Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	4,179,242	C→T	100%	A1322V (GCG→GTG)	rpoC →	RNA polymerase, beta prime subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	4,179,242	0	C	T	100.0%	65.5 / ‑6.7	22	A1322V (GCG→GTG)	rpoC	RNA polymerase, beta prime subunit
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base T (11/10);  minor base G (1/0);  total (12/10)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TCTGCAGGGCGTTAAGATTAACGATAAACACATCGAAGTTATCGTTCGTCAGATGCTGCGTAAAGCTACCATCGTTAACGCGGGTAGCTCCGACTTCCTGGAAGGCGAACAGGTTGAATACTCTCGCGTCAAGATCGCAAACCGCGAACTGGAAGCGAACGGCAAAGTGGGTGCAACTTACTCCCGCGATCTGCTGGGTATCACCAAAGCGTCTCTGGCAACCGAGTCCTTCATCTCCGCGGCATCGTTCCAGGAGACCACTCGCGTGCTGACCGAAGCAGCCGTTGCGGGCAAACGCGACGAACTGCGCGGCCTGAAAGAGAACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACCAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCACCGCAGGTGACTGCAGAAGACGCATCTGCCAGCCTGGCAGAACTGCTGAACGCAGGTCT  >  CP009273/4179003‑4179479                                                                                                                                                                                                                                                |                                                                                                                                                                                                                                              tCTGCAGGGCGTTAAGATTAACGATAAACACATCGAAGTTATCGTTCGTCAGATGCTGCGTAAAGCTACCATCGTTAACGCGGGTAGCTCCGACTTCCTGGAAGGCGAACAGGTTGAATACTCTCGCGTCAAGATCGCAAACCGCGAACTGGAAGCGAACGGCAAAGTGGGTGCAACTTACTCCCGCGATCTGCTGGGTATCACCAAAGCGTCTCTGGTAACCGAGTCCTTCATCTCCGTGGCATCGTTCCAGGAGCCCACACGCGTGCAGACCg                                                                                                                                                                                                            >  1:175771/1‑275 (MQ=255) tCTGCAGGGCGTTAAGATTAACGATAAACACATCGAAGTTATCGTTCGTCAGATGCTGCGTAAAGCTACCATCGTTAACGCGGGTAGCTCCGACTTCCTGGAAGGCGAACAGGTTGAATACTCTCGCGTCAAGATCGCAAACCGCGAACTGGAAGCGAACGGCAAAGTGGGTGCAACTTACTCCCGCGATCTGCTGGGTATCACCAAAGCGCCTCTGGCAACCGAGTCCTTCATCTCCGGGGCATCGTTCCGGGAGACCACTCGCGTGCCGAccc                                                                                                                                                                                                            >  2:123646/1‑274 (MQ=255)                                                           cGTAAAGCTACCATCGTTAACGCGGGTAGCTCCGACTTCCTGGAAGGCGAACAGGTTGAATACTCTCGCGTCAAGATCGCAAACCGCGAACTGGAAGCGAACGGCAACGTGGGTGCAACTTACTCCCGCGATCTGCTGGGTATCACCAAAGCGTCTCTGGCAACCGAGTCCTTCATCGCCGTGGCATCGTTCCAGGAGACCACTCGCGTGCTGACCGAAGCAGCCGTTGCGGGCAAACGCGACGAACAGCGCGGCCTGAAAGAGAACGTTATCg                                                                                                                                                   >  1:207084/1‑274 (MQ=255)                                                                                    gTAGCTCCGACTTCCTGGAAGGCGAACAGGTTGAATACTCTCGCGTCAAGATCGCAAACCGCGAACTGGAAGCGAACGGCAAAGTGGGTGCAACTTACTCCCGCGATCTGCTGGGTATCACCAAAGCGTCTCTGGCAACCGAGTCCTTCATCTCCGTGGCATCGTTCCAGGAGAc                                                                                                                                                                                                                             >  2:311333/1‑175 (MQ=255)                                                                                        cgccGACTGCCTGGAAGACAAACAGGTTGTATACTCCCGCGTCAAGTTCGCAAACCGCGAACTGGAAGCGAACGGCAAAGTGGGTGCAACTTACTCCCGCGATCTGCTGGGTATCACCAAAGCGTCTCTGGCAACCGAGTCCTTCATCTCCGTGGc                                                                                                                                                                                                                                            <  2:93408/154‑1 (MQ=255)                                                                                        cTCCGACTTCCTGGAAGGCGAACAGGTTGAATACTCTCGCGTCAAGATCGCAAACCGCGAACTGGAAGCGAACGGCAAAGTGGGTGCAACTTACTCCCGCGATCTGCTGGGTATCACCAAAGCGTCTCTGGCAACCGAGTCCTTCATCTCCGTGGCATCGTTCCAGGAGACCACt                                                                                                                                                                                                                         <  1:311339/175‑1 (MQ=255)                                                                                              cTTCCTGGAAGGCGAACAGGTTGAATACTCTCGCGTCAAGATCGCAAACCGCGAACTGGAAGCGAACGGCAAAGTGGGTGCAACTTACTCCCGCGATCTGCTGGGTATCACCAAAGCGTCTCTGGCAACCGAGTCCTTCATCTCCGTGGCATCGTTCCAGGAGACCACTCGCGTGCTGACCGAAGCAGCCGTTGCGGGCAAACGCGACGAACTGCGCGGCCTGAAAGAGAACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGt                                                                                                               <  1:123650/275‑1 (MQ=255)                                                                                                                           ctcGCGTCAAGATCGCAAACCGCGAACTGGAAGCGAACGGCAAAGTGGGTGCAACTTACTCCCGCGATCTGCTGGGTATCACCAAAGCGTCTCTGGCAACCGAGTCCTTCATCTCCGTGGCATCGTTCCAGGAGACCACTCGCGTGCTGACCGAAGCAGCCGTTGCgg                                                                                                                                                                                             >  2:267922/1‑168 (MQ=255)                                                                                                                           ctcGCGTCAAGATCGCAAACCGCGAACTGGAAGCGAACGGCAAAGTGGGTGCAACTTACTCCCGCGATCTGCTGGGTATCACCAAAGCGTCTCTGGCAACCGAGTCCTTCATCTCCGTGGCATCGTTCCAGGAGACCACTCGCGTGCTGACCGAAGCAGCCGTTGCGGGCAAACGCGACGAAc                                                                                                                                                                              >  1:181328/1‑183 (MQ=255)                                                                                                                               cgTCAAGATCGCAAACCGCGAACTGGAAGCGAACGGCAAAGTGGGTGCAACTTACTCCCGCGATCTGCTGGGTATCACCAAAGCGTCTCTGGCAACCGAGTCCTTCATCTCCGTGGCATCGTTCCAGGAGACCACTCGCGTGCTGACCGAAGCAGCCGTTGCGGGCaa                                                                                                                                                                                         <  1:267927/168‑1 (MQ=255)                                                                                                                               cgTCAAGATCGCAAACCGCGAACTGGAAGCGAACGGCAAAGTGGGTGCAACTTACTCCCGCGATCTGCTGGGTATCACCAAAGCGTCTCTGGCAACCGAGTCCTTCATCTCCGTGGCATCGTTCCAGGAGACCACTCGCGTGCTGACCGAAGCAGCCGTTGCGGGCAAACGCGACGAACTgcg                                                                                                                                                                          <  2:181323/183‑1 (MQ=255)                                                                                                                                 tCAAGATCGCAAACCGCGTACTGGAAGCGAACGGCAAAGTGGGTGCAACTTACTCCCGCGATCTGCTGGGTATCACCAAAGCGTCTCTGGCAACCGAGTCCTTCATCTCCGTGGCATCGTTCCAGGAGACCACTCGCGTGCTGACCGAAGCAGCCGTTGCGGGCAAACGCGACGAACTGCGCGGCCTGAAAGAGAACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACCAGGATCGTATGCGTCGCCGTGCTGCGGGt                                                                            <  1:153575/275‑1 (MQ=255)                                                                                                                                                                   ccaaGTGGGTGCAACTTACTCCCGCGATCTGCTGGGTATCACCAAAGCGTCTCTGGCAACCGAGTCCTTCATCTCCGTGGCATCGTTCCAGGAGACCACTCGCGTGCTGACCGAAGCAGCCGTTGCgg                                                                                                                                                                                             >  2:348255/3‑128 (MQ=255)                                                                                                                                                                       gTGGGTGCAACTTACTCCCGCGATCTGCTGGGTATCACCAAAGCGTCTCTGGCAACCGAGTCCTTCATCTCCGTGGCATCGTTCCAGGAGACCACTCGCGTGCTGACCGAAGCAGCCGTTGCGGGCaa                                                                                                                                                                                         <  1:348261/128‑1 (MQ=255)                                                                                                                                                                             gCAACTTACTCCCGCGATCTGCTGGGTATCACCAAAGCGTCTCTGGCAACCGAGTCCTTCATCTCCGTGGCATCGTTCCAGGAGACCACTCGCGTGCTGACCGAAGCAGCCGTTGCGGGCAAACGCGACGAAc                                                                                                                                                                              >  2:182946/1‑133 (MQ=255)                                                                                                                                                                                 cTTACTCCCGCGATCTGCTGGGTATCACCAAAGCGTCTCTGGCAACCGAGTCCTTCATCTCCGTGGCATCGTTCCAGGAGACCACTCGCGTGCTGACCGAAGCAGCCGTTGCGGGCAAACGCGACGAACTgcg                                                                                                                                                                          <  1:182951/133‑1 (MQ=255)                                                                                                                                                                                    aCTCCCGCGATCTGCTGGGTATCACCAAAGCGTCTCTGGCAACCGAGTCCTTCATCTCCGTGGCATCGTTCCAGGAGACCACTCGCGTGCTGACCGAAGCAGCCGTTGCGGGCAAACGCGACGAACTGCGCGGCCTGAAAGAGAACGTTATCGTGGGTCGTCTGATCACGGCAg                                                                                                                              >  1:92482/1‑174 (MQ=255)                                                                                                                                                                                                  ctgGGTATCACCAAAGCGTCTCTGGCAACCGAGTCCTTCATCTCCGTGGCATCGTTCCAGGAGACCACTCGCGTGCTGACCGAAGCAGCCGTTGCGGGCAAACGCGACGAACTGCGCGGCCTGAAAGAGAACGTTATCGTGGGTCGTCTGAt                                                                                                                                      >  1:257720/1‑152 (MQ=255)                                                                                                                                                                                                      gTATCACCAAAGCGTCTCTGGCAACCGAGTCCTTCATCTCCGTGGCATCGTTCCAGGAGACCACTCGCGTGCTGACCGAAGCAGCCGTTGCGGGCAAACGCGACGAACTGCGCGGCCTGAAAGAGAACGTTATCGTGGGTCGTCTGATCCCg                                                                                                                                  <  2:257715/152‑1 (MQ=255)                                                                                                                                                                                                            ccAAAGCGTCTCTGGCAACCGAGTCCTTCATCTCCGTGGCATCGTTCCAGGAGACCACTCGCGTGCTGACCGAAGCATCCGTTGCGGGCAAACGCGACGAACTGCGCGGCCTGAAAGAGAACGTTATCGTGGGTCGTCTGATCCCGTCAGGTACCGGTNACGCGTACCACCAGGATCGTATGCGTCGCCGTGCTGCCGGTGAAGCTCCGGCTGCACCGCAGGTGACTGCAGAAGACGCATCTGCCAGCCTGGAAGAACTGCTGAACGCAGGTCt  >  1:367276/1‑274 (MQ=255)                                                                                                                                                                                                                aGCGTCTCTGGCAACCGAGTCCTTCATCTCCGTGGCATCGTTCCAGGAGACCACTCGCGTGCTGACCGAAGCAGCCGTTGCGGGCAAACGCGACGAACTGCGCGGCCTGAAAGAGAACGTTATCGGGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTac                                                                                                             >  2:87543/1‑163 (MQ=255)                                                                                                                                                                                                                    tctcTGGCAACCGAGTCCTTCATCTCCGTGGCATCGTTCCAGGAGACCACTCGCGTGCTGACCGAAGCAGCCGTTGCGGGCAAACGCGACGAACTGCGCGGCCTGAAAGAGAACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTaccacc                                                                                                         <  1:87546/163‑1 (MQ=255)                                                                                                                                                                                                                                                |                                                                                                                                                                                                                                              TCTGCAGGGCGTTAAGATTAACGATAAACACATCGAAGTTATCGTTCGTCAGATGCTGCGTAAAGCTACCATCGTTAACGCGGGTAGCTCCGACTTCCTGGAAGGCGAACAGGTTGAATACTCTCGCGTCAAGATCGCAAACCGCGAACTGGAAGCGAACGGCAAAGTGGGTGCAACTTACTCCCGCGATCTGCTGGGTATCACCAAAGCGTCTCTGGCAACCGAGTCCTTCATCTCCGCGGCATCGTTCCAGGAGACCACTCGCGTGCTGACCGAAGCAGCCGTTGCGGGCAAACGCGACGAACTGCGCGGCCTGAAAGAGAACGTTATCGTGGGTCGTCTGATCCCGGCAGGTACCGGTTACGCGTACCACCAGGATCGTATGCGTCGCCGTGCTGCGGGTGAAGCTCCGGCTGCACCGCAGGTGACTGCAGAAGACGCATCTGCCAGCCTGGCAGAACTGCTGAACGCAGGTCT  >  CP009273/4179003‑4179479

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑