Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,168,855	G→T	13.5%	G242C (GGT→TGT)	PP_5482 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,168,855	0	G	T	13.5%	109.1 / 3.9	37	G242C (GGT→TGT)	PP_5482	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (16/16);  new base T (2/3);  total (18/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.05e-01

GATAAAGTTTCTTGAGGAACGGCTTGAGTTTTTGCTGTTGCCTGGTGGTCGTGTACAGAGGTCGCCCATGATCTCTCTGATTATTACAGGTAATCAAGACCGATTCTTGTATTATTACCCATACTGTAAAGGTTATGCTGGTGAAGCTGGTGTTGTAAAAATGATAGCGGCAGCCAATGAGAAAAAAAGAGATGAAAATGGCCGCTGGCAAGGATTCAAGGTTGATGATGAGTTACACTCTTACTCCTATTATGCTCTTGCAGAT  >  NC_002947/2168725‑2168989                                                                                                                                   |                                                                                                                                       gATAAAGTTTCTTGAGGACCGGCTTGAGTTTTTGCTGTTGCCTGGTGGTCGTGTACAGAGGTCGCCCATGATCTCTCTGATTATTACAGGTAATCAAGACCGATTCTTGTATTATTACCCATACTGTAAAGGTTAt                                                                                                                                   >  1:297738/1‑136 (MQ=255)           cTTGAGGAACGGCTTGAGTTTTTGCTGTTGCCTGGTGGTCGTGTACAGAGGTCGCCCATGATCTCTCTGATTATTACAGGTAATCAAGACCGATTCTTGTATTATTACCCATACTGTAAAGGTTATGCTGGTGAAg                                                                                                                         >  1:164472/1‑136 (MQ=255)              gAGTAACGGCTTGAGTTTTTGCTGTTGCCTGGTGGTCGTGTACAGAGGTCGCCCATGATCTCTCTGATTATTACAGGTAATCAAGACCGATTCTTGTATTATTACCCATACTGTAAAGGTTATGCTGGTGAAGCTg                                                                                                                      <  1:546667/136‑1 (MQ=255)                                                                 cccATGATCTCTCTGATTATTACAGGTAATCAAGACCGATTCTTGTATTATTACCCATACTGTAAATGTTATGCTGGTGAAGCTGGTGTTGTAAAAATGATAGCGGCAGCCAATGAGAAAAAAAGAGATGAAAATg                                                                   >  2:137807/1‑136 (MQ=255)                                                                 cccATGATCTCTCTGATTATTACAGGTAATCAAGACCGATTCTTGTATTATTACCCATACTGTAAATGTTATGCTGGTGAAGCTGGTGTTGTAAAAATGATAGCGGCAGCCAATGAGAAAAAAAGAGATGAAAATg                                                                   >  2:140471/1‑136 (MQ=255)                                                                               tattattACAGGTAATCAAGACCGATTCTTGTATTATTACCCATACTGTAAAGGTTATGCTGGTGAAGCTGGTGTTGTAAAAATGATAGCGGCAGCCAATGAGAAAAAAAGAGATGAAAATGGCCGCTGGCAAGGa                                                     <  2:542694/135‑1 (MQ=255)                                                                               gATTATTACAGGTAATCAAGACCGATTCTTGTATTATTACCCATACTGTAAAGGTTATGCTGGTGAAGCTGGTGTTGTAAAAATGATAGCGGCAGCCAATGAGAAAAAAAGAGATGAAAATGGCCGCTGGCAAGGa                                                     >  1:200962/1‑136 (MQ=255)                                                                               gATTATTACAGGTAATCAAGACCGATTCTTGTATTATTACCCATACTGTAAAGGTTATGCTGGTGAAGCTGGTGTTGTAAAAATGATAGCGGCAGCCAATGAGAAAAAAAGAGATGAAAATGGCCGCTGGCAAGGa                                                     >  1:259056/1‑136 (MQ=255)                                                                                   attaCAGGTAATCAAGACCGATTCTTGTATTATTACCCATACTGTAAAGGTTATGCTGGTGAAGCTGGTGTTGTAAAAATGATAGCGGCAGCCAATGAGAAAAAAAGAGATGAAAATGGCCGCTGGCAAGGATTCa                                                 >  1:164352/1‑136 (MQ=255)                                                                                       cAGGTAATCAAGACCGATTCTTGTATTATTACCCATACTGTAAAGGTTATGCTGGTGAAGCTGGTGTTGTAAAAATGATAGCGGCAGCCAATGAGAAAAAAAGAGATGAAAATGGCCGCTgg                                                           <  1:126035/122‑1 (MQ=255)                                                                                       cAGGTAATCAAGACCGATTCTTGTATTATTACCCATACTGTAAAGGTTATGCTGGTGAAGCTGGTGTTGTAAAAATGATAGCGGCAGCCAATGAGAAAAAAAGAGATGAAAATGGCCGCTgg                                                           >  2:126035/1‑122 (MQ=255)                                                                                             aTCAAGACCGATTCTTGTATTATTACCCATACTGTAAAGGTTATGCTGGTGAAGCTGGTGTTGTAAAAATGATAGCGGCAGCCAATGAGAAAAAAAGAGATGAAAATGGCCGCTGGCAAGGATTCAAGGTtgatga                                       >  1:342348/1‑136 (MQ=255)                                                                                             aTCAAGACCGATTCTTGTATTATTACCCATACTGTAAAGGTTATGCTGGTGAAGCTGGTGTTGTAAAAATGATAGCGGCAGCCAATGAGAAAAAAAGAGATGAAAATGGCCGCTGGCAAGGATTCAAGGTtgatga                                       >  1:56254/1‑136 (MQ=255)                                                                                                 aGACCGATTCTTGTATTATTACCCATACTGTAAAGGTTATGCTGGTTATGCTGGTGTTGTAAAAATGATAGCGGCAGCCAATTAGAAAAAAAGAGATGAAAATGGCCGCTGGCAAGGATTCAAGGTTGATGATGAg                                   <  2:261961/136‑1 (MQ=255)                                                                                                  tacagATTCTTGTATTATTACCAATACTGTAAAGGTTATGCTGGTGAAGGTGGTGTTTTAAAAATGATAGCGGCAGCCAATGAGAAAAAAAGAGATGAAAATGGCCGCTGGCAAGGATTCAAGGTTGATGATGAGt                                  <  1:74605/132‑1 (MQ=255)                                                                                                  tacagATTCTTGTATTATTACCAATACTGTAAAGGTTATGCTGGTGAAGCTGGTGTTGTAAAAATGATAGCGGCAGCCAATGAGAAAAAAAGAGATGAAAATGGCCGCTGGCAAGGATTCAAGGTTGATGATGAGt                                  <  1:147967/132‑1 (MQ=255)                                                                                                  caCCGATTCTTGTATTATTACCCATACTGTAAAGGTTATGCTGGTGAAGCTGGTGTTGTAAAAATGATAGCGGCAGCCAATGAGAAAAAAAGAGATGAAAATGGCCGCTGGCAAGTATTCAAGGTTGATGATGAGt                                  <  1:410771/135‑1 (MQ=255)                                                                                                     cGATTCTTGTATTATTACCCATACTGTAAAGGTTATGCTGGTGAAGCTGGTGTTGTAAAAATGATAGCGGCAGCCAATGAGAAAAAAAGAGATGAAAATGGCCGCTGGCAAGGATTCAAGGTTGATGATGAGTTac                               >  1:360468/1‑136 (MQ=255)                                                                                                     cGATTCTTGTATTATTACCCATACTGTAAAGGTTATGCTGGTGAAGCTGGTGTTGTAAAAATGATAGCGGCAGCCAATGAGAAAAAAAGAGATGAAAATGGCCGCTGGCAAGGATTCAAGGTTGATGATGAGTTaa                               >  1:206543/1‑135 (MQ=255)                                                                                                       aTTCTTGTATTATTACCCATACTGTAAAGGTTATGCTGGTGAAGCTGGTGTTGTAAAAATGATAGCGGCAGCCAATGAGAAAAAAAGAGATGAAAATGGCCGCTGGCAAGGATTCAAGGTTGATGATGAGTTacac                             <  1:165326/136‑1 (MQ=255)                                                                                                       aTTCTTGTATTATTACCCATACTGTAAAGGTTATGCTGGTGAAGCTGGTGTTGTAAAAATGATAGCGGCAGCCAATGAGAAAAAAAGAGATGAAAATGGCCGCTGGCAAGGATTCAAGGTTGATGATGAGTTacac                             <  1:294096/136‑1 (MQ=255)                                                                                                            tGTATTATTACCCATACTGTAAAGGTTATGCTGGTGAAGCTGGTGTTGTAAAAATGATAGCGGCAGCCAATGAGAAAAAAAGAGATGAAAATGGCCGCTGGCAAGGATTCAAGGTTGATGATGAGTTACACTCTTa                        <  2:516639/136‑1 (MQ=255)                                                                                                            tGTATTATTACCCATACTGTAAAGGTTATGCTGGTGAAGCTGGTGTTGTAAAAATGATAGCGGCAGCCAATGAGAAAAAAAGAGATGAAAATGGCCGCTGGCAAGGATTCAAGGTTGATGATGAGTTACACTCTTa                        <  1:50296/136‑1 (MQ=255)                                                                                                               attattACCCATACTGTAAAGGTTATGCTGGTGAAGCTGGTGTTGTAAAAATGATAGCGGCAGCCAATGAGAAAAAAAGAGATGAAAATGGCCGCTGGCAAGGATTCAAGGTTGATGATGAGTTACACTCTTACTc                     >  1:394538/1‑136 (MQ=255)                                                                                                                  attaCCCATACTGTAAAGGTTATGCTGGTGAAGCTGGTGTTGTAAAAATGATAGCGGCAGCCAATGAGAAAAATAGAGATGAAAATGGCCGCTGGCAAGGATTCAAGGTTGATGATGAGTTACACTCTTACTCCta                  <  2:399007/136‑1 (MQ=255)                                                                                                                  attaCCCATACTGTAAAGGTTATGCTGGTGAAGCTGGTGTTGTAAAAATGATAGCGGCAGCCAATGAGAAAAAAAGAGATGAAAATGGCCGCTGGCAAGGATTCAAGGTTGATGATGAGTTACACTCTTACTCCta                  <  2:297738/136‑1 (MQ=255)                                                                                                                              gTAAAGGTTATGCTGGTGAAGCTGGTGTTGTAAAAATGATAGCGGCAGCCAATGAGAAAAAAAGAGATGAAAATGGCCGCTGGCAAGGATTCAAGGTtg                                           >  2:114817/1‑99 (MQ=255)                                                                                                                              gTAAAGGTTATGCTGGTGAAGCTGGTGTTGTAAAAATGATAGCGGCAGCCAATGAGAAAAAAAGAGATGAAAATGGCCGCTGGCAAGGATTCAAGGTtg                                           <  1:114817/99‑1 (MQ=255)                                                                                                                              gTAAAGGTTATGCTGGTGAAGCTGGTGTTGTAAAAATGATAGCGGCAGCCAATGAGAAAAAAAGAGATGAAAATGGCCGCTGGCAAGGATTCAAGGTTGATGATGAGTTACACTCTTACTCCTATTATGCTCTTGc      <  1:267254/136‑1 (MQ=255)                                                                                                                                aaaTGTTATGCTGGTGAAGCTGGTGTTGTAAAAATGATAGCGGCAGCCAATGAGAAAAAAAGAGATGAAAATGGCCGCTGGCAAGGATTCAAGGTTGATGATGAGTTACACTCTTACTCCTATTATGCTCTTGCAg    <  1:147172/136‑1 (MQ=255)                                                                                                                                aaaTGTTATGCTGGTGAAGCTGGTGTTGTAAAAATGATAGCGGCAGCCAATGAGAAAAAAAGAGATGAAAATGGCCGCTGGCAAGGATTCAAGGTTGATGATGAGTTACACTCTTACTCCTATTATGCTCTTGCAg    <  1:140471/136‑1 (MQ=255)                                                                                                                                aaaTGTTATGCTGGTGAAGCTGGTGTTGTAAAAATGATAGCGGCAGCCAATGAGAAAAAAAGAGATGAAAATGGCCGCTGGCAAGGATTCAAGGTTGATGATGAGTTACACTCTTACTCCTATTATGCTCTTGCAg    <  1:137807/136‑1 (MQ=255)                                                                                                                                aaaGGTTATGCTGGTGAAGCTGGTGTTGTAAAAATGATAGCGGCAGCCAATGAGAAAAAAAGAGATGAAAATGGCCGCTGGCAAGGATTCAAGGTTGATGATGAGTTACACTCTTACTCCTATTATGCTCTTGCAg    >  1:89953/1‑136 (MQ=255)                                                                                                                                aaaGGTTATGCTGGTGAAGCTGGTGTTGTAAAAATGATAGCGGCAGCCAATGAGAAAAAAAGAGATGAAAATGGCCGCTGGCAAGGATTCAAGGTTGATGATGAGTTACACTCTTACTCCTATTATGCTCTTGCAg    <  2:342348/136‑1 (MQ=255)                                                                                                                                aaaGGTTATGCTGGTGAAGCTGGTGTTGTAAAAATGATAGCGGCAGCCAATGAGAAAAAAAGAGATGAAAATGGCCGCTGGCAAGGATTCAAGGTTGATGATGAGTTACACTCTAACTCCTATTATGCTCTTGCAg    >  1:335476/1‑136 (MQ=255)                                                                                                                                  aGGTTATGCTGGTGAAGCTGGTGTTGTAAAAATGATAGCGGCAGCCAATGAGAAAAAAAGAGATGAAAATGGCCGCTGGCAAGGATTCAAGGTTGATGATGAGTTACACTCTTACTCCTATTATGCTCTTGCAGAt  >  2:545755/1‑136 (MQ=255)                                                                                                                                  aGGTTATGCTGGTGAAGCTGGTGTTGTAAAAATGATAGCGGCAGCCAATGAGAAAAAAAGAGATGAAAATGGCCGCTGGCAAGGATTCAAGCTTGATGATGAGTTACACTCTAACTCCAATTATGCTCTTGCAGAt  >  2:538902/1‑136 (MQ=255)                                                                                                                                   |                                                                                                                                       GATAAAGTTTCTTGAGGAACGGCTTGAGTTTTTGCTGTTGCCTGGTGGTCGTGTACAGAGGTCGCCCATGATCTCTCTGATTATTACAGGTAATCAAGACCGATTCTTGTATTATTACCCATACTGTAAAGGTTATGCTGGTGAAGCTGGTGTTGTAAAAATGATAGCGGCAGCCAATGAGAAAAAAAGAGATGAAAATGGCCGCTGGCAAGGATTCAAGGTTGATGATGAGTTACACTCTTACTCCTATTATGCTCTTGCAGAT  >  NC_002947/2168725‑2168989

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑