Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	4,235,469	G→A	19.0%	intergenic (+62/‑437)	pgi → / → yjbE	glucosephosphate isomerase/extracellular polysaccharide production threonine‑rich protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,235,469	0	G	A	19.0%	52.6 / 6.0	21	intergenic (+62/‑437)	pgi/yjbE	glucosephosphate isomerase/extracellular polysaccharide production threonine‑rich protein
Reads supporting (aligned to +/- strand):  ref base G (8/9);  new base A (2/2);  total (10/11)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.78e-01

GCAGCCACGATAGCTCGACCAATGGTCTGATTAACCGCTATAAAGCGTGGCGCGGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATCGTATTCGGCAATTAATACATAGCACGATTGATTAAATAACCTTA  >  NC_000913/4235349‑4235564                                                                                                                         |                                                                                                gcagcCACGATAGCTCGACCAATGGTCTGATTAACCGCTATAAAGCGTGGCGCGGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTa                                                                      <  1:204687/148‑1 (MQ=255)                              aTTAACCGCTATAAAGCGTGGCGCGGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACAt                                               >  4:1115850/1‑142 (MQ=255)                              aTTAACCGCTATAAAGCGTGGCGCGGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGACGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACaa                                               <  3:1115850/142‑2 (MQ=255)                                tAACCGCTATAAAGCGTGGCGCGGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGc                                                                         <  4:37133/114‑1 (MQ=255)                                tAACCGCTATAAAGCGTGGCGCGGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGc                                                                         >  3:37133/1‑114 (MQ=255)                                                  gcgcGGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGat                                                       >  4:1021192/1‑114 (MQ=255)                                                  gcgcGGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGat                                                       <  3:1021192/114‑1 (MQ=255)                                                   cgcgGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTAc                                                 >  2:1000266/1‑119 (MQ=255)                                                   cgcgGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTAc                                                 <  1:1000266/119‑1 (MQ=255)                                                         tAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGa                                                                                              >  1:183304/1‑68 (MQ=255)                                                         tAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGa                                                                                              <  2:183304/68‑1 (MQ=255)                                                         tAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGAcg                                                                                            <  2:918039/70‑1 (MQ=255)                                                         tAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGAcg                                                                                            >  1:918039/1‑70 (MQ=255)                                                                                      ggCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATCGTATTCGGCAATTAAt                              <  2:126864/103‑1 (MQ=255)                                                                                      ggCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATCGTATTCGGCAATTAAt                              >  1:126864/1‑103 (MQ=255)                                                                                        cGTTCACGCCGCATCCGGCAACCGATGCCTGATAAGACGCGACCGCGTCGCATCAg                                                                           <  3:185247/56‑1 (MQ=11)                                                                                        cGTTCACGCCGCATCCGGCAACCGATGCCTGATAAGACGCGACCGCGTCGCATCAg                                                                           >  4:185247/1‑56 (MQ=2)                                                                                          ttCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTAt                                                                              >  2:830067/1‑51 (MQ=255)                                                                                          ttCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTAt                                                                              <  1:830067/51‑1 (MQ=255)                                                                                                              gtaggCCTGATAAGACGCGACCGCGTCGCATCAGGCATACAGGTCGATGCCGATATGTACATCGTATTCGGCAATTAATACATAGCACGATTGATTAAATAACCTta  <  3:1040467/103‑1 (MQ=21)                                                                                                              gtaggCCTGATAAGACGCGACCGCGTCGCATCAGGCATACAGGTCGATGCCGATATGTACATCGTATTCGGCAATTAATACATAGCACGATTGATTAAATAACCTta  >  4:1040467/5‑107 (MQ=21)                                                                                                                         |                                                                                                GCAGCCACGATAGCTCGACCAATGGTCTGATTAACCGCTATAAAGCGTGGCGCGGTTAATCATCGTCGATATGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAACCGATGCCTGATGCGACGCGGTCGCGTCTTATCAGGCCTACAGGTCGATGCCGATATGTACATCGTATTCGGCAATTAATACATAGCACGATTGATTAAATAACCTTA  >  NC_000913/4235349‑4235564

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑