Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,092,703	A→G	F41L (TTC→CTC)	frvA ←	putative PTS enzyme IIA component FrvA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,092,703	0	A	G	96.3%	79.4 / ‑3.8	27	F41L (TTC→CTC)	frvA	putative PTS enzyme IIA component FrvA
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base G (9/17);  total (9/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.18e-01

AATAATTTTGCGACACAGTGTGCCGATGATTTTGACCTGATCCTCTTCGCCGCTTTGCGGCACGCCGAGGCAGATCCAGCAATTGACGTCTTCGCCATCGCTGGCTTTCCAGTCAATAGCCTGCGCTTTGCGGGCGAATAATACGAACGGTTGTTTAACGCAGGCGCTTTTACCGTGCGGCACGGCGACACCGGAACCAAATCCAGTAGAGTGCATTTTTTCGCGCAGCAGCAGGGTTTGCAGGAACTGGTGTGAGTCGGTGATAAAACCGTTTTGTAACGCTATTGTCGCCAACTGCTTCAGAACGGAATAAGCGCCATTGCCCTGAATATTCAGGTCAATACAGCTTGCAGTAAGAGCTGCCATTAATCGGACTCCATAAAATATATTTTAATCAATTGTAATGGTGGAGCGATTAAGTGATGAGAGGCGATATGTCGGTAAACAATGACAATTTGAGACAGAGTGAAAGGTCAGATTTGC  >  NC_000913/4092458‑4092940                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                              aataatTTTGCGCCACAGTTTGCCTATGATTTGGACCTTATCCTCGTCGCCTCTTTGCGGCACGCCGAGGCAGATCCAGCACTTGTCGTCTTCGCCATCGCTGGCTTTCCAGTCAATAGCCTGCGCTTTGCGGGCGAATAATACGAACGGTTGTTTAACGCAGGCGCTTTTACCGTGCGGCACGGCGACACCGGAACCAAATCCAGTAGAGTGCATTTTTTCGCGCAGCAGCAGGGTTTGCAGGAGCTGgt                                                                                                                                                                                                                                          <  2:11552/251‑1 (MQ=255)        ttGCGACACAGGGTGCCGTAGATTTTGTACTGTTCCTCTGCTCCGCGTTGCGGCACGTCGAGGCAGATCCAGCATGTGACGTCTTGGGCATCGCTTGCGTTCCCGTCAATAGCCTGCGCTTTGCGGGCGAATAATACGAACGGTTGTTTAACGCAGGCGCTTTTACCGTGCGGCACGGCGACACCGGAACCAAATCCAGTAGAGTGCATTTGTTCTCGCAGCAGCAGGTTTTGCAGGAGCTGGTGTGAGt                                                                                                                                                                                                                                    <  2:108649/250‑1 (MQ=255)            gACACAGTGTGCCGATGATTTTGACCTGATCCTCTTCGCCGCTTTGCGGCACGCCGAGGCAGATCCAGCAATTGACGTCTTCGCCATCGCTGGCTTTCCAGTCAATAGCCTGCGCTTTGCGGGCGAATAATACGAACGGTTGTTTAACGCAGGCGCTTTTACCGTGCGGCACGGCGACACCGGAACCAAATCCAGTAGAGTGCATTTTTTCGCGCAGCAGCAGGGTTTGCAGGAGCTGGTGTGAGTCGGTg                                                                                                                                                                                                                               <  1:245879/251‑1 (MQ=255)                      gtcacggctttgtcactgttcttctTCGCCCCTTGGCGGCGCGCCGTGGCAGATCCAGCAATTGACGTCGTCGCCATCGCTTGCTTTTCAGTCAATAGCCTGCGCCTTTCGGGCGAATAATACGAACGGTTGTTTAACGCAGGCGCTGTTACCGTGCGGCACGGCGACGCCGGACCCAAATCCAGTAGAGTGCATTTTTTCGCGCAGCAGCAGGGTTTGCAGGAGCTGGTGTGAGTCGGTGATAAATCCg                                                                                                                                                                                                                      <  2:258169/228‑1 (MQ=255)                         gatgatTTTGACCTGATACTCTTCGCCGCTTTGCGGCACGCCGAGGCAGATCCAGCAATTGACGTCTTCGCCATCGCTGGCTTTCCAGTCAATAGCCTGCGCTTTGCGGGCGAATAATACGAACGGTTGTTTAACGCAGGCGCTTTTACCGTGCGGCACGGCGACACCGGAACCAAATCCAGTAGAGTGCATTTTTTCGCGCAGCAGCAGGGTTTGCAGGAGCTGGTGTGAGTCGGTGATAAAACCGtttt                                                                                                                                                                                                                  >  1:282584/1‑251 (MQ=255)                           gcatTTTGACCTGTCCCTCTTCGCCTCTTTGCGCCACGCCGAGGCAGATCCAGTCATTGACGTCTTCGCCATCGCTGGCTTTCCAGTCAATAGCCTGCGCTGTGCGGGCGAATAATACGATCGGTTGTTTAACGCAGGCGCTTTTACCTTGCGGCATGGCGACACCGGAACCAAATCCAGTAGAGTGCATTTTTTCGCGCAGCAGCAGGGTTTGCAGGAGCTGGTGTGAGTCGGTGATAAAACCGTTTTgc                                                                                                                                                                                                                <  1:327818/249‑2 (MQ=255)                                  gACCTGATCCTCTTCGCCGCTTTGCGGCACGCCGAGGCAGATCCAGCAATTGACGTCTTCGCCATCGCTGGCTTTCCAGTCAATAGCCTGCGCTTTGCGGGCGAATAATACGAACGGTTGTTTAACGCAGGCGCTTTTACCGTGCGGCACGGCGACACCGGAACCAAATCCAGTAGAGTGCATTTTTTCGCGCAGCAGCAGGGTTTGCAGGAGCTGGTGTGAGTCGGTGATAAAACCGTTTTGTAACGCt                                                                                                                                                                                                          <  1:87592/250‑1 (MQ=255)                                                                         gATCCAGCAATTGACGTCTTCGCCATCGCTGGCTTTCCAGTCAATAGCCTGCGCTTTGCGGGCGAATAATACGAACGGTTGTTTAACGCAGGCGCTTTTACCGTGCGGCACGGCGACACCGGAACCAAATCCAGTAGAGTGCATTTTTTCGCGCAGCAGCAGGGTTTGCAGGAGCTGGTGTGAGTCGGTGATAAAACCGTTTTGTAACGCTATTGTCGCCAACTGCTTCAGAACGGAATAAGCGCCATTGc                                                                                                                                                                  <  1:274043/251‑1 (MQ=255)                                                                            ccAGCAATTGACGTCTTCGCCATCGCTGGCTTTCCAGTCAATAGCCTGCGCTTTGCGGGCGAATAATACGAACGGTTGTTTAACGCAGGCGCTTTTACCGTGCGGCACGGCGACACCGGAACCAAATCCAGTAGAGTGCATTTTTTCGCGCAGCAGCAGGGTTTGCAGGAGCTGGTGTGAGTCGGTGATAAAACCGTTTTGTAACGCTATTGTCGCCAACTGCTTCAGAACGGAATAAGCGCCATTGCCCt                                                                                                                                                               <  1:80401/251‑1 (MQ=255)                                                                                                   cGCTGGCTTTCCAGTCAATAGCCTGCGCTTTGCGGGCGAATAATACGAACGGTTGTTTAACGCAGGCGCTTTTACCGTGCGGCACGGCGACACCGGAACCAAATCCAGTAGAGTGCATTTTTTCGCGCAGCAGCAGGGTTTGCAGGAGCTGGTGTGAGTCGGTGATAAAACCGTTTTGTAACGCTATTGTCGCCAACTGCTTCAGAACGGAATAAGCGCCATTGCCCTGAATATTCAGGTCAATACAGCtt                                                                                                                                        <  1:309345/251‑1 (MQ=255)                                                                                                      tGGCTTTCCAGTCAATAGCCTGCGCTTTGCGGGCGAATAATACGAACGGTTGTTTAACGCAGGCGCTTTTACCGTGCGGCACGGCGACACCGGAACCAAATCCAGTAGAGTGCATTTTTTCGCGCAGCAGCAGGGTTTGCAGGAGCTGGTGTGAGTCGGTGATAAAACCGTTTTGTAACGCTATTGTCGCCAACTGCTTCAGAACGGAATAAGCGCCATTGCCCTGAATATTCAGGTCAATACAGCTTGc                                                                                                                                      >  1:71367/1‑250 (MQ=255)                                                                                                         cTTTCCAGTCAATAGCCTGCGCTTTGCGGGCGAATAATACGAACGGTTGTTTAACGCAGGCGCTTTTACCGTGCGGCACGGCGACACCGGAACCAAATCCAGTAGAGTGCATTTTTTCGCGCAGCAGCAGGGTTTGCAGGAGCTGGTGTGAGTCGGTGATCAAACCGTTTTGTAACGCTATTGTCGCCAACTGCTTCAGAACGGAATAAGCGCCATTGCCCTGAATTTTCAGGTCAATAAAGCTTGCAGt                                                                                                                                   >  2:216526/1‑250 (MQ=255)                                                                                                                gTCAATAGCCTGCGCTTTGCGGGCGAATAATACGAACGGTTGTTTAACGCAGGCGCTTTTACCGTGCGGCACGGCGACACCGGAACCAAATCCAGTAGAGTGCATTTTTTCGCGCAGCAGCAGGGTTTGCAGGAGCTGGTGTGAGTCGGTGATAAAACCGTTTTGTAACGCTATTGTCGCCAACTGCTTCAGAACg                                                                                                                                                                                  >  2:59532/1‑196 (MQ=255)                                                                                                                gTCAATAGCCTGCGCTTTGCGGGCGAATAATACGAACGGTTGTTTAACGCAGGCGCTTTTACCGTGCGGCACGGCGACACCGGAACCAAATCCAGTAGAGTGCATTTTTTCGCGCAGCAGCAGGGTTTGCAGGAGCTGGTGTGAGTCGGTGATAAAACCGTTTTGTAACGCTATTGTCGCCAACTGCTTCAGAACg                                                                                                                                                                                  <  1:59532/196‑1 (MQ=255)                                                                                                                                 tGCGGGCGAATAATACGAACGGTTGTCTAACGCAGGCGCTTTTACCGTACGGCACGGCGACACCGGAACCAAATCCAGTAGAGTGCATTTGTTCGCGCAGCAGCAGGGTTTCCAGGAGCTGGTGTGAGTCGGTGATAAAACCGTTTTGTAACGCTATTGTCGCCAACTGCTTCAGAACGGAATAAGCGCCATTGCCCTGAATATTCAGGTCAATACAGCTTGCAGTAAGCGCTGCCATTAATCGGACtac                                                                                                           <  2:110090/250‑3 (MQ=255)                                                                                                                                    gggCGAATAATACGAACGGTTGTTTAACGCAGGCGCTTTTACCGTGCGGCACGGCGACACCGGAACCAAATCCAGTAGAGTGCATTTTTTCGCGCAGCAGCAGGGTTTGCAGGAGCTGGTGTGAGTCTGTGATAAAACCGTTTTGTAACGCTATTGTCGCCAACTGCTTCAGAACGGAATAAGCGCCATTGCCCTGAATATTCAGGTCAATACAGCTTGCAGTAAGAGCTGCCATTAATCGGACTCCATaa                                                                                                       <  1:124955/251‑1 (MQ=255)                                                                                                                                    gggCGAATAATACGAACGGTTGTTTAACGCAGGCGCTTTTACCGTGCGGCACGGCGACACCGGAACCAAATCCAGTAGAGTGCATTTTTTCGCGCAGCAGCAGGGTTTGCAGGAGCTGGTGTGAGTCGGTGATAAAACCGTTTTGTAACGCTATTGTCGCCAACTGCTTCAGAACGGAATAAGCGCCATTGCCCTGAATATTCAGGTCAATACAGCTTGCAGTAAGAGCTGCCATTAATCGGACTCCATaa                                                                                                       <  1:216526/251‑1 (MQ=255)                                                                                                                                     ggCGAATAATACGAACGGTTGTTTAACGCAGGCGCTTTTACCGTGCGGCACGGCGACACCGGAACCAAATCCAGTAGAGTGCATTTTTTCGCGCAGCAGCAGTGTTTGCAGGAGCTGGTGTGAGTCGGTGATAAAACCGTTTTGTAACGCTATTGTCGCCAACTGCTTCAGAACGGAATAAGCGCCATTGCCCTGAATATTCAGGTCAATACAGCTTGCAGTAAGAGCTGCCATTAATCGGACTCCATaaa                                                                                                      <  1:206593/251‑1 (MQ=255)                                                                                                                                                    cGGTTGTTTAACGCAGGCGCTTTTACCGTGCGGCACGGCGACACCGGAACCAAATCCAGTAGAGTGCATTTTTTCGCGCAGAAGCAGGGTTTGCAGGAACTGGTGTGAGTCGGTGATAAA‑CCGTTTTGTAACGCTATTGTCGCCAACTGCTTCAGAACGGAATAAGCGCCACTGCCCTGAATATTCAGGTCAATACAGCTTGCAGTAAGAGCTGCCTTTAATCGGACTCCATAAAATATATTTTAATCAAt                                                                                      <  1:173671/251‑1 (MQ=255)                                                                                                                                                                   ggCGCTTTTACCGTGCGGCACGGCGACACCGGAACCAAATCCAGTAGAGTGCATTTTTTCGCGCAGCAGCAGGGTTTGCAGGAGCTGGTGTGAGTCGGTGATAAAACCGTTTTGTAACGCTATTGTCGCCAACTGCTTCAGAACGGAATAAGCGCCATTGCCCTGAATATTCAGGTCAATACAGCTTGCAGTAAGAGCTGCCATTAATCGGACTCCAt                                                                                                         >  1:193036/1‑218 (MQ=255)                                                                                                                                                                                      aCGGCGACACCGGAACCAAATCCAGTAGAGTGCATTTTTTCGCGCAGCAGCAGGGTTTGCAGGAGCTGGTGTGCGTCGGTGATAAAACCGTTTTGTAACGCTATTGTCGCCAACTGCTTCAGAACGGAATAAGCGCCATTGCCCTGAATATTCAGGTCAATACAGCTTGCAGTAAGAGCTGCCATTAATCGGACTCCATAAAATATATTTTAATCAATTGTAATGGTGGAGCGATTAAGTGATGAGAGGCg                                                     >  1:341883/1‑251 (MQ=255)                                                                                                                                                                                                 ggAACCAAATCCAGTAGAGTGCATTTTTTCGCGCAGCAGCAGGGTTTGCAGGAGCTGGTGTGAGTCGGTGATAAAACCGTTTTGTAACGCTATTGTCGCCAACTGCTTCAGAACGGAATAAGCGCCATTGCCCTGAATATTCAGGTCAATACAGCTTGCAGTAAGAGCTGCCATTAATCGGACTCCATAAAATATATTTTAATCAATTGTAATGGTGGAGCGATTAAGTGATGAGAGGCGATATGTCGGTa                                          <  1:55685/251‑1 (MQ=255)                                                                                                                                                                                                      cAAATCCAGTATAGTGCATTTTTTCGCGCAGCAGCAGGGTTTGCAGGAGCTGGTGTGAGTCGGTGATAAAACCGTGTTGTAACGCTATTGTCGCCAACTGCTTCAGAACGGAATAAGCGCCATTGCCCTGAATATTCAGGTCAATACAGCTTGCAGTAAGAGCTGCCATTAATCGGACTCCATAAAATATATTTTAATCACTTGTAATGGTGGAGCGATTAAGTGATGAGAGGCGATATTTCGGTAAACa                                      >  2:285082/1‑250 (MQ=255)                                                                                                                                                                                                       aaaTCCAGTAGAGTGCATTTTTTCGCGCAGCAGCAGGGTTTGCAGGAGCTGGTGTGAGTCGGTGATAAAACCGTTTTGTAACGCTATTGTCGCCAACTGCTTCAGAACGGAATAAGCGCCATTGCCCTGAATATTCAGGTCAATACAGCTTGCAGTAAGAGCTGCCATTAATCGGACTCCATAAAATATATTTTAATCAATTGTAATGGTGGAGCGATTAAGTGATGAGAGGCGATATGTCGGTAAACAAt                                    >  1:302338/1‑251 (MQ=255)                                                                                                                                                                                                                      cATTTTTTCGCGCAGCAGCAGGGTTTGCAGGAGCTGGTGTGAGTCGGTGATAAAACCGTTTTGTAACGCTATTGTCGCCAACTGCTTCAGAACGGAATAAGCGCCATTGCCCTGAATATTCAGGTCAATACAGCTTGCAGTAAGAGCTGCCATTAATCGGACTCCATAAAATATATTTTAATCAATTGTAATGGTGGAGCGATTAAGTGATGAGAGGCGATATGTCGGTAAACAATGACAATTTGAGACag                     <  1:283574/251‑1 (MQ=255)                                                                                                                                                                                                                                  cagcagcagGGATTGCAGGAGCTGGTGTGAGTCGGTGATAAAACCGTTTTGTAACGCTATTGTCGCCACCTGCTTCAGCACGGAATAAGCGCCATTGCCCTGAATATTCCGGTCAATACAGCTTGCAGTACGAGCTGCCATTAATCGGACTCCATAAAATATATTTTAATCAATTGTAATGGTGGAGCGATTAAGTGATGAGAGGCGATATGTCGGTAAACAATGACAATTTGAGACAGAGTAAAAAGTcc         >  1:324350/1‑250 (MQ=255)                                                                                                                                                                                                                                         agGGTTTGCAGGAGCTGGTGTGAGTCAGTGATAAAACCGTTTTGTAACGCTATTGTCGCCAACTGCTTCAGAACGGAATAAGCGCCAGTGCCCTGAATATTCAGGTCAATACAGCTTGCAGTAAGAGCTGCCATTAATCGGACTCCATAAAATATATTTTAATCAATTGTAATGGTGGAGCGATTAAGTGATGAGAGGCGATATGTCGGTAAACAATGACAATTTGAGACAGAGTGAAAGGTCAGATTTGc  <  2:79315/251‑1 (MQ=255)                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                              AATAATTTTGCGACACAGTGTGCCGATGATTTTGACCTGATCCTCTTCGCCGCTTTGCGGCACGCCGAGGCAGATCCAGCAATTGACGTCTTCGCCATCGCTGGCTTTCCAGTCAATAGCCTGCGCTTTGCGGGCGAATAATACGAACGGTTGTTTAACGCAGGCGCTTTTACCGTGCGGCACGGCGACACCGGAACCAAATCCAGTAGAGTGCATTTTTTCGCGCAGCAGCAGGGTTTGCAGGAACTGGTGTGAGTCGGTGATAAAACCGTTTTGTAACGCTATTGTCGCCAACTGCTTCAGAACGGAATAAGCGCCATTGCCCTGAATATTCAGGTCAATACAGCTTGCAGTAAGAGCTGCCATTAATCGGACTCCATAAAATATATTTTAATCAATTGTAATGGTGGAGCGATTAAGTGATGAGAGGCGATATGTCGGTAAACAATGACAATTTGAGACAGAGTGAAAGGTCAGATTTGC  >  NC_000913/4092458‑4092940

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑