Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	2,706,728	G→A	64.1%	P228L (CCA→CTA)	rseB ←	anti‑sigma factor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	2,706,728	0	G	A	64.1%	31.7 / 38.8	39	P228L (CCA→CTA)	rseB	anti‑sigma factor
Reads supporting (aligned to +/- strand):  ref base G (3/11);  new base A (13/12);  total (16/23)
Fisher's exact test for biased strand distribution p-value = 9.30e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.91e-01

TCGATAGGCATGTTGTCCATCGTCGGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTGGCAACCAGGTTGGCGTCCAGCTGAATTTAGCTTTTTCACCTACAGGAACAGAAAGCAA  >  W3110S.gb/2706662‑2706786                                                                   |                                                           tCGATAGGCATGTTGTCCATCGTCGGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTAGCaa                                                        >  1:2840248/1‑71 (MQ=255) tCGATAGGCATGTTGTCCATCGTCGGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTAGCaa                                                        >  1:1822130/1‑71 (MQ=255) tCGATAGGCATGTTGTCCATCGTCGGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTAGCaa                                                        >  1:1442684/1‑71 (MQ=255)   gATAGGCATGTTGTCCATCGTCGGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTGGCAAc                                                       <  1:125997/70‑1 (MQ=255)   gATAGGCATGTTGTCCATCGTCGGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTGGCAAc                                                       <  1:1901393/70‑1 (MQ=255)   gATAGGCATGTTGTCCATCGTCGGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTGGCAAc                                                       <  1:575076/70‑1 (MQ=255)    aTAGGCATGTTGTCCATCGTCGGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTAGCAACCa                                                     <  1:2093554/71‑1 (MQ=255)        gCATGTTGTCCATCGTCGGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTAGCAAcc                                                      <  1:302890/66‑1 (MQ=255)        gCATGTTGTCCATCGTCGGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTAGCAAcc                                                      <  1:2501424/66‑1 (MQ=255)        gCATGTTGTCCATCGTCGGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTAGCAAcc                                                      <  1:1423569/66‑1 (MQ=255)         cATGTTGTCCATCGTCGGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTAGCAACCAg                                                    <  1:1309860/67‑1 (MQ=255)         cATGTTGTCCATCGTCGGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTAGCAACCAg                                                    <  1:2739206/67‑1 (MQ=255)         cATGTTGTCCATCGTCGGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTAGCAACCAg                                                    <  1:3066781/67‑1 (MQ=255)         cATGTTGTCCATCGTCGGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTAGCAACCAg                                                    <  1:3306695/67‑1 (MQ=255)             ttgtCCATCGTCGGTAGCGGACGTCGACTACTGGAAACTTGGCTAAAACCCTGTAGCAACCAGGTTGGCGt                                            >  1:98330/1‑71 (MQ=255)             ttgtCCATCGTCGGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTGGCAACCAGGTTGGCGt                                            >  1:426579/1‑71 (MQ=255)             ttgtCCATCGTCGGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTAGCAACCAGGTTGGCg                                             >  1:1188750/1‑70 (MQ=255)             ttgtCCATCGTCGGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTAGCAACCAGGTTGGCGt                                            >  1:1407912/1‑71 (MQ=255)             ttgtCCATCGTCGGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTAGCAACCAGGTTGGCGt                                            >  1:2041351/1‑71 (MQ=255)                  gaTCGTCGGTAGCGGACGTCGACTAATGGAAACTTCGCTAAAACCCTGTAGCAACCAg                                                    <  1:1090469/57‑1 (MQ=255)                    tcgtcgGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTGGCAACCAGGTTGGCGTCCAGCTg                                     <  1:3059312/71‑1 (MQ=255)                     cgtctGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTAGCAACCAg                                                    <  1:1207053/55‑1 (MQ=255)                      gtcgGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTGGCAACCAGGTTGGCGTCCAGCTGaa                                   >  1:391370/1‑71 (MQ=255)                      gtcgGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTAGCAACCAGGTTGGCGTCCAGCtca                                    >  1:3599250/1‑68 (MQ=255)                      gtcgGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTAGCAACCAGGTTGGCGTCCAGCTGaa                                   >  1:3343331/1‑71 (MQ=255)                      gtcgGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTAGCAACCAGGTTGGCGTCCAGCTGaa                                   >  1:2565165/1‑71 (MQ=255)                      gtcgGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTAGCAACCAGGTTGGCGTCCAGCTGaa                                   >  1:1113550/1‑71 (MQ=255)                      gtcgGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTAGCAACCAGGTTGGCGTCCAGCTGa                                    >  1:2731102/1‑70 (MQ=255)                          gTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTGGCAACCAGGTTGGCGTCCAGCTGAATTTa                               <  1:1530662/71‑1 (MQ=255)                                       actactGGAAACTTCGCTAAAACCCTGTGGCAACCAGGTTGGCGTCCAGCTGAATTTAGCTTTTTCACCTa                  <  1:2943925/71‑1 (MQ=255)                                       actactGGAAACTTCGCTAAAACCCTGTGGCAACCAGGTTGGCGTCCAGCTGAATTTAGCTTTTTCACCTa                  <  1:2694865/71‑1 (MQ=255)                                       actactGGAAACTTCGCTAAAACCCTGTGGCAACCAGGTTGGCGTCCAGCTGAATTTAGCTTTTTCACCTa                  <  1:3618829/71‑1 (MQ=255)                                        ctactGGAAACTTCGCTAAAACCCTGTGGCAACCAGGTTGGCGTCCAGCTGAATTTAGCTTTTTCACCTAc                 <  1:2551545/71‑1 (MQ=255)                                        ctactGGAAACTTCGCTAAAACCCTGTGGCAACCAGGTTGGCGTCCAGCTGAATTTAGCTTTTTCACCTAc                 <  1:1854721/71‑1 (MQ=255)                                           ctGGAAACTTCGCTAAAACCCTGTGGCAACCAGGTTGGCGTCCAGCTGAATTTAGCTTTTTCACCTACAgg              <  1:737789/71‑1 (MQ=255)                                           ctGGAAACTTCGCTAAAACCCTGTAGCAACCAGGTTGGCGTCCAGCTGAAttt                                <  1:183471/53‑1 (MQ=255)                                           ctGGAAACTTCGCTAAAACCCTGTAGCAACCAGGTTGGCGTCCAGCTGAATTTAGCTTTTTCACCTACAg               >  1:2746367/1‑70 (MQ=255)                                                             cccTGTGGCAACCAGGTTGGCGTCCAGCTGAATTTAGCTTTTTCACCTACAGGAACAGAAAGCaa  >  1:3625704/1‑65 (MQ=255)                                                              ccTGTAGCAACCAGGGTGGCGTCCAGCTGAATTTAGCt                            <  1:2103546/38‑1 (MQ=37)                                                                   |                                                           TCGATAGGCATGTTGTCCATCGTCGGTAGCGGACGTCGACTACTGGAAACTTCGCTAAAACCCTGTGGCAACCAGGTTGGCGTCCAGCTGAATTTAGCTTTTTCACCTACAGGAACAGAAAGCAA  >  W3110S.gb/2706662‑2706786

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑