Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,956,019	T→C	V230A (GTT→GCT)	ilvA →	threonine deaminase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,956,019	0	T	C	97.8%	146.4 / ‑4.3	46	V230A (GTT→GCT)	ilvA	threonine deaminase
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base C (20/25);  total (20/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.26e-01

GTGCCAGTCGGCGGCGGCGGTCTGGCTGCTGGCGTGGCGGTGCTGATCAAACAACTGATGCCGCAAATCAAAGTGATCGCCGTAGAAGCGGAAGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGTTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGAAACCTTCCGTTTATGCCAGGAGTATCTCGACGACATCATCACCGTCGATAGCGATGCGATCTGTGCGGCGATGA  >  NC_000913/3955883‑3956153                                                                                                                                         |                                                                                                                                       gtgCCAGTCGGCGGCGGCGGTCTGGCTGCTGGCGTGGCGGTGCTGATCAAACAACTGATGCCGCAAATCAAAGTGATCGCCGTAGAAGCGGAAGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGCTGa                                                                                                                                     >  1:299188/1‑140 (MQ=255)    ccAGTCGGCGGCGGCGGTCTGGCTGCTGGCGTGGCGGTGCTGATCAAACAACTGATGCCGCAAATCAAAGTGATCGCCGTAGAAGCGGAAGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGGCATCCGGCTGATCt                                                                                                                                  >  2:576295/1‑140 (MQ=255)       gTCGGCGGCGGCGGTCTGGCTGCTGGCGTGGCGGTGCTGATCAAACAACTGATGCCGCAAATCAAAGTGATCGCCGTAGAAGCGGAAGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGCTGATCTGcc                                                                                                                               >  1:64972/1‑140 (MQ=255)       gTCGGCGGCGGCGGTCTGGCTGCTGGCGTGGCGGTGCTGATCAAACAACTGATGCCGCAAATCAAAGTGATCGCCGTAGAAGCGGAAGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGCTGATCTGcc                                                                                                                               >  1:345854/1‑140 (MQ=255)        tCGGCGGCGGCGGTCTGGCTGCTGGCGTGGCGGTGCTGATCAAACAACTGATGCCGCAAATCAAAGTGATCGCCGTAGAAGCGGAAGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGCTGATCTGCcg                                                                                                                              <  2:345854/140‑1 (MQ=255)             ggcggcggTCTGGCTGCTGGCGTGGCGGTGCTGATCAAACAACTGATGCCGCAAATCAAAGTGATCGCCGTAGAAGCGGAAGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGCTGATCTGCCGCGCGt                                                                                                                         <  2:420244/140‑1 (MQ=255)                  cggTCTGGCTGCTGGCGTGGCGGTGCTGATCAAACAACTGATGCCGCAAATCAAAGTGATCGCCGTAGAAGCGGAAGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGCTGATCTGCCGCGCGTAGGGc                                                                                                                    <  2:608744/140‑1 (MQ=255)                     tCTGGCTGCTGGCGTGGCGGTGCTGATCAAACAACTGATGCCGCAAATCAAAGTGATCGCCGTAGAAGCGGAAGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGCTGATCTGCCGCGCGTAGGGCTAt                                                                                                                 <  1:327618/140‑1 (MQ=255)                                   tggcgGTGCTGATCAAACAACTGATGCCGCAAATCAAAGTGATCGCCGTAGAAGCGGAAGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGCTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTa                                                                                                   >  2:904576/1‑140 (MQ=255)                                     gcgGTGCTGATCAAACAACTGATGCCGCAAATCAAAGTGATCGCCGTAGAAGCGGAAGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGCTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGc                                                                                                 >  1:62026/1‑140 (MQ=255)                                     gcgGTGCTGATCAAACAACTGATGCCGCAAATCAAAGTGATCGCCGTAGAAGCGGAAGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGCTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGc                                                                                                 >  2:863756/1‑140 (MQ=255)                                                cAAACAACTGATGCCGCAAATCAAAGTGATCGCCGTAGAAGCGGAAGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGCTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCa                                                                                      >  1:448278/1‑140 (MQ=255)                                                   acaacTGATGCCGCAAATCAAAGTGATCGCCGTAGAAGCGGAAGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGCTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCg                                                                                   <  2:299188/140‑1 (MQ=255)                                                     aacTGATGCCGCAAATCAAAGTGATCGCCGTAGAAGCGGAAGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGCTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGt                                                                                 >  2:806232/1‑140 (MQ=255)                                                        tGATGCCGCAAATCAAAGTGATCGCCGTAGAAGCGGAAGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGCTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGAc                                                                              >  1:310391/1‑140 (MQ=255)                                                        tGATGCCGCAAATCAAAGTGATCGCCGTAGAAGCGGAAGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGCTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGAc                                                                              >  2:75165/1‑140 (MQ=255)                                                          aTGCCGCAAATCAAAGTGATCGCCGTAGAAGCGGAAGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGCTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGa                                                                            >  1:375306/1‑140 (MQ=255)                                                           tGCCGCAAATCAAAGTGATCGCCGTAGAAGCGGAAGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGCTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGaa                                                                           <  2:310391/140‑1 (MQ=255)                                                            gCCGCAAATCAAAGTGATCGCCGTAGAAGCGGAAGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGCTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGaaa                                                                          <  2:62026/140‑1 (MQ=255)                                                            gCCGCAAATCAAAGTGATCGCCGTAGAAGCGGAAGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGCTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGaaa                                                                          >  1:891799/1‑140 (MQ=255)                                                                 aaaTCAAAGTGATCGCCGTAGAAGCGGAAGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGCTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGAAACCTTc                                                                     <  2:528330/140‑1 (MQ=255)                                                                     cAAAGTGATCGCCGTAGAAGCGGAAGACTCCGCCTGCCTGAAAGCAGCGCCGGATGCGGGTCATCCGGTTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGAAACCTTCCGtt                                                                 <  2:893945/140‑1 (MQ=255)                                                                          tGATCGCCGTAGAAGCGGAAGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGCTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGAAACCTTCCGTTTATGc                                                            <  2:64972/140‑1 (MQ=255)                                                                             tCGCCGTAGAAGCGGAAGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGCTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGAAACCTTCCGTTTATGCCAg                                                         >  1:370413/1‑140 (MQ=255)                                                                              cGCCGTAGAAGCGGAAGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGCTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGAAACCTTCCGTTTATGCCAgg                                                        <  1:75165/140‑1 (MQ=255)                                                                                         cGGAAGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGCTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGAAACCTTCCGTTTATGCCAGGAGTATCTcgac                                             <  1:904576/140‑1 (MQ=255)                                                                                         cGGAAGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGCTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGAAACCTTCCGTTTATGCCAGGAGTATCTcgac                                             <  2:570812/140‑1 (MQ=255)                                                                                           gAAGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGCTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGAAACCTTCCGTTTATGc                                                            <  1:390554/123‑1 (MQ=255)                                                                                           gAAGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGCTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGAAACCTTCCGTTTATGc                                                            >  2:390554/1‑123 (MQ=255)                                                                                           gAAGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGCTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGAAACCTTCCGTTTATGCCAGGAGTATCTcgacga                                           >  2:656661/1‑140 (MQ=255)                                                                                           gAAGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGCTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGAAACCTTCCGTTTATGCCAGGAGTATCTcgacga                                           >  1:36388/1‑140 (MQ=255)                                                                                                  ccGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGCTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGAAACCTTCCGTTTATGCCAGGAGTATCTCGACGACatcatc                                    <  2:190611/140‑1 (MQ=255)                                                                                                   cGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGCTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGAAACCTTCCGTTTATGCCAGGAGTATCGCGACGACAtcagca                                   >  2:864464/1‑140 (MQ=255)                                                                                                         cctgAAAGCAGCGCTGGATGCGGGTCATCCGGCTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGAAACCTTCCGTTTATGCCAGGAGTATCTCgacgac                                          <  2:949733/127‑1 (MQ=255)                                                                                                         cctgAAAGCAGCGCTGGATGCGGGTCATCCGGCTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGAAACCTTCCGTTTATGCCAGGAGTATCTCgacgac                                          >  1:949733/1‑127 (MQ=255)                                                                                                          ctgAAAGCAGCGCTGGATGCGGGTCATCCGGCTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGAAACCTTCCGTTTATGCCAGGAGTATCTCGACGACATCATCACCGTCGa                            <  1:299580/140‑1 (MQ=255)                                                                                                            gAAAGCAGCGCTGGATGCGGGTCATCCGGCTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGAAACCTTCCGTTTATGCCAGGAGTATCTCGACGACATCATCACCGTCGATa                          <  2:36388/140‑1 (MQ=255)                                                                                                            gAAAGCAGCGCTGGATGCGGGTCATCCGGCTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGAAACCTTCCGTTTATGCCAGGAGTATCTCGACGACATCATCACCGTCGATa                          <  1:863756/140‑1 (MQ=255)                                                                                                              aaGCAGCGCTGGATGCGGGTCATCCGGCTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGAAACCTTCCGTTTATGCCAGGAGTATCTCGACGACATCATCACCGTCGATAgc                        <  2:380630/140‑1 (MQ=255)                                                                                                                   gcgcTGGATGCGGGTCATCCGGCTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGAAACCTTCCGTTTATGCCAGGAGTATCTCGACGACATCATCACCGTCGATAgcgatgc                   <  1:656661/140‑1 (MQ=255)                                                                                                                   gcgcTGGATGCGGGTCATCCGGCTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGAAACCTTCCGTTTATGCCAGGAGTATCTCGACGACATCATCACCGTCGATAgcgatgc                   <  1:576295/140‑1 (MQ=255)                                                                                                                                   aTCCGGCTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGAAACCTTCCGTTTATGCCAGGAGTATCTCGACGACATCATCACCGTCGATAGCGATGCGATCTGTgcgg        <  2:455481/135‑1 (MQ=255)                                                                                                                                   aTCCGGCTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGAAACCTTCCGTTTATGCCAGGAGTATCTCGACGACATCATCACCGTCGATAGCGATGCGATCTGTgcgg        >  1:455481/1‑135 (MQ=255)                                                                                                                                   aTCCGGCTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGAAACCTTCCGTTTATGCCAGGAGTATCTCGACGACATCATCACCGTCGATAGCGATGCGATCTGTGCGGCGATg   <  2:375306/140‑1 (MQ=255)                                                                                                                                   aTCCGGCTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGAAACCTTCCGTTTATGCCAGGAGTATCTCGACGACATCATCACCGTCGATAGCGATGCGATCTGTGCGGCGATg   <  2:370413/140‑1 (MQ=255)                                                                                                                                   aTCCGGCTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGAAACCTTCCGTTTATGCCAGGAGTATCTCGACGACATCATCACCGTCGATAGCGATGCGATCTGTGCGGCGATg   <  1:366943/140‑1 (MQ=255)                                                                                                                                    tCCGGCTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGAAACCTTCCGTTTATGCCAGGAGTATCTCGACGACATCATCACCGTCGATAGCGATGCGATCTGTGCGGCGATGa  >  1:356351/1‑140 (MQ=255)                                                                                                                                         |                                                                                                                                       GTGCCAGTCGGCGGCGGCGGTCTGGCTGCTGGCGTGGCGGTGCTGATCAAACAACTGATGCCGCAAATCAAAGTGATCGCCGTAGAAGCGGAAGACTCCGCCTGCCTGAAAGCAGCGCTGGATGCGGGTCATCCGGTTGATCTGCCGCGCGTAGGGCTATTTGCTGAAGGCGTAGCGGTAAAACGCATCGGTGACGAAACCTTCCGTTTATGCCAGGAGTATCTCGACGACATCATCACCGTCGATAGCGATGCGATCTGTGCGGCGATGA  >  NC_000913/3955883‑3956153

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑