Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	1,290,774	A→G	intergenic (‑65/‑9)	ychJ ← / → rssA	conserved hypothetical protein/conserved hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	1,290,774	0	A	G	100.0%	158.5 / NA	46	intergenic (‑65/‑9)	ychJ/rssA	conserved hypothetical protein/conserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (21/25);  total (21/25)

CAAATAATCTCCCTGGAAACAATAACGGCGTATTAACCGCCTGAGTAGCACTATGTTAACCGAGCAGTAGCGATGTGGCTACGATTGCATTCCAGGGGAATCTTGCGGGAATAATGAGAAAGATAAAAA  >  W3110S.gb/1290709‑1290837                                                                  |                                                                caAATGATCTCCCTGGAAACAATAACGGCGTATTAACCGCCTGAGTAGCACTATGTTAACCGAGCGGTAGc                                                            <  1:1696665/71‑1 (MQ=255)  aaaTAATCTCCCCGGAAACAATAACGGCGTATTAACCGCCTGAGTAGCACTATGTTAACCGAGCGGTAGCg                                                           <  1:613108/71‑1 (MQ=255)   aataatCTCCCTGGAAACAATAACGGCGTATTAACCGCCTGAGTAGCACTATGTTAACCGAGCGTTAGCGa                                                          <  1:1618999/71‑1 (MQ=255)   aataatCTCCCTGGAAACAATAACGGCGTATTAACCGCCTGAGTAGCACTATGTTAACCGAGCGGTAGCGa                                                          <  1:226892/71‑1 (MQ=255)    ataatCTCCCTGGAAACAATAACGGCGTATTAACCGCCTGAGTAGCACTATGTTAACCGAGCGGTAGCGAt                                                         <  1:4454471/71‑1 (MQ=255)     taatCTCCCTGGAAACAATAACGGCGTATTAACCGCCTGAGTAGCACTATGTTAACCGAGCGGTAGCGAtg                                                        >  1:795212/1‑71 (MQ=255)       atCTCCCTGGAAACAATAACGGCGTATTAACCGCCTGAGTAGCACTATGTTAACCGAGCGGTAGCGAtgtg                                                      >  1:642986/1‑71 (MQ=255)            ccTGGAAACAATAACGGCGTATTAACCGCCTGAGTAGCACTATGTTAACCGAGCGGTAGCGATGTGGCTAc                                                 <  1:675803/71‑1 (MQ=255)            ccTGGAAACAATAACGGCGTATTAACCGCCTGAGTAGCACTATGTTAACCGAGCGGTAGCGATGTGGCTAc                                                 <  1:682869/71‑1 (MQ=255)             cTGGAAACAATAACGGCGTATTAACCGCCTGAGTATCACTATGTTAACCGAGCGGTAGCGATCTGGCTACg                                                <  1:237012/71‑1 (MQ=255)              tGGAAACAATAACGGCGTATTAACCGCCTGAGTAGCACTATGTTAACCGAGCGGTAGCGATGTGGCTACGa                                               >  1:3070200/1‑71 (MQ=255)              tGGAAACAATAACGGCGTATTAACCGCCTGAGTAGCACTATGTTAACCGAGCGGTAGCGATGTGGCTACGa                                               >  1:3961812/1‑71 (MQ=255)                   aCAATAACGGCGTATTAACCGCCTGAGTAGCACTATGTTAACCGAGCGGTAGCGATGTGGCTACGATTGCa                                          >  1:1341349/1‑71 (MQ=255)                   aCAATAACGGCGTATTAACCGCCTGAGTAGCACTATGTTAACCGAGCGGTAGCGATGTGGCTACGATTGCa                                          >  1:769423/1‑71 (MQ=255)                       tAACGGCGTATTAACCGCCTGAGTAGCACTATGTTAACCGAGCGGTAGCGATGTGGCTACGATTg                                            <  1:1368773/65‑1 (MQ=255)                       tAACGGCGTATTAACCGCCTGAGTAGCACTATGTTAACCGAGCGGTAGCGATGTGGCTACGATTGCATTcc                                      <  1:1297144/71‑1 (MQ=255)                         aCGGCGTATTAACCGCCTGAGTAGCACTATGTTAACCGAGCGGTAGCGATGTGGCTACGATTGCATTCCAg                                    >  1:1280971/1‑71 (MQ=255)                               tATTAACCGCCTGAGTAGCACTATGTTAACCGAGCGGTAGCGATGTGGCTACGATTg                                            <  1:1698757/57‑1 (MQ=255)                                 ttAACCGCCTGAGTAGCACTATGTTAACCGAGCGGTAGCGATGTGGCTACGATTGCATTCCAGGGGAATCt                            >  1:1253219/1‑71 (MQ=255)                                 ttAACCGCCTGAGTAGCACTATGTTAACCGAGCGGTAGCGATGTGGCTACGATTGCATTCCAGGGGAATCt                            >  1:2838060/1‑71 (MQ=255)                                              tAGCACTATGTTAACCGAGCGGTAGCGATGTGGCTACGATTGCATTCCAGGGGAATCTTGCGGGaataat                >  1:1158295/1‑70 (MQ=255)                                               aGCACTATGTTAACCGAGCGGTAGCGATGTGGCTACGATTGCATTCCAGGGGAATCTTGCGGGaataat                >  1:381929/1‑69 (MQ=255)                                                gCACTATGTTAACCGAGCGGTAGCGATGTGGCTACGATTGCATTCCAGGGGAAt                              >  1:3631605/1‑54 (MQ=255)                                                gCACTATGTTAACCGAGCGGTAGCGATGTGGCTACGATTGCATTCCAGGGGAATCTTGCGGGaataat                >  1:3496625/1‑68 (MQ=255)                                                  aCTATGTTAACCGAGCGGTAGCGATGTGGCTACGATTGCATTCCAGGGGAATCTTGCGGGAATAATgaga            <  1:3173884/70‑1 (MQ=255)                                                  aCTATGTTAACCGAGCGGTAGCGATGTGGCTACGATTGCATTCCAGGGGAATCTTGCGGGAATAATgag             >  1:2672259/1‑69 (MQ=255)                                                   cTATGTTAACCGAGCGGTAGCGATGTGGCTACGATTGCATTCCAGGGGAATCTTGCGGGaataat                <  1:1591503/65‑1 (MQ=255)                                                   cTATGTTAACCGAGCGGTAGCGATGTGGCTACGATTGCATTCCAGGGGAATCTTGCGGGaataat                <  1:628902/65‑1 (MQ=255)                                                    tATGTTAACCGAGCGGTAGCGATGTGGCTACGATTGCATTCCATGGGAATCTTGCGGGaat                   <  1:719365/61‑1 (MQ=255)                                                    tATGTTAACCGAGCGGTAGCGATGTGGCTACGATTGCATTCCAGGGGAATCTTGCGGGaataat                <  1:3083546/64‑1 (MQ=255)                                                    tATGTTAACCGAGCGGTAGCGATGTGGCTACGATTGCATTCCAGGGGAATCTTGCGGGaat                   <  1:2684808/61‑1 (MQ=255)                                                    tATGTTAACCGAGCGGTAGCGATGTGGCTACGATTGCATTCCAGGGGAATCTTGCGGGaat                   <  1:3934730/61‑1 (MQ=255)                                                     aTGTTAACCGAGCGGTAGCGATGTGGCTACGATTGCATTCCAGGGGAATCTTGCGGGAATAATgaga            >  1:4594391/1‑67 (MQ=255)                                                     aTGTTAACCGAGCGGTAGCGATGTGGCTACGATTGCATTCCAGGGGAATCTTGCGGGAATAATgaga            >  1:3501096/1‑67 (MQ=255)                                                     aTGTTAACCGAGCGCTAGCGATGTGGCTACGATTGCATTCCAGGGGAATCTTGCGGGAATAATgaga            >  1:2347416/1‑67 (MQ=255)                                                      tGTTAACCGAGCGGTAGCGATGTGGCTACGATTGCATTCCAGGGGAATCTTGCGGGAATAATGAGAAAGa        >  1:3069048/1‑70 (MQ=255)                                                      tGTTAACCGAGCGGTAGCGATGTGGCTACGATTGCATTCCAGGGGAATCTTGCGGGAATAATGAGAAAGa        >  1:3740615/1‑70 (MQ=255)                                                      tGTTAACCGAGCGGTAGCGATGTGGCTACGATTGCATTCCAGGGGAATCTTGCGGGAATAATGAGAAAGAt       <  1:2314403/71‑1 (MQ=255)                                                       gTTAACCGAGCGGTAGCGATGTGGCTACGATTGCATTCCAGGGGAATCTTGCGGGAATAATGAGAAAGa        <  1:224835/69‑1 (MQ=255)                                                        ttAACCGAGCGGTAGCGATGTGGCTACGATTGCATTCCAGGGGAATCTTGCGGGAATAATGAGAAAGATa      >  1:1678718/1‑70 (MQ=255)                                                         tAACCGAGCGGTAGCGATGTGGCTACGATTGCATTCCAGGGGAATCTTGCGGGAATAATGAGAAAGATa      >  1:2135443/1‑69 (MQ=255)                                                           aCCGAGCGGTAGCGATGTGGCTACGATTGCATTCCAGGGGAATCTTGCGGGAATAATGAGAAAGATaaaaa  <  1:4016686/71‑1 (MQ=255)                                                           aCCGAGCGGTAGCGATGTGGCTACGATTGCATTCCAGGGGAATCTTGCGGGAATAATGAGAAAGATaaaaa  <  1:3798920/71‑1 (MQ=255)                                                           aCCGAGCGGTAGCGATGTGGCTACGATTGCATTCCAGGGGAATCTTGCGGGAATAATGAGAAAGATaaaaa  <  1:2190231/71‑1 (MQ=255)                                                           aCCGAGCGGTAGCGATGTGGCTACGATTGCATTCCAGGGGAATCTTGCGGGAATAATGAGAAAGATaaaaa  <  1:1073157/71‑1 (MQ=255)                                                           aCCGAGCGGTAGCGATGTGGCTACGATTGCATTCCAGGGGAATCTTGCGGGAATAATGAGAAAGATaaaa   <  1:1005094/70‑1 (MQ=255)                                                                  |                                                                CAAATAATCTCCCTGGAAACAATAACGGCGTATTAACCGCCTGAGTAGCACTATGTTAACCGAGCAGTAGCGATGTGGCTACGATTGCATTCCAGGGGAATCTTGCGGGAATAATGAGAAAGATAAAAA  >  W3110S.gb/1290709‑1290837

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑