Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	2,985,002	G→T	100%	D126Y (GAT→TAT)	ygeG →	SycD‑like chaperone family TPR‑repeat‑containing protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	2,985,002	0	G	T	67.8%	15.8 / 21.5	25	D126Y (GAT→TAT)	ygeG	SycD‑like chaperone family TPR‑repeat‑containing protein
Reads supporting (aligned to +/- strand):  ref base G (1/7);  new base T (11/6);  total (12/13)
Fisher's exact test for biased strand distribution p-value = 3.02e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.42e-03
Rejected as polymorphism: Not supported by required number of reads on both strands.

AAAGATTTTGCATCAGTATGTCAGCCCAAAAAGAAATATCAACAAGCATATGACCTTTACAAACTAAGTTACAATTACTTCCCGTATGATGACTATTCAGTTATTTATCGTATGGGTCAATGTCAGATTGGGGCTAAAAATATCGATAACGCAATGCAATGTTTCTATCACATTATTAACAATTGTGAGGATGATAGTGTTAAGAGTAAAGCGCAGGCATATATTGAACTCTTAAACGATAATTCAGAAGATAATGGCTAAGCATTACAATCATTTGGTTAAATTTGCTGGTT  >  CP009273/2984858‑2985150                                                                                                                                                 |                                                                                                                                                     aaaGATTTTGCATCAGTATGTCAGCCCAAAAAGAAATATCAACAAGCATATGACCTTTACAAACTAAGTTACAATTACTTCCCGTATGATGACTATTCAGTTATTTATCGTATGGGTCAATGTCAGATTGGGGCTAAAAATATCTATaa                                                                                                                                                  >  1:240179/1‑149 (MQ=255)             tCATTATGGCAGACCAAAAAGAATTATCATCAAGCATATGACCTGTACAAACGAACTAACAATTACTTCCCGTATGATGACTATTCAGTTATTTATCGTATGGGTCAATGTCAGATTGGGGCTAAAAATATCTATAACgcaat                                                                                                                                            <  2:188867/143‑1 (MQ=255)                 tATGTCAGCCCAAAAAGAAATATCAACAAGCATATGACCTTTACAAACTAAGTTACAATTACTTCCCGTATGATGACTATTCAGTTATTTATCGTATGGGTGACTGTCAGATTGGGGCTAAAAATTTCTATAAACGAATGCGATGTTTc                                                                                                                                  >  1:105412/1‑149 (MQ=255)                           cAAAAAGAAATATCAACAAGCATATGACCTTTACAAACTAAGTTACAATTACTTCCCGTATGATGACTATTCAGTTATTTATCGTATGGGTCAATGTCAGATTGGGGCTAAAAATATCTATAACGCAATGCAATGTTTCTATCAAatta                                                                                                                        >  1:74832/1‑149 (MQ=255)                               aaGAAATATCAACAAGCATATGACCTTTACAAACTAAGTTACAATTACTTCCCGTATGATGACTATTCAGTTATTTATCGTATGGGTCAATGTCAGATTGGGGCTAAAAATATCTATAACGCAATGCAATGTTTCTATCACATTATTaa                                                                                                                    <  1:138425/149‑1 (MQ=255)                                 gAAATATCCACCAGCATACGCCCTTTACAAACTAAGTTACAATTACTTCCCGTATGACCACTATTCAGTTATTTATCGTATCGGTCAATCTCAGATTGGGGCTAAAAATATCTATAACGCAATGCAATGTTTCTATCCCatta                                                                                                                        <  2:35770/143‑1 (MQ=255)                                     tatCAACAAGCATATGACCTTTACAAACTAAGTTACAATTACTTCCCGTATGATGACTATTCAGTTATTTATCGTATGGGTCAATGTCAGATTGGGGCTAAAAATATCTATAACGCAATGCAATGTTTATATGACATTATTACCAAGtg                                                                                                              >  1:59857/1‑149 (MQ=255)                                        caacaaGCATATGACCTTTACAAACTAAGTTACAATTACTTCCCGTATGATGACTATTCAGTTATTTATCGTATGGGTCAATGTCAGATTGGGGCTAAAAATATCGATAACGCAATGCAATGTTTCTATCACATTATTAACAATTGTGa                                                                                                           <  1:173346/149‑1 (MQ=255)                                              gCATATGACCTTTACAAACTAAGTTACAATTACTTCCCGTATGATGACTATTCAGTTATTTATCGTATGGGTCAATGTCAGATTGGGGCTAAAAATATCGATAACGCAATGCAATGTTTCTATCACATTATTAACAATTGTGa                                                                                                           <  2:275817/143‑1 (MQ=255)                                                atatGACCTTTACAAACTAAGTTACAATTACTTCCCGTATGATGACTATTCAGTTATTTATCGTATGGGTCAATGTCAGATTGGGGCTAAAAATATCGATAACGCAAGGCAATGTTTCTATCACATTATTAACAATTGTGAgg                                                                                                         <  2:176313/143‑1 (MQ=255)                                                            cAAACTAAGTTACAATTACTTCCCGTATGATGACTATTCAGTTATTTATCGTATGGGTCAATGTCAGATTGGGGCTAAAAAGATCGATAACGCAATGCAATGTTTCTATCACATTATTAACAATTGTGAGGATGATAGTGTTa                                                                                             <  2:119742/143‑1 (MQ=255)                                                               aCTAAGTTACAATTACTTCCCGTATGATGACTATTCAGTTATTTATCGTATGGGTCAATGTCAGATTGGGGCTAAAAATATCGATAACGCAATGCAATGTTTCTATCACATTATTAACAATTGTGAGGATGATAGTGTTAAGAGTAAAg                                                                                    <  1:44476/149‑1 (MQ=255)                                                                 tAAGTTACAATTACTTCCCGTATGATGACTATTCAGTTATTTATCGTATGGGTCAATGTCAGATTGGGGCTAAAAATATCTATAACGCAATGCAATGTTTCTATCACATTATTAACAATTGTGAGGATGATAGTGTTAAGAGTAAAgcg                                                                                  >  1:327575/1‑149 (MQ=255)                                                                 tAAGTTACAATTACTTCCCGTATGATGACTATTCAGTTATTTATCGTATGGGTCAATGTCAGATTGGGGCTAAAAATATCTATAACGCAATGCAATGTTTCTATCACATTATTAACAATTGTGAGGATGATAGTGTTAAGAGTAAAacg                                                                                  >  1:182129/1‑149 (MQ=255)                                                                    gTTACAATTACTTCCCGTATGATGACTATTCAGTTATTTATCGTATGGGTCAATGTCAGATTGGGGCTAAAAATATCGATAACGCAATGCAATGTTTCTATCACATTATTAACAATTGTGAGGATGATAGTGTTAAGAGTaaa                                                                                     <  2:160338/143‑1 (MQ=255)                                                                    gTTACAACTACTTCCCGTATGATGACTATTCAGTTATTTATCGTATGGGTCAATGTCAGATTGGGGCTAAAAATATCTATAACGCAATGCAATGTTTCTATCACATTATTAACAATTGTGAGGATGATAGTGTTAAGAGTaaa                                                                                     <  2:256290/143‑1 (MQ=255)                                                                      tACAATTACTTCCCGTATGATGCCTATTCGGTTATTTATCGTATGGGTCAATGTCAGATTGGGGCTAAAAATATCTATAACGCAATGCAATGTTTCTATCACATTATTAACAATTGTGAGGATGATAGTGTTAAGAGTAAAGCGCAgga                                                                             >  1:328661/1‑148 (MQ=255)                                                                               ttCCCGTATGATGACTATTCAGTTATTTATCGTATGGGTCAATGTCAGATTGGGGCTAAAAATATCTATAACGCAATGCAATGTTTCTATCAAATTATTAACAATTGTGAGGATGATAGTGTTAAGAGTAAAGCGCAGGCata                                                                          >  2:292110/1‑143 (MQ=255)                                                                                              tATTCAGTTATTTATCGTATGGGTCAATGTCAGATTGGGGCTAAAAATATCTATAACGCAATGCAATGTTTCTATCACATTATTAACAATTGTGAGGATGATAGTGTTAAGAGTAAAGCGCAGGCATATATTGAACTCTTaaa                                                           >  2:154864/1‑143 (MQ=255)                                                                                                                aTGGGTCAATGTCAGATTGGGGCTAAAAATATCTATAACGCAATGCAATGTTTCTATCACATTATTAACAATTGTGAGGCTGATAGTGTTAAGAGTAAAGCGCAGGCATATATTGAACTCTTAAACGATACTTCAGAAAATAATGGCTa                                   >  1:139523/1‑149 (MQ=255)                                                                                                                   ggTCAATGTCAGATTGGGGCTAAAAATATCGATAACGCAATGCAATGTTTCTATCACATTATTAACAATTGTGAGGATGATAGTGTTAAGAGTAAAGCGCAGGCATATATTGAACTCTTAAACGATAATTCAGAAGATAATGGCTAAGc                                <  1:134458/149‑1 (MQ=255)                                                                                                                                ttGGGGCTAAAAATATCTATAACGCAATGCAATGTTTCTATCACATTATTAAAAATTGTGAGGATGATAGTGTTCAGAGGAAAGCGCAGGCATATATTGAAATCTTAAACGATAATTAAGAAGATAATGGCTAAGCATTACaa                         >  2:263986/1‑143 (MQ=255)                                                                                                                                     gCTAAAAATATCTATAACGCAATGCAATGTTTCTATCACATTATTAACAATTGTGAGGATGATAGTGTTAAGAGTAAAGCGCAGGCATATATTGAACTCTTAAACGATAATTCAGAAGATACTGGCCAAGCATTACAATCAtt                    <  2:257395/143‑1 (MQ=255)                                                                                                                                       tAAAAATATCTATAACGCAATGCAATGTTTCTATCACATTATTAACAATTGTGAGGATGATAGTGTTAAGAGTAAAGCGCAGGCATATATTGAACTCTTAAACGATAATTCAGAAGATAATGGCTAAGCATTACAATCATTTGGTTaaa            <  1:176377/149‑1 (MQ=255)                                                                                                                                       tAAAAATATCGATAACGCAAGGCAATGTTTATATCAGATTATTAACAATTGTGAGGATGATAGTGTTAAGAGTAAAGCGCAGGCATATATTGAACTCTTAAACGGTAGTTCAGAAGATAGTGGCTAAGCATTACAATGATTTTGGTaaa            >  1:142868/1‑149 (MQ=255)                                                                                                                                                 gATAACGCAATGCAATGTTTCTATCACATTATTAACAATTGTGAGGATGATAGGTTGAAGAGTAAAGCGCAGGCATATATTGAACTCTTAAACGATAATTCAGAAGATAATGGCTAAGCATTACAATCATTTGGTTAAATTTGCTGGtt  <  1:76588/149‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                     AAAGATTTTGCATCAGTATGTCAGCCCAAAAAGAAATATCAACAAGCATATGACCTTTACAAACTAAGTTACAATTACTTCCCGTATGATGACTATTCAGTTATTTATCGTATGGGTCAATGTCAGATTGGGGCTAAAAATATCGATAACGCAATGCAATGTTTCTATCACATTATTAACAATTGTGAGGATGATAGTGTTAAGAGTAAAGCGCAGGCATATATTGAACTCTTAAACGATAATTCAGAAGATAATGGCTAAGCATTACAATCATTTGGTTAAATTTGCTGGTT  >  CP009273/2984858‑2985150

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: ‑