Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,189,296	C→T	V161I (GTA→ATA)	phoQ ←	sensor histidine kinase PhoQ

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,189,296	0	C	T	92.9%	31.6 / NA	14	V161I (GTA→ATA)	phoQ	sensor histidine kinase PhoQ
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base T (3/10);  minor base G (0/1);  total (3/11)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.57e-01

GCGGTTATGTTCTTCCAGTTCGCGGACTTCTTTTGCCAGGGCTTCGATGGGGCGTAAACTCCACCAGGCGGCGACCCACAGCAGCGGGATCACTAACAGCAGATTGGCTGAGAGCACATAGATAAACCAGCTCCAGACCATATAGGAACTTTTTAGCTCCACCGGAATGGTATCCACCACCACAATGGTTAATTTTGGCATCCGCGATGTTGCCGGGTAGACGTTTACTGCCACCGAGTGGGTCATCTCCGCGTCGTCATCATCTTCCCGCACTTCCTGCAACTGTTGCTGTATCGAATGATCTCCACTCAGCAAGAGGCTGGTATCGTTAACATCCGCTTCAATTTCATGAAAACCATTCGATTTCAGCCAGTCAGGCTGGATCATCTTCATCAGCCAGGGCACGTCACGTTGCGCCCATAAAAGCTGCCCGTTCTCATCATAAATTAGCGTCATGGTGGG  >  NC_000913/1189069‑1189530                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                           gcgGTTATGTTCTTCCAGTTCGCGGACTTCTTTTGCCAGGGCTTCGATGGGGCGTAAACTCCACCAGGCGGCGACCCACAGCAGCGGGATCACTAACAGCAGATTGGCTGAGAGCACATAGATAAACCAGCTCCAGACCATATAGGAACTTTTTAGCTCCACCGGAATGGTATCCACCACCACAATGGTTAATTTTGGCATCCGCGATGTTGCCTGGTAGACGTTTATTGCCACCGAGTGGGTCATCTCcg                                                                                                                                                                                                                     <  1:287454/251‑1 (MQ=255)                                      aGGGCTTCGATGGGGCGTAAACTCCACCAGGCGGCGACCCACAGCAGCGGGATCACTAACAGCAGATTGGCTGAGAGCACATAGATAAACCAGCTCCAGACCATATAGGAACTTTTTAGCTCCACCGGAATGGTATCCACCACCACAATGGTTAATTTTGGCATCCGCGATGTTGCCGGGTAGACGTTTATTGCCACCGAGTGGGTCATCTCCGCGTCGTCATCATCTTcc                                                                                                                                                                                                    <  1:182680/231‑1 (MQ=255)                                                                ccaGGCGGCGACCCACAGCAGCGGGATCACTAACAGCAGATTGGCTGAGAGCACATAGATAAACCAGCTCCAGACCATATAGGAACTTTTTAGCTCCACCGGAATGGTATCCACCACCACACTGGTTAATTTTGGCATCCGCGATGTTGCCGGGTAGACGTTTATTGCCACCGAGTGGGTCATCTCCGCGTCGTCATCATCTTCCCGCACTTCCTGCAACTGTTGCTGTATCGAATGATCTCCACTCAGc                                                                                                                                                       >  1:180217/1‑250 (MQ=255)                                                                                                      gATTGGCTGAGAGCACATAGATAAACCAGCTCCAGACCATATAGGAACTTTTTAGCTACACCGGAATGGCATCCACCAGCACAATGGTTAATTTTCGCCTCCGCGATGTTGCCGGGTAGACGTTTATTGCCACCGAGTGGGTCCTCTCCGCGTCGTCATCATCTTCCCGCACTTCCTGCCACTGTTGCTGTATCGAATGAtc                                                                                                                                                                 >  1:396944/1‑202 (MQ=255)                                                                                                           gCTGAGAGCACATAGATAAACCAGCTCCAGACCATATAGGAACTTTTTAGCTCCACCGGAATGGTATCCACCACCACAATGGTTAATTTTGGCATCCGCGATGTTGCCGGGTAGACGTTTATTGCCACCGAGTggg                                                                                                                                                                                                                              >  1:447113/1‑136 (MQ=255)                                                                                                                            aaaCCAGCTCCAGACCATATAGGAACTTTTTAGCTCCACCGGAATGGTATCCACCACCACAATGGTTAATTTTGGCATCCGCGATGTTGCCGGGTAGACGTTTATTGCCACCGAGTGGGTCATCTCCGCGTCGTCATCATCTTCCCGCACTTCCTGCAACTGTTGCTGTATCGAATGATCTCCACTCAGCAAGAGGCTGGTATCGTTAACATCCGCTTCAATTTCATGAAAAc                                                                                                            <  1:2171/233‑1 (MQ=255)                                                                                                                                           cATATAGGAACTTTTTAGCTCCACCGGAATGGTATCCACCACCACAATGGTTAATTTTGGCATCCGCGATGTTGCCGGGTAGACGTTTATTGCCACCGAGTGGGTCATCTCCGCGTCGTCATCATCTTCCCGCACTTCCTGCAACTGTTGCTGGATCGAATGATCTCCACTCAGCAAGAGGCTGGTATCGTTAACATCCGCTTCAATTTCATGAAAACCATGCGATTTCAGCCAGTCAGGCTGGATCATCt                                                                           <  1:416958/251‑1 (MQ=255)                                                                                                                                              ataGGAACTTTTTAGCTCCACCGGAATGGTATCCACCACCACAATGGTTAATTTTGGCATCCGCGATGTTGCCGGGTAGACGTTTATTGCCACCGAGTGGGTCATCTCCGCGTCGTCATCATCTTCCCGCACTTCCTGCAACTGTTGCTGTATCGAATGATCTCCACTCAGCAAGAGGCTGGTATCGTTAACATCCGCTTCAATTTCATGAAAACCATTCGATTTCAGCCAGTCAGGCTGGATCATCTtc                                                                         <  1:334227/250‑1 (MQ=255)                                                                                                                                                    aCTTTTTAGCTCCACCGGAATGGTATCCACCACCACAATGGTTAATTTTGGCATCCGCGATGTTGCCGGGTAGACGTTTATTGCCACCGAGTGGGTCATCTCCGCGTCGTCATCATCTTcn                                                                                                                                                                                                    <  1:116321/121‑2 (MQ=255)                                                                                                                                                               ccACCGGAATGGTATCCACCACCACAATGGTTAATTTTGGCATCCGCGATGTTGCCGGGTAGACGTTTATTGCCACCGAGTGGGTCATCTCCGCGTCGTCATCATCTTCCCGCACGTCCTGCAACTGTTGCTg                                                                                                                                                                             <  1:139020/133‑1 (MQ=255)                                                                                                                                                                         ggTATCCACCACCACAATGGTTAATTTTGGCATCCGCGATGTTGCCGGGTAGACGTTTAGTGCCACCGAGTGGGTCATCTCCGCGTCGTCATCATCTTCCCGCACTTCCTGCAACTGTTGCTGTATCGAATGATCTCCACTCAGCAagagn                                                                                                                                                 <  1:38516/151‑2 (MQ=255)                                                                                                                                                                                  caccacAATGGTTAAGTTTGGCATCCGCGATGGTGCCGTGTAGACTTTTATTTCCACCGAGTGGGTCATCTCCGCGTCGTCATCATCTGCCCTCACGTCCTGCAACTGTTGCTTTAGCGAATGATCTCCACTCAGCAAGAGGCTGGTATCGTTAACATCCGCTTCAAttt                                                                                                                     <  1:431253/170‑1 (MQ=255)                                                                                                                                                                                                                    ggcGGGTAGACGTTTATTGCCTCCGAGTGGGTCATCTCCGCGTCGTCATCATCTTCCCGCACTTCCGGCATCTGTTGCTGTATCGAATGATCTCCACTCAGCAAGAGGCTGGTATCGTTAACATCCGCTTCAATTTCATGAAAACCATTCGATTTCAGCCAGTCAGGCTGGATCATCTTCATCAGCCAGGGCACGTCACGTTGCGCCCATAAAAGCTGCCCGTTCACATCATAAATTAGCGTCAtggtggn  <  1:109111/249‑2 (MQ=255)                                                                                                                                                                                                                              cGTTTATTGCCACCGAGTGGGTCATCTCCGCGTCGTCATCATCTTCCCGCACTTCCTGCAACTGTTGCTGTATCGAATGATCTCCACTCAGCAAGAGGCTGGTATCGTTAACATCCGCTTCAATTTCATGAAAACCATTCGATTTCAGCCAGTCAGGCTGGATCATCTnc                                                                         <  1:348068/170‑1 (MQ=255)                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                           GCGGTTATGTTCTTCCAGTTCGCGGACTTCTTTTGCCAGGGCTTCGATGGGGCGTAAACTCCACCAGGCGGCGACCCACAGCAGCGGGATCACTAACAGCAGATTGGCTGAGAGCACATAGATAAACCAGCTCCAGACCATATAGGAACTTTTTAGCTCCACCGGAATGGTATCCACCACCACAATGGTTAATTTTGGCATCCGCGATGTTGCCGGGTAGACGTTTACTGCCACCGAGTGGGTCATCTCCGCGTCGTCATCATCTTCCCGCACTTCCTGCAACTGTTGCTGTATCGAATGATCTCCACTCAGCAAGAGGCTGGTATCGTTAACATCCGCTTCAATTTCATGAAAACCATTCGATTTCAGCCAGTCAGGCTGGATCATCTTCATCAGCCAGGGCACGTCACGTTGCGCCCATAAAAGCTGCCCGTTCTCATCATAAATTAGCGTCATGGTGGG  >  NC_000913/1189069‑1189530

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: ‑