Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,499,978	C→T	D436D (GAC→GAT)	pyrS →	sensor histidine kinase PyrS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,499,978	0	C	T	95.7%	77.9 / NA	23	D436D (GAC→GAT)	pyrS	sensor histidine kinase PyrS
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base T (11/11);  minor base G (0/1);  total (11/12)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGCCCTGCAAAGCAAAATTAATCCCCATTTTCTGTTTAACGCTCTGAACGCTATTTCATCGTCAATCCGTCTGAATCCGGATACCGCTCGCCAGTTGATCTTTAATCTGTCGCGTTATCTGCGCTATAACATTGAATTAAAAGACGATGAGCAAATCGATATCAAAAAAGAGCTGTATCAAATTAAAGACTATATTGCCATTGAGCAGGCCCGCTTTGGTGACAAGCTGACGGTTATCTATGATATTGATGAAGAGGTGAATTGCTGCATTCCCAGCCTGCTGATCCAGCCGTTGGTGGAGAACGCCATTGTCCACGGTATTCAGCCTTGCAAAGGTAAAGGCGTTGTCACCATCAGCGTTGCAGAGTGCGGAAATC‑GGGTACGCATTGCGGTGCGAGATACCGGGCACGGCATCGATCCAAAGGTGATTGAGCGGGTCGAAGCGAATGAAATGCCGG  >  NC_000913/2499756‑2500213                                                                                                                                                                                                                               |                                                                                                                                                                                                                                             cgcCCTGCAAAGCAAAATTAATCCCCATTTTCTGTTTAACGCTCTGAACGCTATTTCATCGTCAATCCGTCTGAATCCGGATACCGCTCGCCAGTTGATCTTTAATCTGTCGCGTTATCTGCGCTATAACATTGAATTAAAAGACGATGAGCAAATCGATATCAAAAAAGAGCTGTATCAAATTAAAGACTATATTGCCATTGAGCAGGCCCGCTTTGGTGATAAGCTGACGGTTATCTATGATATtgatg                                                                                                                                                                                                                  <  2:84077/251‑1 (MQ=255)             caaaATTAATCCCCATTTTCTGTTTAACGCTCTGAACGCTATTTCATCGTCAATCCGTCTGAATCCGGATACCGCTCGCCAGTTGATCTTTAATCTGTCGCGTTATCTGCGCTATAACATTGAATTAAAAGACGATGAGCAAATCGATATCAAAAAAGAGCTGTATCAAATTAAAGACTATATTGCCATTGAGCAGGCCCGCTTTGGTGATAAGCTGACGGTTATCTATGATATTGATGAaga                                                                                                                                                                                                              >  1:285478/1‑243 (MQ=255)             caaaATTAATCCCCATTTTCTGTTTAACGCTCTGAACGCTATTTCATCGTCAATCCGTCTGAATCCGGATACCGCTCGCCAGTTGATCTTTAATCTGTCGCGTTATCTGCGCTATAACAGTGAATTAAAAGACGATGAGCAAATCGATATCAAAAAAGAGCTGTATCAAATTAAAGACTATATTGCCATTGAGCAGGCCCGCTTTGGTGATAAGCTGACGGTTATCTATGATATTGATGAaga                                                                                                                                                                                                              <  2:285478/243‑1 (MQ=255)                       ccccATTTTCTGTTTAACGCTCTGAACGCTATTTCATCGTCAATCCGTCTGAATCCGGATACCGCTCGCCAGTTGATCTTTAATCTGTCGCGTTATCTGCGCTATAACATTGAATTAAAAGACGATGAGCAAATCGATATCAAAAAAGAGCTGTATCAAATTAAAGACTATATTGCCATTGAGCAGGCCCGCTTTGGTGATAAGCTGACGGTTATCTATGATATTGATGAAGGGGTGAATTGCTGCATTcc                                                                                                                                                                                            <  2:90822/251‑1 (MQ=255)                        cccATTTTCTGTT‑AACGCTCTGAACGCTATTTCATCGTCAATCCGTCTGAATCCGGATACCGCTCGCCAGTTGATCTTTAATCTGTCGCGTTATCTGCGCTATAACATTGAATTAAAAGACGATGAGCAAATCGATATCAAAAAAGAGCTGTATCAAATTAAAGACTATATTGCCATTGAGCAGGCCCGCTTTGGTGATAAGCTGACGGTTATCTATGATATTGATGAAGAGGTGAATTGCTGCATTCCCa                                                                                                                                                                                          <  2:166516/251‑1 (MQ=255)                                      aaCGCTCTGAACGCTATTTCATCGTCAATCCGTCTGAATCCGGATACCGCTCGCCAGTTGATCTTTAATCTGTCGCGTTATCTGCGCTATAACATTGAATTAAAAGACGATGAGCAAATCGATATCAAAAAAGAGCTGTATCAAATTAAAGACTATATTGCCATTGAGCAGGCCCGCTTTGGTGATAAGCTGACGGTTATCTATGATATTGATGAAGAGGTGAATTGCTGCATTCCCAGCCTGCTGATCCa                                                                                                                                                                             <  1:95927/251‑1 (MQ=255)                                             tGAACGCTATTTCATCGTCAATCCGTCTGAATCCGGATACCGCTCGCCAGTTGATCTTTAATCTGTCGCGTTATCTGCGCTATAACATTGAATTAAAAGACGATGAGCAAATCGATATCAAAAAAGAGCTGTATCAAATTAAAGACTATATTGCCATTGAGCAGGCCCGCTTTGGTGATAAGCTGACGGTTATCTATGATATTGATGAAGAGGTGAATTGCTGCATTCCCAGCCTGCTGATCCAGCCGTtg                                                                                                                                                                      >  1:118582/1‑251 (MQ=255)                                                aCGCTATTTCATCGTCAATCCGTCTGAATCCGGATACCGCTCGCCAGTTGATCTTTAATCTGTCGCGTTATCTGCGCTATAACATTGAATTAAAAGACGATGAGCAAATCGATATCAAAAAAGAGCTGTATCAAATTAAAGACTATATTGCCATTGAGCAGGCCCGCTTTGGTGATAAGCTGACGGTTATCTATGATATTGATGAAGAGGTGAATTGCTGCATTCCCAGCCTGCTGATCCAGCCGTtggtg                                                                                                                                                                   <  1:74614/251‑1 (MQ=255)                                                                aaTCCGTCTGAATCCGGATACCGCTCGCCAGTTGATCTTTAATCTGTCGCGTTATCTGCGCTATAACATTGAATTAAAAGACGATGAGCAAATCGATATCAAAAAAGAGCTGTATCAAATTAAAGACTATATTGCCATTGAGCAGGCCCGCTTTGGTGATAAGCTGACGGTTATCTATGATATTGATGAAGAGGTGAATTGCTGCATTCCCAGCCTGCTGATCCAGCCGTTGGTGGAGAACGCCATTGTcc                                                                                                                                                   >  1:32485/1‑251 (MQ=255)                                                                                                 gATCTTTAATCTGTCGCGTTATCTGCGCTATAACATTGAATTAAAAGACGATGAGCAAATCGATATCAAAAAAGAGCTGTATCAAATTCACGACTATATTGCCATTGAGCAGGCCCGCATTGGTGATAAGCTGCCGGTTATCTATGATATTGATGAAGGGGTGAATTGCTGCATTCCCAGCCTGCTGATCCAGCCGTTGGCGGAGAACGCCATTGTCCACGGCATTCAGCCTTGCAAAGGTAAAGGCGTTg                                                                                                                  >  1:259398/1‑251 (MQ=255)                                                                                                               cgcgTTATCTGCGCTATAACATTGAATTAAAAGACGATGAGCAAATCGATATCAAAAAAGAGCTGTATCAAATTAAAGACTATATTGCCATTGAGCAGGCCCGCTTTGGTGATAAGCTGACGGTTATCTATGATATTGATGAAGAGGTGAATTGCTGCATTCCCAGCCTGCTGATCCAGCCGTtggtg                                                                                                                                                                   <  1:307705/188‑1 (MQ=255)                                                                                                               cgcgTTATCTGCGCTATAACATTGAATTAAAAGACGATGAGCAAATCGATATCAAAAAAGAGCTGTATCAAATTAAAGACTATATTGCCATTGAGCAGGCCCGCTTTGGTGATAAGCTGACGGTTATCTATGATATTGATGAAGAGGTGAATTGCTGCATTCCCAGCCTGCTGATCCAGCCGTtggtg                                                                                                                                                                   >  2:307705/1‑188 (MQ=255)                                                                                                                    tATCTGCGCTATAACATTGAATTAAAAGACGATGAGCAAATCGATATCAAAAAAGAGCTGTATCAAATTAAAGACTATATTGCCATTGAGCAGGCCCGCTTTGGTGATAAGCTGACGGTTATCTATGATATTGATGAAGAGGTGAATTGCTGCATTCCCAGCCTGCTGATCCAGCCGTTGGTGGAGAACGCCATTGTCCACGGTATTCAGCCTTGCAAAGGTAAAGGCGTTGTCACCATCAGCGTTGCag                                                                                                <  2:252790/250‑1 (MQ=255)                                                                                                                                        aTTAAAAGACGATTAGCAAATCGATATCAAAAAAGAGCTGTATCTAATTAAAGACGATATTGCCATTGAGCAGGCCCGCTTTGGTGATAAGCTGACGGTTATCTATGATATTGATGAAGAGGTGAATTGCTGCATTCCCAGCCTGCTGATCCAGCCTTTGGTGGAGAACGCCATTGTCCACGGTATTCAGCCGTGCAAAGGTAAAGGCGTTGTCACCATCAGCGTTGCAGAGTGCGGAAATC‑GGGTACGCa                                                                          <  2:49768/251‑1 (MQ=255)                                                                                                                                        aTTAAAAGACGATGAGCAAATCGATATCAAAAAAGAGCTGTATCAAAATAATGACTATTTTGCCATTGAGCAGGCCCGCTTTGGTGATAAGCTGACGGTTATCTATGATATGGATGAAGAGGTGAATTGCTGCATTCCCAGCCTGCTGATCCAGCCGTTGGTGTAGAACGCCATTGTCCACGGTATTCAGCCTTGCAAAGGTAAAGGCGTTGTCCCCATTAGCGTTGCAGAGTGCGGAAATC‑GGGTACGCa                                                                          <  1:287125/251‑1 (MQ=255)                                                                                                                                         ttAAAAGACGATGAGCAAATCGATATCAAAAAAGAGCTGTATCAAATTAAAGACTATATTGCCATTGAGCAGGCCCGCTTTGGTGATAAGCTGACGGTTATCTATGATATTGATGAAGAGGTGAATTGCTGCATTCCCAGCCTGCTGATCCAGCCGTTGGTGGAGAACGCCATTGTCCACGGTATTCAGCCTTGCAAAGGTAAAGGCGTTGTCACCATCAGCGTTGCAGAGTGCGGAAATC‑GGGTACGCAt                                                                         >  2:263122/1‑251 (MQ=255)                                                                                                                                         ttAAAAGACGATGAGCAAATCGATATCAAAAAAGAGCTGTATCAAATTAAAGACTATATTGCCATTGAGCAGGCCCGCTTTGGTGATAAGCTGACGGTTATCTATGATATTGATGAAGAGGTGAATTGCTGCATTCCCAGCCTGCTGATCCAGCCGTTGGTGGAGAACGCCATTGTCCACGGTATTCAGCCTTGCAAAGGTAAAGGCGTTGTCACCATCAGCGTTGCAGAGTGCGGAAATC‑GGGTACGCAt                                                                         >  1:119545/1‑251 (MQ=255)                                                                                                                                                            tCGATATCAAAAAAGAGCTGTATCAAATTAAAGACTATATTGCCATTGAGCAGGCCCGCTTTGGTGATAAGCTGACGGTTATCTATGATATTGATGAAGAGGTGAATTGCTGCATTCCCAGCCTGCTGCTCCAGCCGTAGGTGGAGAACGCCATTGTCCACGGTATTCAGCCTTGCAAAGGTAAAGGCGTTGTCACCATCAGCGTTGCAGAGTGCGGAAATC‑GGGTACGCATTGCGGTGCGAGATACCggg                                                      >  2:256256/1‑251 (MQ=255)                                                                                                                                                                               gTATCAAATTAAAGACTATAGTGCCATTGAGCAGGCCCGGTTTTGTGAGAAGCTGTCGGTTATCTATGATATTGATGAAGAGGTGAATTGCTGCAGTCTTAGCCTGCTGATCTAGCCGTTGGTGGAGAACGCCATGGTCCACGTTATTCAGCCTTGCATAGGTAAAGGCGTTGTCTCCATCAGCATTGCAGAGTGTGGATATCTGGGT‑CGCAGTTCGGTGCGAGATACCGGGCACGGCATCGATCCAAAg                                    <  1:202815/250‑1 (MQ=255)                                                                                                                                                                                        tAAAGACTATATTGCCATTGAGCAGGCCCGCTTTGGTGATAAGCTGACGGTTATCTATGATATTGATGAAGAGGTGAATTGCTGCATTCCCAGCCTGCTGATCCAGCCGTTGGTGGAGAACGCCATTGTCCACGGTATTCAGCCTTGCAAAGGGAAAGGCGTTGTCACCATCAGCGTTGCAGAGTGCGGAAATC‑GGGTACGCATTGCGGTGCGAGATACCGGGCACGGCATCGATCCAAAGGTGATTGAg                           <  2:118582/250‑1 (MQ=255)                                                                                                                                                                                            gACTATATTGCCATTGAGCAGGCCCGCTTTGGTCATACGCTGACGGTTATATATGATATTGATGAAGAGGAGAATTGCTGCATTCCCAGCCTGCTGATCCAGCCGTTGGTGGAGAACGCCATTGTCCACGGTATTCAGCCTTGCAACGGCAAAGGCGTTGTCACCATCAGCGTTGCAGAGTGCGGAAATA‑GGGTACGCATTGCGGTGCGAGATACCGGGCACGGCATCGATCCAAAGGTGATTGAGCGGGt                      >  1:291159/1‑251 (MQ=255)                                                                                                                                                                                             aCTATATTGCCATTGAGCAGGCCCGCTTTGGTGATAAGCTGACGGTTATCTATGATATTGATGAAGAGGTGACTTGCTGCATTCCCAGCATGCTGATCCAGCCGTTGGTGGAGAACGCCCTTGTCCACGGTATTCAGCCTTGCAAAGGTAAAGGCGTTGTCACCATCAGCGTTGCAGAGTGCGGAAATC‑GGGTACGCATTGCGGTGCGAGATACCGGGCACGGCATCGCTCCACAGGTGATTGAGCGGGTc                     >  2:266149/1‑251 (MQ=255)                                                                                                                                                                                                                ggCCCGCTTTGGTGATAAGCTGACGGTTATCTATGATATTGATGAAGAGGTGAATTGCTGCATTCCCAGCCTGCTGATCCAGCCGTTGGTGGAGAACGCCATTGTCCACGGTATTCAGCCTTGCAAAGGTAAAGGCGTTGTCACCATCAGCGTTGCAGAGTGCGGAAATC‑GGGTACGCATTGCGGTGCGAGATACCGGGCACGGCATCGATCCAAAGGTGATTGAGCGGGTCGAAGCGAATGAAATGCCgg  >  1:101616/1‑251 (MQ=255)                                                                                                                                                                                                                               |                                                                                                                                                                                                                                             CGCCCTGCAAAGCAAAATTAATCCCCATTTTCTGTTTAACGCTCTGAACGCTATTTCATCGTCAATCCGTCTGAATCCGGATACCGCTCGCCAGTTGATCTTTAATCTGTCGCGTTATCTGCGCTATAACATTGAATTAAAAGACGATGAGCAAATCGATATCAAAAAAGAGCTGTATCAAATTAAAGACTATATTGCCATTGAGCAGGCCCGCTTTGGTGACAAGCTGACGGTTATCTATGATATTGATGAAGAGGTGAATTGCTGCATTCCCAGCCTGCTGATCCAGCCGTTGGTGGAGAACGCCATTGTCCACGGTATTCAGCCTTGCAAAGGTAAAGGCGTTGTCACCATCAGCGTTGCAGAGTGCGGAAATC‑GGGTACGCATTGCGGTGCGAGATACCGGGCACGGCATCGATCCAAAGGTGATTGAGCGGGTCGAAGCGAATGAAATGCCGG  >  NC_000913/2499756‑2500213

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑