Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,732,992	G→A	I394I (ATC→ATT)  I394I (ATC→ATT)	clpB ← clpB ←	chaperone protein ClpB chaperone protein ClpB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,732,992	0	G	A	95.0%	47.8 / NA	20	I394I (ATC→ATT)  I394I (ATC→ATT)	clpB clpB	chaperone protein ClpB chaperone protein ClpB
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (7/12);  minor base C (1/0);  total (8/12)
Fisher's exact test for biased strand distribution p-value = 4.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.95e-01

CAGAAAGCGATGCCTTCTCTGCTTTCCACTCTTCTTCTAACTCGGAGTACTGACGTTCTTTGTCGCTCAGTTCTTCGTTGAGCATATCCAGACGTTTTTTACTGGCTTCATCAGACTCTTTCATTAACGCCTGTTGTTCCAGTTTGAGCTGGATGATACGACGATCGAGTCGGTCGAGTTCTTCTGGTTTTGAGTCAATCTGCATACGAATGCTGGATGCTGCTTCATCGATCAGGTCGATGGCTTTATCCGGCAGCTGACGGTCAGCAATGTAGCGATGAGACAACGTCGCCGCTGCAACAATTGCCGGGTCAGTAATTTGCACATGGTGGTGCAATTCGTAACGTTCTTTCAGGCCACGCAGAATCGCAATGGTATCTTCAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATCTTTTTCAATGTACTGGCG  >  NC_000913/2732763‑2733216                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                 cAGAAAGCGATGCCTTCTCTGCTTTCCACTCTTCTTCTAACTCGGAGTACTGACGTTCTTTGTCGCTCAGTTCTTCGTTGAGCATATCCAGACGTTTTTTACTGGCTTCATCAGACTCTTTCATTAACGCCTGTTGTTCCAGTTTGAGCTGGATGATACGACGATCGAGTCGGTCGAGTTCTTCTGGTTTTGAGTCAATCTGCATACGAATGCTGGATGCTGCTTCATCAATCAGGTCGATGGCTTTATcc                                                                                                                                                                                                             <  1:104158/251‑1 (MQ=255)          aTGCCTTCTCTGCTTTCCACTCTTCTTCTAACTCGGAGTACTGATGTTCTTTGTCGCTCAGTTCTTCGTTGAGCATATACAGACGTTTTTTAATGGCTTCATCAGACTATTTCATTAACGCCTGTTGTTCCAGGTTGAGCTGGATGATACGACGATCGAGTCGGTCGAGTTCTTCTGGTTTTGAGTCAATCTGCATACGAATGCTGGATGCTGCTTAATCAATCAGGTCGATGGCTTTATCCGGCAGCTg                                                                                                                                                                                                     >  1:203413/1‑250 (MQ=255)                                                           tttGTCGCTCAGTTCTTCGTTGAGCATATCCAGACGTTTTTTACTGGCTTCATCAGACTCTTTCATTAACGCCTGTTGTTCCAGTTAGAGCTGGATGATACGACGATCGAGTCGGTCGAGTTCTTCTGGTTTTGATTCAATCTGCATACGAATGCTGGATGCTGCTTCATCAATCAGGTCGATGGCTTTATCCGGCAGCTGACGGTCAGCAATGTAGCGATGAGACAACGTcgcc                                                                                                                                                                   <  1:449604/235‑1 (MQ=255)                                                            ttGTCGCTCAGTTCTTCGTTGAGCATATCCAGACGTTTTTTACTGGCTTCATCAGACTCTTTCATTAACGCCTGTTGTTCCAGTTTGAGCTGGATGATACGACGATCGAGTCGGTCGAGTTCTTCTGGTTTTGAGTCAATCTGCATACGAATGCTGGATGCTGCTTCATCAATCAGGTCGATTGCTTTATCCGGCAGCTGACGGTCAGCAATGTAGCGATGAGACAACGTcgccgc                                                                                                                                                                 <  1:421120/236‑1 (MQ=255)                                                               ncGCTCAGTTCTTCGTTGAGCATATACAGAAGTTTTTTACTGGCTTCATCAGACTCTTTCATTAACGCCTGTTGTTCCAGTTTGAGCTGGATGATACGACGATCGAGTCGGTCGGGTTCTTCTGGTTTTGAGTCAATCTGCATACGAATGCTGGATGCTGCTTCATCAATCAGGTCGATGGCtt                                                                                                                                                                                                                  >  1:132452/2‑184 (MQ=255)                                                                           tcGTTGAGCATATCCAGACGTTTTTTACTGGCTTCATCAGACTCTTTCATTAACGCCTGTTGTTCCAGTGTGAGCTGGATGATACGACGATCGAGTCGGTCGAGTTCTTCTGGTTTTGAGTCAATCTGCATACGAATGCTGGATGCTGCTTCATCAATCAGGTCGATGGCTTTATCCGGCAGCTGACGGGCAGCAATGTAGCGATGAGACAACGTCGCCGCTGCATCAATTGTCGGGTCAGTAATTTg                                                                                                                                      <  1:376214/248‑1 (MQ=255)                                                                                  gCATATCCAGACGTTTTTTACTGGCTTCATCAGACTCTTTCATTAACGCCTGTTGTTCCAGTTTGAGCTGGATGATACGACGATCGAGTCGGTCGAGTTCTTCTGGTTTTGAGTCAATCTGCATACGAATGCTGTATGCTGCTTCATCAATCAGGTCGATGGCTTTATCCGGCAGCTGACGGTCAGCAATGTAGCGATGAGACAACGTCGCCGCTGCAACAATTGCCGGGTCAGTAATTTGCACAtggtgg                                                                                                                            <  1:32616/251‑1 (MQ=255)                                                                                              gTTTTTTACTGTCTTCATCAGACTCTTTCATTAACGCTTGTTGTTCCAGTTTGAGTTGGATGAGACGGCGAGCGATTCGGTCGAGTTCTTCTGGTTTGGAGTCAAGCTGCATTCGAATGCTGGATGCTTCTTCATCAATCAGGTCGATGGCTTTATCCGGCAGCGGACGGTCAGCaa                                                                                                                                                                                          <  1:243024/177‑1 (MQ=255)                                                                                                            tcatcaGACTCTTTCATTAACGCCTGTTGTTCCAGTTTGAGCTGGATGATACGACGATCGAGTCGGTCGAGTTCTTCTGGTTTTGAGTCAATCTGCATACGAATGCTGGATGCTGCTTCATCAATCAGGTCGATGGCTTTATCCGGCAGCTGACGGTCAGCAATGTAGCGATGAGACAACGTCGCCGCTGCAACAATTGCCGGGTCAGTAATTTGCACATGGTGGTGCAATTCGTAACGTTCTTTCAgg                                                                                                    <  1:169743/249‑1 (MQ=255)                                                                                                                            ttAACGCCTGTTGTTCCCGTTTGAGCTGGATGATACGACGATCGAGTCGGTCGAGTTCTTCTGGTTTTGAGTCAATCTGCCTACGAATGATGGATGCTGCTTCATCAATCAGGTCGATGGCTTTATACGGCAGNGGANNNNNAgnnnnnnnnnn                                                                                                                                                                                   >  2:272305/1‑144 (MQ=255)                                                                                                                                                    gCTGGATGATACGACGATCGAGTCGGTAGAGTTCTTCTGGTTTTGAGTCAATCTGCATACGCATGCTGGATGCTGCTTCATCAATCAGGTCGCTGGCTTTATCCGGCAGCTGACGGTCAGCCATGTAGCGATGAGACAACGt                                                                                                                                                                       >  1:363708/1‑142 (MQ=255)                                                                                                                                                     cTGGATGATACGACGATCGAGTCGGTCGAGTTCTTCTGGTTTTGAGTCAATCTGCATACGAAGGCTGGATGCTGCTTCATCAATCAGTTCGATGGCTTTATCCGGCAGCTGACGGTCAGCAATGTAGCGATTAGACAACGTCTCCGCTGCAACAATTGCCggg                                                                                                                                                 <  1:369285/163‑1 (MQ=255)                                                                                                                                                               cgacgaTCGAGTCGGTCGAGTTCTTCTGGTTTTGAGTCAANCTGNATACNAANGCTGGATGCTGCTTCNTCAATCAGGTCGATGGCTTTATCCGGCAGCTGACGGTCAGCAATNNANNNANGAGACAAc                                                                                                                                                                         <  2:314706/129‑1 (MQ=255)                                                                                                                                                               cgacgaTCGAGTCGGTCGAGTTCTTCTGGTTTTGAGCCAAACTGCAAACGCCTGATGGATTCTGATTCATACATCAGGTCGATGGCTATATCCGGAAGCTGACGGGCAGCAATGAAGCGATGAGACaaa                                                                                                                                                                         >  1:314706/1‑128 (MQ=255)                                                                                                                                                                gacgaTCGAGTCGGTCGAGTTCTTCTGGGTTTGAGTCAATCTGCATACGAATGCTGGATGCTGCTTCATCAATCAGGTCGATGGCTTTATCCGGCAGCTGACGGGCAGCAATGTAGCGATGAGACAAAGTCGCCGCTGCAACAATTGCCGGGTCAGTAATTTGcaaa                                                                                                                                  >  1:13536/1‑165 (MQ=255)                                                                                                                                                                         gtctgtcgAGTTCTTCTGGTTTTGAGTCAATCTGCATACGAATGCTGGATGCTGCTTCATCAATCAGGTCGATGGCTTTATCCGGCAGCTGACGGTCAg                                                                                                                                                                                             <  1:138527/95‑1 (MQ=255)                                                                                                                                                                           cggtcgAGTTCTTCTGGTTTTGAGTCAATCTGCATACGAATGCTGGATGCTGCTTCATCAATCAGGTCGATGGCTTTATCCGGCAGCTGACGGTCAGCAATGTAGCGATGAGACAACGTCGCCGCTGCAACAATTGCCGGGTCAGTAATTTGCACATGGTGGTGCAATTCGTAACGTTCTTTCAGGCCACGCAGAATCGCAATGGTATCTTCAACAGAAGGCTCGGCAACAAAAACTTTCTGGAAacgacg                                   >  1:387651/1‑251 (MQ=255)                                                                                                                                                                                       tctGGTTTTGAGTCAATCTGCATACGAATGCTGGATGCTGCTTCATCAATCAGGTCGATGGCTTTATCCGGCAGCTGACGGTCAGCAATGTAGCGATGAGACAACGTCGCCGCTGCAACAATTGCCGGGTCAGTAATTTGCACATGGTGGTGCAATTCGTAACGTTCTTTCAGGCCACGCAGAATCGCAATGGTATCTTCAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCgcan                        <  1:272305/250‑2 (MQ=255)                                                                                                                                                                                        ctGGTTTTGAGTCAAGCTGCATACGAATGCTGGATGCTGCTTCATCAATCAGGTCGATGGCTTTATCCGGCAGCTGACGGTCAGCAATGTAGCGATGAGACAACGTCGCCGCTGCAACAATTGCCGGGTCAGTAATTTGCACATGGTGGTGCAATTCGTAACGTTCTTTCAGGCCACGCAGAATCGCAATGGTATCTTCAACAGAAGGCTCGGCAACAAACACTTTCTGGAAac                                       <  1:226162/234‑1 (MQ=255)                                                                                                                                                                                                            aTACGAATGCTGGATGCTGCTTCATCAATCAGGTCGATGGCTTTATCCGGCAGCTGACGGTCAGCAATGTAGCGATGCGACAACGTCGCCGCTGCAACAATTGCCGGGTCAGTAATTTGCACATGGTGGAGCAATTCGTAACGTTCTTTCAGGCCACGCAGAATCGCAATGGTATCTTCAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATCTTTTTCAATGTACTGGCg  >  1:233752/1‑251 (MQ=255)                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                 CAGAAAGCGATGCCTTCTCTGCTTTCCACTCTTCTTCTAACTCGGAGTACTGACGTTCTTTGTCGCTCAGTTCTTCGTTGAGCATATCCAGACGTTTTTTACTGGCTTCATCAGACTCTTTCATTAACGCCTGTTGTTCCAGTTTGAGCTGGATGATACGACGATCGAGTCGGTCGAGTTCTTCTGGTTTTGAGTCAATCTGCATACGAATGCTGGATGCTGCTTCATCGATCAGGTCGATGGCTTTATCCGGCAGCTGACGGTCAGCAATGTAGCGATGAGACAACGTCGCCGCTGCAACAATTGCCGGGTCAGTAATTTGCACATGGTGGTGCAATTCGTAACGTTCTTTCAGGCCACGCAGAATCGCAATGGTATCTTCAACAGAAGGCTCGGCAACAAACACTTTCTGGAAACGACGTTCCAGCGCAGCATCTTTTTCAATGTACTGGCG  >  NC_000913/2732763‑2733216

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑