Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	3,849,032	A→T	19.6%	L100H (CTC→CAC)	yidG ←	inner membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	3,849,032	0	A	T	19.6%	47.2 / 4.4	25	L100H (CTC→CAC)	yidG	inner membrane protein
Reads supporting (aligned to +/- strand):  ref base A (10/10);  new base T (2/3);  total (12/13)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01

AATCGGCAGGTTGCAGAGCATCCTTGTACTCTACAACCAGTTTATGCCTGTCCTCTTCAGCATCAATGACCTGACTTCCTGTCATGCGACTCTCTCAATAAATACGATAAGTTGATGTATATGCGTTACAGCAAACAGTATTGCGAGAGATAACACCGCGAGGGAGATCAAAAATTTGTCACGGACTACGTGAAATTGGGAAAAATCGCTATTCGTGACATCCATTAAATTGCGATTACGGGTGTAGTGCCAGAGGATCAGCGCCACGATGGCGAGAATGCCAATCGAAA  >  CP009273/3848887‑3849176                                                                                                                                                  |                                                                                                                                                 aaTCGGCAGGTTGCAGAGCATCCTTGTACTCTACAACCAGTTTATGCCTGTCCTCTTCAGCATCAATGACCTGACTTCCTGTCATGCGACTCTCTCAATAAATACGATAAGTTGATGTATATGCGTTACAGCAAACAGTATTGCgagag                                                                                                                                               >  1:164235/1‑149 (MQ=255)        aGGTTGCAGAGCATCCTTGTACTCTACAACCAGTTTATGCCTGTCCTCTTCAGCATCAATGACCTGACTTCCTGTCATGCGACTCTCTCAATAAATACGATAAGTTGATGTATATGCGTTACAGCAAACAGTATTGCGAGAGAt                                                                                                                                             <  2:112591/144‑1 (MQ=255)                   cATACTTGTACTCGACAACCAGTTTATGCCTGCTCTCTTCAGCATCAATGCCCTGACTTCCTGTCATGCCACTCTCTCAACAAATACGATAAGTTGATGTATATGCGTTACAGCAAACAGTATTGCGAGAGATAACACCGCGAg                                                                                                                                  <  2:113826/144‑1 (MQ=255)                      ccTTGTACTCTACAACCAGTTTATGCCTGTCCTCTTCAGCATCAATGACCTGACTTCCTGTCATGCGACTCTCTCAATAAATACGATAAGTTGATGTATATGCGTTACAGCAAACAGTATTGCGTGAGATAACACCGCGAGGga                                                                                                                               >  2:30518/1‑144 (MQ=255)                      ccTTGTACTCTACAACCAGTTTATGCCTGTCCTCTTCAGCATCAATGACCTGACTTCCTGTCATGCGACTCTCTCAATAAATACGATAAGTTGATGTATATGCGTTACAGCAAACAGTATTGCGTGAGATAACACCGCGAGGga                                                                                                                               >  2:30513/1‑144 (MQ=255)                      ccTTGTACTCTACAACCAGTTTATGCCTGTCCTCTTCAGCATCAATGACCTGACTTCCTGTCATGCGACTCTCTCAATAAATACGATAAGTTGATGTATATGCGTTACAGCAAACAGTATTGCGAGAGATAACACCGCGAGGga                                                                                                                               >  2:47352/1‑144 (MQ=255)                               ctACAACCAGTTTATGCCTGTCCTCTTCAGCATCAATGACCTGACTTCCTGTCATGCGACTCTCTCAATAAATACGATAAGTTGATGTATATTCGTTACAGCCAACAGTATTGCGAGAGATAACACCGCGAGGGGGATAAAAAATTTGt                                                                                                                 >  1:33065/1‑149 (MQ=255)                                               ccTGTCCTCTTCAGCATCAATGACCTGACTTCCTGTCATGCGACTCTCTCAATAAATACGATAAGTTGATGTATATGCGTTACAGCAAACAGTATTGCGAGAGATAACACCGCGAGGGAGATCAAAAATTTGTCACGGACTACGTGaaa                                                                                                 <  1:44932/149‑1 (MQ=255)                                                         tCAGCATCAATGACCTGACTTCCCGTCAGGCGACTCTCTCAAGAAATACGATAAGTTGATGTATATGCGTTACAGCAAACAGTATTGCGAGAGATAACACCGCGAGGGAGATCAAAAACTTCACACGGACTACGAGAAATTggg                                                                                            >  2:346396/1‑144 (MQ=255)                                                                      ccTGACTTCCTGTCATGCGACTCTCTCAATAAATACGATAAGTTGATGTATATGCGTTACAGCAAACAGTATTGCGAGAGATAACACCGCGAGGGAGATCAAAAATTTGTCACGGACTACGTGAAATTGGGAAAAAGCGCTAtt                                                                               >  2:256096/1‑144 (MQ=255)                                                                          aCTTCCTGTCATGCGACTCTCTCAATAAAGACGATAATTTTATATCTATGCGGTGCAGCAAACAGTATTGCGAGAGATAACACCGCGAGGGAGATCAAAAATTTGTCACGGACTACGTGAAATTGGGAAAAATCGCTATTCGGGACATc                                                                      <  1:53241/149‑1 (MQ=255)                                                                              ccTGTCATGCGACTCTCTCAATAAATACGATAAGTTGATGTATATGCGTTACAGCAAACAGTATTGCGAGAGATAACACCGCGAGGGAGATCAAAAATTTGTCACGGACTACGTGAAATTGGGAAAAATCGCTATTCGTGACATCCAtt                                                                  <  1:246629/149‑1 (MQ=255)                                                                                   cATGCGACTCTCTCAATAAATACGATAAGTTGATGTATATGCGTTACAGCAAACAGTATTGCGAGAGATAACACCGCGAGGGAGATCAAAAATTTGTCACGGACTACGTGAAATTGGGAAAAATCGCTATTCGTGACATCCATTAAAtt                                                             <  1:63090/149‑1 (MQ=255)                                                                                      gCGACTCTCTCAATAAATACGATAAGTTGATGTATATGCGTTACAGCAAACAGTATTGCGAGAGATAACACCGCGAGGGGGATCAAAAATTTGTCACGGACTACGGGAAATTGGGAAAAATCGCTATTCGTGCCATCCATTAAATTGCg                                                          >  1:104612/1‑149 (MQ=255)                                                                                                cAATAAATACGATAAGTTGATGTATATGCGTTACAGCAAACAGTATTGCGAGAGATAACACCGCGAGGGAGATCAAAAATTTGTCACGGACTACGTGAAATTGGGAAAAATCGCTATTCGTGACATCCATTAAATTGCGATTACGGgtg                                                >  1:179077/1‑149 (MQ=255)                                                                                                      ataCGATAAGTTGATGTATATGCGTTACAGCAAACAGTATTGCGAGAGATCAAACCGCGCGGGAGATCAAAAATTTGTCACGGACTACGTGAAATTGGGAAAAATCGCTATTCGTGACATCCATTAAATTGCGATTACGGgtgt                                               >  2:307114/1‑144 (MQ=255)                                                                                                            tAAGTTGAGGTATATGCGTTACAGCAAACAGTATTGCGAGAGATAACACCGCGAGGGAGATCAAAAATTTGTCACGGACTACGTGAAATTGGGAAAAATCGCTATTCGTGACATCCATTAAATTGCGATTACGGGTGTAGTGCCAGAgg                                    <  1:187122/149‑1 (MQ=255)                                                                                                                ttGATGTATATGCGTTACAGCAGACAGTATTGCGAGAGATAACACCGCGAGGGAGATCAAAAATTTGTCACGGACTACGTGAAATTGGGAAAAATCGCTATTCGTGACATCCATTAAATTGCGATTACGGGTGTAGTGCCagtg                                     >  2:313563/1‑142 (MQ=255)                                                                                                                      tataTGCGTTACAGCAAACAGTATTGCGAGAGATAACACCGCGAGGGAGATCAAAAATTTGTCACGGACTACGTGAAATTGGGAAAAATCGCTATTCGTCACATCCATTAAATTGCGATTACGGGTGTAGTGCCAGAGGATCAGCGCCa                          <  1:284731/149‑1 (MQ=255)                                                                                                                         atGCGTTACAGCAAACAGTATTTCGTGAGATAACACCGCGAGGGAGATAAAAAATTTGTCACGGACTACGTGAAATTGGGAAAAATCGCTATTCGTGACATCCATTAAATTGCGATTACGGGTGTAGTGCCAGAGGATCAgcgc                            <  2:158137/144‑1 (MQ=255)                                                                                                                         atGCGTTACAGCAAACAGTATTGCGAGAGATAACACCGCGAGGGAGATCAAAAATTTGTCACGGACTACGTGAAATTGGGAAAAATCGCTATTCGTGACATCCATTAAATTGCGATTACTGGTGTAGTGCCAGAGGATCAGCGCCACGa                       >  1:356123/1‑149 (MQ=255)                                                                                                                            cGTTACAGCAAACAGTATTGCGAGAGATACCACCGCGAGGGAGATCAAAAATTTGTCACGGACTACGTGAAATTGGGAAAAATCGCTATTCGTGACATCCATTGAATTGCGATTACGGGGGTGCTGCCAGAGCATCAGCGCCAc                         >  2:44089/1‑144 (MQ=255)                                                                                                                                       aCAGGATGGCGAGAGATAACACCGCGAGGGAGATCAAAAATTTGTCACGGACAACGTAAAATTGGGAAAAATCGCTATTCGTGACATCCATTAAATTGCGATTACGGGTGTAGTGCCAGAGGATCAGCGCCACGATGGCGAGaa              <  2:127/144‑1 (MQ=255)                                                                                                                                           tATTGCGTGAGATAACACCGCGAGGGAGATCAAAAATTTGTCACGGACTACGTGAAATTGGGAAAAATCGCTATTCGTGACATCCATTAAATTGCGATTACGGGTGTAGTGCCAGAGGATCAGCGCCACGATGGCGAGAATGCCAATCg     <  1:34244/149‑1 (MQ=255)                                                                                                                                           tATTGCGTGAGATAACACCGCGAGGGAGATCAAAAATTTGTCACGGACTACGTGAAATTGGGAAAAATCGCTATTCGTGACATCCATTAAATTGCGATTACGGGTGTAGTGCCAGAGGATCAGCGCCACGATGGCGAGAATGCCAATCg     <  1:34238/149‑1 (MQ=255)                                                                                                                                              tGCGAGAGATAACACCGCGAGGGAGATCAAAAATTTGTCACGGACTACGTGAAATTGGGAAAAATCGCTATTCGTGACATCCATTAAATTGCGATTACGGGTGTAGTGCCAGAGGATCAGCGCCACGATGGCGAGAATGCCAATCGaaa  <  1:66535/149‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                 AATCGGCAGGTTGCAGAGCATCCTTGTACTCTACAACCAGTTTATGCCTGTCCTCTTCAGCATCAATGACCTGACTTCCTGTCATGCGACTCTCTCAATAAATACGATAAGTTGATGTATATGCGTTACAGCAAACAGTATTGCGAGAGATAACACCGCGAGGGAGATCAAAAATTTGTCACGGACTACGTGAAATTGGGAAAAATCGCTATTCGTGACATCCATTAAATTGCGATTACGGGTGTAGTGCCAGAGGATCAGCGCCACGATGGCGAGAATGCCAATCGAAA  >  CP009273/3848887‑3849176

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑