Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	4,140	A→T	18.2%	D136V (GAT→GTT)	thrC →	L‑threonine synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	4,140	0	A	T	18.2%	55.8 / 6.7	26	D136V (GAT→GTT)	thrC	L‑threonine synthase
Reads supporting (aligned to +/- strand):  ref base A (10/11);  new base T (2/3);  total (12/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.79e-01

AGTGCGAAGATCCTCTCGGCGTTTATTGGTGATGAAATCCCACAGGAAATCCTGGAAGAGCGCGTGCGCGCGGCGTTTGCCTTCCCGGCTCCGGTCGCCAATGTTGAAAGCGATGTCGGTTGTCTGGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTTCGGCGGTCGCTTTATGGCACAAATGCTGACCCATATTGCGGGTGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGATACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTACCGAATGTGAAAGTGGTTATCCTCTATCCACGAGGCAAAATCAGTCCACTGCAAGAAAAACTGTTCTGTACATTGGGCGGCAATATCGAAACTGTTGCCATCGACGGCGATTTCGATGCCTGTCAGGCGCTGGTGAAGCAGGCGTTTGATGATGAAGAACTGAAAGTGGCGCTAGGGTTAAACTCGGCTAACTCGATTAACATCAGCCGTTTGC  >  CP009273/3896‑4391                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                                            agggggAAGATCCTTTTGGCGTTTATTGGTGATGAAATCCCACAGGAAAGCCTGGAAGGGCGCGTGCGCGCGGCGTTTGCCTTCCCGGCTCCGGTCGCCAATGTTGAAAGCGATGNCGGTTGTCTGGCATTGTTCCACGGGCCAACGCTGGCATTTAAAGAGTTCGGCGGTCGCTTTATGGCACAAATGCTGACCCATATTGCGGGTGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGATACCGGAGCGGCAGTGGCTCATGCTTTCt                                                                                                                                                                                                                                <  1:479116/269‑1 (MQ=255)                                          acaGGAAATCCTGGAAGAGCGCGTGCGCGCGGCGTTTGCCTTCCCGGCTCCGGTCGCCAATGTTGAAAGCGATGTCGGTTGTCTGGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTTCGGCGGTCGCTTTATGGCACAAATGCTGACCCATATTGCGGGTGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGATACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTACCGAATGTGAAAGTGGTTATCCTCTATCCACGa                                                                                                                                                                                       >  1:194061/1‑274 (MQ=255)                                                                 tGCGCGCGGCGTTTGCCTTCCCGGCTCCGGTCGCCAATGTTGAAAGCGATGTCGGTTGTCTGGAATTGTGCCACGGGCCAACGCTGGCATTTAAAGATTTCGGCGGTCGCTTTATGGCACAAATGCTGACCCATATTGCGGGTGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGATACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTACCGAATGTGAAAGTGGTTAt                                                                                                                                                                                                    <  1:50533/238‑1 (MQ=255)                                                                           gTTTGCCTTCCCGGCTCCGGTCGCCAATGTTGAAAGCGATGTCGGTTGGCTGGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTTCGGCGGTCGCTTTATGGCACAAATGCTGACCCATATTGCGGGTGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGATACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTACCGAATGTGAAAGTGGTTATCCTCTATCCACGAGGCAAAATCAGTCCACTGCAAGAAAAACTGTTc                                                                                                                                                      <  1:284274/274‑1 (MQ=255)                                                                                                                            gtgtgaTTGNTCCACGGGCCAACGCTTGAATTTAAAGATTTTGGCGGTCGCTTTATGGTCCAAATGCTGACCCATATTGCGGGTGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGATACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTACCGAATGTGAAAGTGGTTATCCTCTATCCACGAGGCAAAATCAGTCCACTGCAAGAAAAACTGTTCTGTACATTGGGCGGCAATATCGAAACTGTTGCCATCGACGGCGATTTCGa                                                                                                    <  2:194058/270‑1 (MQ=255)                                                                                                                                    gTTCCACGGGCCAACGCTGGCATTTAAAGATTTTGGCGGTCGCTTTATGGCACTAATGCTGACCCATATTGCGGGTGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGATAACGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTACCGAATGTGAAAGTGGTTATCCTCTATCCACGAGGCAAAATCAGTCCACTGCAAGAAAAACTGTTCTGTACATTGGGCGGCAATATCGAAACTGTTGCCATCGACGGCGATTTCGATGCCTGt                                                                                             <  1:87728/274‑1 (MQ=255)                                                                                                                                     ttCCACGGGCCAACGCTGGCATTTAAAGATTTCGGCGGTCGCTTTATGGCACAAATGCTGACCCATATTGCGGGTGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGATACCGGAGCGGCAGTg                                                                                                                                                                                                                                             >  2:81016/1‑129 (MQ=255)                                                                                                                                         aCGGGCCAACGCTGGCATTTAAAGATTTCGGCGGTCGCTTTATGGCACAAATGCTGACCCATATTGCGGGTGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGATACCGGAGCGGCAGTGGCTc                                                                                                                                                                                                                                         <  1:81016/129‑1 (MQ=255)                                                                                                                                                                                           aTGCTGACCCATATTGCGGGTGATAAGCTAGTGACCATTCTGACCGCGACCTCCGGTGATACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTACCGAATGTGAAAGt                                                                                                                                                                                                          >  1:400584/1‑110 (MQ=255)                                                                                                                                                                                               tGACCCATATTGCGGGTGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGATACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTACCGAATGTGAAAGTGGtt                                                                                                                                                                                                      <  2:400575/110‑1 (MQ=255)                                                                                                                                                                                                 aCCCATATTGCGGGTGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGATACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTACCGAATGTGAAAGTGGTTATCCTCTATCCACGAGGCAAAATCAGTCCACTGCAAGAAAAACTGTTCTGTACATTGGGCGGCAATATCGAAACTGTTGCCATCGACGGCGATTTCGATGCCTGTCAGGCGCTGGTGAAGCAGGCGGTTGATGATGAAGAACTGAAAGTGGCGCTTggggagaatgc                               >  2:75749/1‑267 (MQ=255)                                                                                                                                                                                                           cGGGTGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGATACCGGAGCGGCAGTGGCTCATGCt                                                                                                                                                                                                                                    >  1:132563/1‑68 (MQ=255)                                                                                                                                                                                                             ggTGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGTTACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTACCGAATGTGAAAGTGGTTATCCTCTATCCACGAGGCAAAATCAGTCCACTGCAAGAAAAACTGTTCTGTACATTGGGCGGCa                                                                                                                                      >  1:168012/1‑160 (MQ=255)                                                                                                                                                                                                             ggTGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGATACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTACCGAATGTGAAAGTg                                                                                                                                                                                                         >  2:338860/1‑93 (MQ=255)                                                                                                                                                                                                             ggTGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGATACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTACCGAATGTGAAAGTGGTTATCCTCTATCCACGAGGCAAAATCAGTCCACTGCAAGAAAAACTGTTCTGTACATTGGGCGGCAATATCGAAACTGTTGCCATCGACGGCGATTCCGATGCCTGt                                                                                             >  2:385053/1‑201 (MQ=255)                                                                                                                                                                                                             ggTGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGATACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTACAGAATGTGAAAGTGGTTATCATCTATCCACGAGGCAAACTCAGTCCACTGCAAGAAAAACTGTTCTGTACATTGGGCGGCAATATCGAAACTGTTGCCATCGACGGCGATTTAGATGCCTGTCAGGCGCTGGTGAAGCAGGCGATTGATGATGAAGAACAGAAAGTGGCGATAGGGTTAAAATCGGCTACATCGAt                   >  1:55223/1‑275 (MQ=255)                                                                                                                                                                                                               tGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGATACCGGAGCGGCAGTGGCTCATGCTTTCt                                                                                                                                                                                                                                <  2:132562/68‑1 (MQ=255)                                                                                                                                                                                                                 aTAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGTTACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTACCGAATGTGAAAGTGGTTATCCTCTATCCACGAGGCAAAATCAGTCCACTGCAAGAAAAACTGTTCTGTACATTGGGCGGCAatat                                                                                                                                  <  2:168011/160‑1 (MQ=255)                                                                                                                                                                                                                 aTAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGATACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTACCGAATGTGAAAGTGGTTa                                                                                                                                                                                                     <  1:338865/93‑1 (MQ=255)                                                                                                                                                                                                                 aTAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGATACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTACCGAATGTGAAAGTGGTTATCCTCTATCCACGAGGCAAAATCAGTCCACTGCAAGAAAAACTGTTCTGTACATTGGGCGGCAATATCGAAACTGTTGCCATCGACGGCGATTTCGATGCCTGTCAgg                                                                                         <  1:385061/201‑1 (MQ=255)                                                                                                                                                                                                                          tGACCATTCTGACCGCGACCTCCGGTGATACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTACCGAATGTGAAAGTGGTTATCCTCTATCCACGAGGCAAAATCAGTCCACTGCAAGAAAAACTGTTCTGTAc                                                                                                                                                 >  1:72858/1‑136 (MQ=255)                                                                                                                                                                                                                              catgccgccnGCGACCTTCGGCGTGACCGGGGCGGCAGTGGCTCATGCTTTCTAAGGTTTGACGAATGTGAAAGTGGTTATCCTCTATCAACGAGGCAAAATCAGACCACTGCAAGAAAAACTGTTCTGTACGTTGGGCGGCAATATCGAAGCTGTTGCCATCGACGGCGATTTCGATGCCTGTCAGGCGCTGGTGAAGCAGGCGTTTGATGATGAAGAACTGAAAGTGGCGCTAGGGTTAACCTCGGCTAACTCGATTAACATCAGCCGTTTGc  <  2:202064/267‑1 (MQ=255)                                                                                                                                                                                                                              cATTCTGACCGCGACCTCCGGTGATACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTACCGAATGTGAAAGTGGTTATCCTCTATCCACGAGGCAAAATCAGTCCACTGCAAGAAAAACTGTTCTGTACATTg                                                                                                                                             <  2:72858/136‑1 (MQ=255)                                                                                                                                                                                                                                 tCTGACCGCGACCTCCGGTGATACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTACCGAATGTGAAAGTGGTTATCCTCTATCCACGAGGCAAAATCAGTCCACTGCAAGAAAAACTGTTCTGTACATTGGGCGGCAATATCGAAACTGTTGCCATCGACGGCGATTTCGATGCCTGTCAGGCGCTGGTGAAGCAGGCGTTTGATGATGAAGAACTGAAAGTGGCGCTAGGGTTAAACTCGGCTAACACGATTAACATCAGCCGt      >  1:202067/1‑268 (MQ=255)                                                                                                                                                                                                                                         cgACCTCCGGTGTTACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTACCGAATGTGAAAGTGGTTATCCTCTATCCACGAGGCAAAATCAGTCCACTGCAAGaaa                                                                                                                                                              >  1:467542/1‑108 (MQ=255)                                                                                                                                                                                                                                             cTCCGGTGTTACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTACCGAATGTGAAAGTGGTTATCCTCTATCCACGAGGCAAAATCAGTCCACTGCAAGAAAAACt                                                                                                                                                          <  2:467533/108‑1 (MQ=255)                                                                                                                                                                                                                                                     aTACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTACCGAATGTGAAAGTGGTTATCCTCTATCCACGAGGCAAAATCAGTCCACTGCAAGAAAAACTGTTCTGTACATTGGGCGGCAATATCGAAACTGTTGCCATCGACGGCGATTTCGATGCCTGt                                                                                             >  1:160506/1‑161 (MQ=255)                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                                            AGTGCGAAGATCCTCTCGGCGTTTATTGGTGATGAAATCCCACAGGAAATCCTGGAAGAGCGCGTGCGCGCGGCGTTTGCCTTCCCGGCTCCGGTCGCCAATGTTGAAAGCGATGTCGGTTGTCTGGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTTCGGCGGTCGCTTTATGGCACAAATGCTGACCCATATTGCGGGTGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGATACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTACCGAATGTGAAAGTGGTTATCCTCTATCCACGAGGCAAAATCAGTCCACTGCAAGAAAAACTGTTCTGTACATTGGGCGGCAATATCGAAACTGTTGCCATCGACGGCGATTTCGATGCCTGTCAGGCGCTGGTGAAGCAGGCGTTTGATGATGAAGAACTGAAAGTGGCGCTAGGGTTAAACTCGGCTAACTCGATTAACATCAGCCGTTTGC  >  CP009273/3896‑4391

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑