:136716/143‑1 (MQ=255)                                atgatTACACCTATCTGGCGGTGGAAATTATCCGTGGCGATACCATCCGTTACGCGCTGCTGGAGATCCCATCAGATAAAGTGCCGCGCTTTGTGAATTTACCGCCAGAAGCGCCGCGTCGACGCAAGCCGATGATTCTTCTg                                                                                                           <  1:43866/143‑1 (MQ=255)                                 tgatTACACCTATCTGGCGGTGGACATTATCCGTGGCGATACCCTCCGTTACGCGCTGCTGGAGATCCCGTCAGATAAAGTGCCGCGCTCTGTGCATTTACCCCTAGAAGCGCACCGACGCCGCAAGCGCATCATTCTTCTgg                                                                                                          >  2:350184/1‑143 (MQ=255)                                     tACACCTATCTGGCGGTGGAAATTATCCGTGGCGATACCATCCGTTACGCGCTGCTGGAGATCCCATCAGATAAAGTGCCGCGCTTTGTGAATTTACCGCCAGAAGCGCCGCGTCGACGCAAGCCGATGATTCTTCTGGATaa                                                                                                      >  1:43187/1‑143 (MQ=255)                                         ccTATCTGGCGGTGGAAATTATCCGTGGCGATACCATCCGTTACGCGCTGCTGGAGATCCCATCCGATCAAGTGCCGCGCTTCGTGAACTTACCGCCAGAAGCGCCGCGTCGACGCCCGCCGATGACTCGTCTGGATCAccgt                                                                                                  >  2:195755/1‑140 (MQ=255)                                         ccTATCGGGCGGTGGAAAGTATCCGTGGCGGGACCATCCGTCACGCGCTGCTGGAGAGCCCAGCAGATAAAGTGCCGCGCTTTGTGAATTGACCGCCAGACGCGCCGCGGCGACGCAAGCCGATGATTCTTCTGGATAACAtt                                                                                                  <  1:80684/143‑1 (MQ=255)                                           tATCTGGAGGTGGAAATTATCCGTGGCTATACCATCCGTTACGCGCTGCTGGAGATCCCATCAGATAAAGTGCCGCGCTTTGTGAATTTACCGCCAGAAGCGCCGCGTCGACGCAAGCCGATGATTCTTCTGGATAACATTCt                                                                                                <  2:622099/143‑1 (MQ=255)                                                      ggAAAGTATCCGTGGCGATACCATCCGTTACGCGCTGCTGGAGATCCCATCAGATAAAGTGCCGCGCTTTGTGAATTTACCGCCAGAAGCGCCGCGTCGACGCAAGCCGATGATTCTTCTGGATAACATTCTGCGTTACTGcc                                                                                     <  1:620346/143‑1 (MQ=255)                                                              tCCGTGGCGATACCATCCGTTACGCGCTGCTGGAGATCCCATCAGATAAAGTGCCGCGCTTTGTGAATTTACCGCTAGAAGCGCCGCGTCGACGCAAGCCGATGATTGTGATGGGTGACGTTCTGCGTTACTGCCTTgatgat                                                                             >  1:509121/1‑143 (MQ=255)                                                                       aTACCATCCGTTACGCGCTGCTGGAGATCCCATCAGATAAAGTGCCGCGCTTTGTGAATTTACCGCTAGAAGCGCCGCGTCGACGCAAGCCGATGATTCTTCTGGATAACATTCTGCGTTACTGCCTTGATGCTATCTTCaaa                                                                    >  1:400241/1‑143 (MQ=255)                                                                                   aCGCGCTGCTGGAGATCCCATCAGATAAAGTGCCGCGCCTTGTGAATTTACCGCCAGAAGCGCCGCGTCGACTCGAGCCGATGATTCTTCTGGATAACATTCTGCGTTACTGCCTTGATGATATTTTCAAAGGCTTCTTTGAt                                                        <  1:92422/143‑1 (MQ=255)                                                                                            tgGAGATCCCATCAGATAAAGTGCCGCGCTTTGTGAATTTACCGCCAGAAGCGCCGCGTCGACGCAAGCCGATGATTCTTCTGGATAACATTCTGCGTTACTGCCTTGATGATATTTTCAAAGGCTTCTTTGATTATGAcgcg                                               >  2:411602/1‑143 (MQ=255)                                                                                                    ctatgaGATAAAGTGCCGCGCTTTGTGAATTTCCCGCTAGAAGCGCCGCGTCGACGCAACCCGATGATTCTTCTGGATAACATTCTGCGTTACTGCCTTGATGATATTTTCAAAGGCTTCTTTGATTATGACGCGCTGAATGc                                       <  2:323984/138‑1 (MQ=255)                                                                                                    ccATCAGATAAAGTGCCGCGCTTTGTGAATTTACCGCTAGAAGCGCCGCGTCGACGCACGCCGATGATTCTTCTGGATAACATTCTGCGTTACTGCCTTGATGATATTTTCAAAGGCTTCTTTGATTATGACGCGCTGAATGc                                       >  1:399196/1‑143 (MQ=255)                                                                                                    ccATCAGACAAAGTGCCGCGCTTTGTGAATTTACCGCCAGAAGCGCCGCGTCGACGCAAGCCGATGATTCTTCTGGATAACATTCTGCGTTACTGTCTTGATGATATTTTCAAAGGCTTCTTTGATTATGACGCGCTGAATGc                                       <  1:628707/143‑1 (MQ=255)                                                                                                    ccATCACTTAACGTGCCGCGCCTTGTGAATTTACCGCTAGAAGCGCCGCGCCGACGCAAGCGGATGATTCTTCTGGATAACATTCTGCGTTACTGCCTTGATGAGATTTTCAAAGGCTTCTTTGATTATGACGCGCTGAATGc                                       <  2:79654/143‑1 (MQ=255)                                                                                                               aGTGCCGCGCTTTGTGAATTTACCGCCAGAAGCGCCGCGTCGACGCAAGCCGATGATTCTTCTGGATAACATTCTGCGTTACTGCCTTGATGATATTTTCAAAGGCTTCTTTGCTTATGACGCGCTGAATGCCTATTCAATGa                            >  1:369319/1‑143 (MQ=255)                                                                                                                 tGCCGCGCTTTGTGAATTTACCGCTAGAAGCGCCGCGTCGACGCAAGCCGATGATTCTTCTGGATAACATTCTGCGTTACTGCCTTGATGATATTTTCAAAGGCTTCTTTGATTATGACGCGCTGAATGCCTATTCAATGAAg                          <  2:107827/143‑1 (MQ=255)                                                                                                                     gcgcTTTGTGAATTTACCGCTAGAAGCGCCACGACGACGCAAGACGATAATTCTTCTAGATAACATTCTGCGTTACTGCCTTGATGATATTTTCAAAGGCTTCTTTTATTATGACGAGATGAATACCAATAAAATAAAAATGa                      >  2:171321/1‑143 (MQ=255)                                                                                                                         tttGTGAATTTACCGCCAGAAGCGCCGCGTCGACGCAAGCCGATGATTCTTCTGGATAACATTCTGCGTTACTGCCTTGATGATATTTTCAAAGGCTGCTTTGATTATGACTCGCTGCATGCCAATTCAATGACGGTGGcccc                  >  2:113415/1‑142 (MQ=255)                                                                                                                               aaTTTACCGCTAGAAGCGCCGCGTCGACGCAAGCCGATGATTCTTCTGGATAACATTCTGCGTTACTGCCTTGATGATATTTTCAAAGGCTTCTTTGGTTATCACGCGCGGAATGCCTATTCAATGAAGATGACCCGCGATGc            >  2:45327/1‑143 (MQ=255)                                                                                                                                 tttACCGCTAGAAGCGCCGCGTCGACGCAAGCCGATGATTCTTCTGGATAACATTCTGCGTTACTGCCTTGATGATATTTTCAAAGGCTTCTTTGATTATGACGCGCTGAATGCCTATTCAATGAAGATGACCCGCGATGCCg          >  1:425574/1‑143 (MQ=255)                                                                                                                                 tttACCGCCAGAAGCGCCGCGTCGACGCAAGCCGATGATTCTTCTGGATAACATTCTGCGTTACTGCCTTGATGATATTTTCAAAGGCTTCTTTGATTATGACGCGCTGGAGGCCTATTCAATGCAGATGACCcgccctcccc          >  1:176730/1‑136 (MQ=255)                                                                                                                                         cAGAAGCGCCGCGTCGACGCAAGCCGATGATTCTTCTGGATAACATTCTGCGTTACTGCCTTGGTGATATTTTCAAAGGCTTCTTTGATTATGACGCGCTGAATGCCTATTCAATGAAGATGACCCGCGATGCCGAATACGAt  >  1:376654/1‑143 (MQ=255)                                                                                                                                         |                                                                                                                                               CCTGACACTGACTTAGTGCAGTTCCTGAAAGATGATTACACCTATCTGGCGGTGGAAATTATCCGTGGCGATACCATCCGTTACGCGCTGCTGGAGATCCCATCAGATAAAGTGCCGCGCTTTGTGAATTTACCGCCAGAAGCGCCGCGTCGACGCAAGCCGATGATTCTTCTGGATAACATTCTGCGTTACTGCCTTGATGATATTTTCAAAGGCTTCTTTGATTATGACGCGCTGAATGCCTATTCAATGAAGATGACCCGCGATGCCGAATACGAT  >  NC_000913/2623467‑2623745

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑