Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,964,868	T→C	K96K (AAA→AAG)	thyA ←	thymidylate synthetase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,964,868	0	T	C	93.9%	102.8 / ‑1.6	34	K96K (AAA→AAG)	thyA	thymidylate synthetase
Reads supporting (aligned to +/- strand):  ref base T (1/1);  new base C (14/17);  total (16/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01

TAATGCGGCGCGAATCCGGGTCGTTTTTCAGCTGGTTCAGTACCGTAGTGATCTGGTCAATATGACGACCATCTGGCGTTGGCCAGGCGCGCCACTGTTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGATGGTGACATTGTTTTCGTGTAGATAAGCAATGTTAG  >  NC_000913/2964771‑2964956                                                                                                  |                                                                                         taatGCGGCGCGAATCCGGGTCGTTTTTCAGCTGGTTCAGTACCGTAGTGATCTGGTCAATATGACGACCATCTGGCGTTGGCCAGGCGCGCCACTGctt                                                                                        <  1:83974/100‑1 (MQ=255)    tGCGGCGCGAATCCGGGTCGTTTTTCAGCTGGTTCAGTACCGTAGTGATCTGGTCAATATGACGACCATCTGGCGTTGGCCAGGCGCGCCACTGCTTAcc                                                                                     >  2:419759/1‑100 (MQ=255)    tGCGGCGCGAATCCGGGTCGTTTTTCAGCTGGTTCAGTACCGTAGTGATCTGGTCAATATGACGACCATCTGGCGTTGGCCAGGCGCGCCACTGCTTAcc                                                                                     <  2:1151204/100‑1 (MQ=255)     gcggcgCGAATCCGGGTCGTTTTTCAGCTGGTTCAGTACCGTAGTGATCTGGTCAATATGACGACCATCTGGCGTTGGCCAGGCGCGCCACTGCTTACCa                                                                                    <  2:561367/100‑1 (MQ=255)         cgcgAATCCGGGTCGTTTTTCAGCTGGTTCAGTACCGTAGTGATCTGGTCAATATGACGACCATCTGGCGTTGGCCAGGCGCGCCACTGCTTACCATaca                                                                                <  2:420666/100‑1 (MQ=255)                  gggTCGTTTTTCAGCTGGTTCAGTACCGTAGTGATCTGGTCAATATGACGACCATCTGGCGTTGGCCAGGCGCGCCACTGCTTACCATACACTGGCCCGa                                                                       <  1:799113/100‑1 (MQ=255)                    gTCGTTTTTCAGCTGGTTCAGTACCGTAGTGATCTGGTCAATATGACGACCATCTGGCGTTGGCCAGGCGCGCCACTGCTTACCATACACTGGCCCGAgg                                                                     <  1:953577/100‑1 (MQ=255)                     tCGTTTTTCAGCTGGTTCAGTACCGTAGTGATCTGGTCAATATGACGACCATCTGGCGTTGGCCAGGCGCGCCACTGCTTACCATACACTGGCCCGAGGt                                                                    >  2:8873/1‑100 (MQ=255)                      cGTTTTTCAGCTGGTTCAGTACCGTAGTGATCTGGTCAATATGATGACCATCTGGCGTTGGCCAGGCGCGCCACTGCTTACCATACACTGGCCCGAGGTc                                                                   <  1:424240/100‑1 (MQ=255)                      cGTTTTTCAGCTGGTTCAGTACCGTAGTGATCTGGTCAATATGATGACCATCTGGCGTTGGCCAGGCGCGCCACTGCTTACCATACACTGGCCCGAGGTc                                                                   <  1:424243/100‑1 (MQ=255)                                  ggTTCAGTTCCGTAGTGATCTGGTCAATCTGACGACCATCTGGCGTTGGCCAGGCGCGCCACTTCTTACCATACGCTGGCCCGGGGTCGCCGGTTTc                                                          <  2:1010103/97‑1 (MQ=255)                                  ggTTCAGTACCGTAGTGATCTGGTCAATATCCCGACCATCTGGCTTTGGCCAGGCGCGCCACTGGTTACCATACACTGGCCCGAGGTCGcc                                                                >  2:1102832/1‑91 (MQ=255)                                    ttCATTACCGTAGTGAGCTTGTCAATATGACGACCATCTGGCGTTGGCCAGGCGCGCCACTGCTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCgg                                                     <  1:564585/100‑1 (MQ=255)                                     tCAGTACCGCAGTGATCTGGTCAATATGACGACCATCTGGCGTTGGCCAGGCGCGCCACTGCTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGc                                                    <  1:531810/100‑1 (MQ=255)                                             gTAGTGATCTGGTCAATATGACGACCATCTGGCGTTGGCCAGGCGCGCCACTGCTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGt                                            >  1:211079/1‑100 (MQ=255)                                                 tGATCTGGTCAATATGACGACCATCTGGCGTTGGCCAGGCGCGCCACTGCTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCa                                        >  1:1008793/1‑100 (MQ=255)                                                    tCTGGTCAATATGACGACCATCTGGCGTTGGCCAGGCGCGCCACTGCTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGAt                                     >  2:728637/1‑100 (MQ=255)                                                        gTCAATATGACGACCATCTGGCGTTGGCCAGGCGCGCCACTGCTTACCATACGCTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGATGGTg                                 >  2:505453/1‑100 (MQ=255)                                                        gTCAATATGACGACCATCTGGCGTTGGCCAGGCGCGCCACTGCTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGATGGTg                                 >  1:438951/1‑100 (MQ=255)                                                               tGACGACCATCTGGCGTTGGCCAGGCGCGCCACTGCTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGATGGTGACATTg                           >  2:829625/1‑99 (MQ=255)                                                                gacgacCATCTGGCGTTGGCCAGGCGCGCCACTGCTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGACCCATTCGTCCCAGATGGTGACATTGtt                         >  1:564556/1‑100 (MQ=255)                                                                  cgacCATCTGGCGTTGGCCAGGCGCGCCACTGCTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGATGGTGACATTGtttt                       >  1:1164717/1‑100 (MQ=255)                                                                    acCATCTGGCGTTGGCCAGGCGCGCCACTGCTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGATGGTGACATTGTTTTCg                     <  1:146326/100‑1 (MQ=255)                                                                      cATCTGGCGTTGGCTAGGCGCGCCACTGCTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGATGGTGACATTGTTTTCg                     <  2:362096/98‑1 (MQ=255)                                                                        tCTGGCGTTGGCCAGGCGCGCCACTGCTTACCATCCACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGATGGTGACATTGTTTTCGTGTa                 <  1:419763/100‑1 (MQ=255)                                                                           ggCGTTGGCCAGGCGCGCCACTGCTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGATGGTGACATTGTTTTCGTGTAGAt              >  2:898504/1‑100 (MQ=255)                                                                              gTTGGCCAGGCGCGCCACTGCTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGATGGTGACATTGTTTTCGTGTAGATAAg           >  1:1119919/1‑100 (MQ=255)                                                                               ttGGCCGGGCGCGCCACTGCTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGATGGTGACATTGTTTTCGTGTAGATAAGc          <  1:775694/100‑1 (MQ=255)                                                                                cgatctggCGCGCCACTGCTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGATGGTGACATTGTTTTCGTGTAGATAAGCa         <  1:271704/94‑1 (MQ=255)                                                                                 ggCCAGGCGCGCCACTGCTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGATGGTGACATTGTTTTCGTGTAGATAAGCaa        >  1:40755/1‑100 (MQ=255)                                                                                   ccAGGCGCGCCACTGCTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGATGGTGACATTGTTTTCGTGTAGATAAGCAATg      <  2:309947/100‑1 (MQ=255)                                                                                    cAGGCGCGCCACTGTTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGATGGTGACATTGTTTTCGTGTAGATAAGCAATGt     >  1:55303/1‑100 (MQ=255)                                                                                      ggCGCGCCACTGCTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGATGGTGACATTGTTTTCGTGTAGATAAGCaagatcg   >  2:271701/1‑95 (MQ=255)                                                                                       gcgcgcCTCTGTTTCCCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGATGGTGACATTGTTTTCGTGTGGATAAGCAATGTTAg  <  2:600478/100‑1 (MQ=255)                                                                                        cgcgcCACTGCTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGATGGTGACATTGTTTTCGTGTAGATAAGCAATGTTAg  <  2:621578/99‑1 (MQ=255)                                                                                                  |                                                                                         TAATGCGGCGCGAATCCGGGTCGTTTTTCAGCTGGTTCAGTACCGTAGTGATCTGGTCAATATGACGACCATCTGGCGTTGGCCAGGCGCGCCACTGTTTACCATACACTGGCCCGAGGTCGCCGTTTTCATCGGCCCATTCGTCCCAGATGGTGACATTGTTTTCGTGTAGATAAGCAATGTTAG  >  NC_000913/2964771‑2964956

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: ‑