Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,405,833	A→G	9.3%	E74G (GAA→GGA)	ureA →	Urease subunit gamma

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,405,833	0	A	G	9.3%	128.3 / 5.0	43	E74G (GAA→GGA)	ureA	Urease subunit gamma
Reads supporting (aligned to +/- strand):  ref base A (23/16);  new base G (2/2);  total (25/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.27e-01

TGAAACTAAATCATCCTGAGGCATTAGCTTTAATCAGCGATGAATTATTAGAAGGTGCACGCGATGGTAAGACCGTTGCAGAGTTAATGAGTTATGGTAGACAAATTCTAAACAAAGAAGATGTCATGGATGGTGTCGAACACATGATTACAGATATCGAAATCGAGGCTACGTTCCCCGATGGTACTAAGTTAATCACAGTACATCACCCTATTGTTTAAAGGAGGCAGTCAAATGATACCAGGAGAAATTATTACAAAAAGTACAGAGGTTGAAA  >  USA300TCH1516_ALE/2405695‑2405971                                                                                                                                           |                                                                                                                                           tGAAACTAAATCCTCCTGAGGCATTAGCTTTAATCAGCGATGAATTATTAGAAGGTGCACGCGATGGTAAGACCGTTGCAGAGTTAATGAGTTATGGTAGACAAATTCTAAACAAAGAAGATGTCATGGATGGTGTCGAac                                                                                                                                          <  1:55310/141‑1 (MQ=255)    aaCTAAATCATCCTGAGGCATTAGCTTTAATCAGCGATGAATTATTAGAAGGTGCACGCGATGGTAAGACCGTTGCAGAGTTAATGAGTTATGGTAGACAAATTCTAAACAAAGAAGATGTCATGGATGGTGTCGAAcaca                                                                                                                                       >  1:211177/1‑141 (MQ=255)               ccTGAGGCATTAGCTTTAATCAGCGATGAATTATTAGAAGGTGCACGCGATGGTAAGACCGTTGCAGAGTTAATGAGTTATGGTAGACAAATTCTAAACAAAGAAGATGTCATGGATGGTGTCGAACACATGATTACAGat                                                                                                                            <  1:90616/141‑1 (MQ=255)               ccTGAGGCATTAGCTTTAATCAGCGATGAATTATTAGAAGGTGCACGCGATGGTAAGACCGTTGCAGAGTTAATGAGTTATGGTAGACAAATTCTAAACAAAGAAGATGTCATGGATGGTGTCGAACACATGATTACAGat                                                                                                                            <  1:301448/141‑1 (MQ=255)                  gAGGCCTTAGCTTTAATCAGCGATGAATTATTAGAAGGTGCACGCGATGGTAAGACCGTTGCAGAGTTAATGAGTTATGGTAGACAAATTCTAAACAAAGAAGATGTCATGGATGGTGTCGACCACATGATTACAGCTATc                                                                                                                         >  2:274101/1‑141 (MQ=255)                  gAGGCATTAGCTTTAATCAGCGATGAATTATTAGAAGGTGCACGCGATGGTAAGACCGTTGCAGAGTTAATGAGTTATGGTAGACAAATTCTAAACAAAGAAGATGTCATGGATGGTGTCGAACACATGATTACAGATATc                                                                                                                         >  2:181051/1‑141 (MQ=255)                         tAGCTTTAATCAGCGATGAATTATTAGAAGGTGCACGCGATGGTAAGACCGTTGCAGAGTTAATGAGTTATGGTAGACAAATTCTAAACAAAGAAGATGTCATGGATGGTGTCGGACACATGATTACAGATATCGAAATCg                                                                                                                  >  1:188296/1‑141 (MQ=255)                         tAGCTTTAATCAGCGATGAATTATTAGAAGGTGCACGCGATGGTAAGACCGTTGCAGAGTTAATGAGTTATGGTAGACAAATTCTAAACAAAGAAGATGTCATGGATGGTGTCGGACACATGATTACAGATATCGAAATCg                                                                                                                  >  1:326040/1‑141 (MQ=255)                              ttAATCAGCGATGAATTATTAGAAGGTGCACGCGATGGTAAGACCGATGCAGCGTTAATGAGTTATGGGAGACAAATTCTAAACAAAGAAGCTGTCATGGATGGTGTCGAACACATGATTACAGATATCGAAATCGAGGCt                                                                                                             >  1:450035/1‑141 (MQ=255)                               tAATCAGCGATGAATTATTAGAAGGTGCACGCGATGGTAAGACCGTTGCAGAGTTAATGAGTTATGGTAGACAAATTCTAAACAAAGAAGATGTCATGGATGGTGTCGAACACATGATTACAGATATCGAAATCGAGGCTa                                                                                                            >  2:84272/1‑141 (MQ=255)                               tAATCAGCGATGAATTATTAGAAGGTGCACGCGATGGTAAGACCGTTGCAGAGTTAATGAGTTATGGTAGACAAATTCTAAACAAAGAAGATGTCATGGATGGTGTCGAACACATGATTACAGATATCGAAATCGAGGCTa                                                                                                            >  2:104671/1‑141 (MQ=255)                                   cAGCGATGAATTATTAGAAGGTGCACGCGATGGTAAGACCGTTGCAGAGTTAATGAGTTATGGTAGACAAATTCTAAACAAAGAAGATGTCATGGATGGTGTCGAACACATGATTACAGATATCGAAATCGAGGCTACGtt                                                                                                        >  2:328196/1‑141 (MQ=255)                                    aGCGATGAATTATTAGAAGGTGCACGCGATGGTAAGACCGTTGCAGAGTTAATGAGTTATGGTAGACAAATTCTAAACAAAGAAGATGTCATGGATGGTGTCGAACACATGATTACAGATATCGAAATCGAGGCTACGTTc                                                                                                       >  2:455927/1‑141 (MQ=255)                                    aGCGATGAATTATTAGAAGGTGCACGCGATGGTAAGACCGTTGCAGAGTTAATGAGTTATGGTAGACAAATTCTAAACAAAGAAGATGTCATGGATGGTGTCGAACACATGATTACAGATATCGAAATCGAGGCTACGTTc                                                                                                       >  1:70601/1‑141 (MQ=255)                                     gCGATGAATTATTAGAAGGTGCACGCGATGGTAAGACCGTTGCAGAGTTAATGAGTTATGGTAGACAAATTCTAAACAAAGAAGATGTCATGGATGGTGTCGAACACATGATTACAGATATCGAAATCGAGGCTACGTTcc                                                                                                      <  2:106555/141‑1 (MQ=255)                                     gCGATGAATTATTAGAAGGTGCACGCGATGGTAAGACCGTTGCAGAGTTAATGAGTTATGGTAGACAAATTCTAAACAAAGAAGATGTCATGGATGGTGTCGAACACATGATTACAGATATCGAAATCGAGGCTACGTTcc                                                                                                      <  1:16257/141‑1 (MQ=255)                                      cGATGAATTATTAGAAGGTGCACGCGATGGTAAGACCGTTGCAGAGTTAATGAGTTATGGTAGACAAATTCTAAACAAAGAAGATGTCATGGATGGTGTCGAACACATGATTACAGATATCGAAATCGAGGCTACGTTccc                                                                                                     >  2:106950/1‑141 (MQ=255)                                      cGATGAATTATTAGAAGGTGCACGCGATGGTAAGACCGTTGCAGAGTTAATGAGTTATGGTAGACAAATTCTAAACAAAGAAGATGTCATGGATGGTGTCGAACACATGATTACAGATATCGAAATCGAGGCTACGTTccc                                                                                                     >  1:270634/1‑141 (MQ=255)                                      cGATGAATTATTAGAAGGTGCACGCGATGGTAAGACCGTTGCAGAGTTAATGAGTTATGGTAGACAAATTCTAAACAAAGAAGATGTCATGGATGGTGTCGAACACATGATTACAGATATCGAAATCGAGGCTACGTTccc                                                                                                     >  2:2938/1‑141 (MQ=255)                                      cGATGAATTATTAGAAGGTGCACGCGATGGTAAGACCGTTGCAGAGTTAATGAGTTATGGTAGACAAATTCTAAACAAAGAAGATGTCATGGATGGTGTCGAACACATGATTACAGATATCGAAATCGAGGCTACGTTccc                                                                                                     >  1:423424/1‑141 (MQ=255)                                       gATGAATTATTAGAAGGTGCACGCGATGGTAAGACCGTTGCAGAGTTAATGAGTTATGGTAGACAAATTCTAAACAAAGAAGATGTCATGGATGGTGTCGAACACATGATTACAGATATCGAAATCGAGGCTACGTTcccc                                                                                                    <  1:8014/141‑1 (MQ=255)                                              tattaGAAGGTGCACGCGATGGTAAGACCGTTGCAGAGTTAATGAGTTATGGTAGACAAATTCTAAACAAAGAAGATGTCATGGATGGTGTCGAACACATGATTACAGATATCGAAATCGAGGCTACGTTCCCCGATGGTa                                                                                             <  2:26907/141‑1 (MQ=255)                                                           aCGCGATGGTAAGACCGTTGCAGAGTTAATGAGTTATGGTAGACAAATTCTAAACAAAGAAGATGTCATGGATGGTGTCGAACACATGATTACAGATATCGAAATCGAGGCTACGTTCCCCGATGGTACTAAGTTAATcac                                                                                >  1:266974/1‑141 (MQ=255)                                                                 tGGTAAGACCGTTGCAGAGTTAATGAGTTATGGTAGACAAATTCTAAACAAAGAAGATGTCATGGATGGTGTCGAACACATGATTACAGATATCGAAATCGAGGATACGTTCCCCGATGGTACTAAGTTAATCACAGTACa                                                                          <  2:197125/141‑1 (MQ=255)                                                                            ttGCAGAGTTAATGAGTTATGGTAGACAAATTCTAAACAAAGAAGATGTCATGGATGGTGTCGAACACATGATTACAGATATCGAAATCGAGGCTACGTTCCCCGATGGTACTAAGTTAATCACAGTACATCACCCTATTg                                                               <  1:263347/141‑1 (MQ=255)                                                                                   gTTAATGAGTTATGGTAGACAAATTCTAAACAAAGAAGATGTCATGGATGGTGTCGAACACATGATTACAGATATCGAAATCGAGGCTACGTTCCCCGATGGTACTAAGTTAATCACAGTACATCACCCTATTGTTTAAag                                                        <  1:267797/141‑1 (MQ=255)                                                                                   gTTAATGAGTTATGGTAGACAAATTCTAAACAAAGAAGATGTCATGGATGGTGTCGAACACATGATTACAGATATCGAAATCGAGGCTACGTTCCCCGATGGTACTAAGTTAATCACAGTACATCACCCTATTGTTTAAag                                                        <  1:199928/141‑1 (MQ=255)                                                                                                  tAGACAAATTCTAAACAAAGAAGATGTCATGGATGGTGTCGAACACATGATTACAGATATCGAAATCGAGGCTACGTTCCCCGATGGTACTAAGTTAATCACAGTACATCACCCTATTGTTTAAAGGAGGCAGTCAAATGa                                         >  1:155959/1‑141 (MQ=255)                                                                                                           tCTAAACAAAGAAGATGTCATGGATGGTGTCGAACACATGATTACAGATATCGAAATCGAGGCTACGTTCCCCGATGGTACTAAGTTAATCACAGTACATCACCCTATTGTTTAAAGGAGGCAGTCAAATGATACCAGgag                                <  2:173337/141‑1 (MQ=255)                                                                                                                    agaagaTGTCATGGATGGTGTCGAACACATGATTACAGATATCGAAATCGAGGCTACGTTCCCCGATGGTACTAAGTTAATCACAGTACATCACCCTATTGTTTAAAGGAGGCAGTCAAATGATACCAGGAGAAAttatta                       <  1:182681/141‑1 (MQ=255)                                                                                                                      aagaTGTCATGGATGGTGTCGAACACATGATTACAGATATCGAAATCGAGGCTACGTTCCCCGATGGTACTAAGTTAATCACAGTACATCACCCTATTGTTTAAAGGAGGCAGTCAAATGATACCAGGAGAAATTATTACa                     >  1:181061/1‑141 (MQ=255)                                                                                                                            tCATGGATGGTGTCGAACACATGATTACAGATATCGAGATCGAGGCTACGTTCCCCGATGGTACTAAGTTAATCACAGTACAACACCCTATTGTTTAAAGGAGGCAGTCAAATGATACCAGGAGAAATTATTACAAAAAGt               >  1:332102/1‑141 (MQ=255)                                                                                                                            tCATGGATGGTGTCGAACACATGATTACAGATATCGAAATCGAGGCTACGTTCCCCGATGGTACTAAGTTAATCACAGTACATCACCCTATTGTTTAAAGGAGGCAGTCAAATGATACCAGGAGAAATTATTACAAAAAGt               >  1:95803/1‑141 (MQ=255)                                                                                                                            tCATGGATGGTGTCGAACACATGATTACAGATATCGAAATCGAGGCTACGTTCCCCGATGGTACTAAGTTAATCACAGTACATCACCCTATTGTTTAAAGGAGGCAGTCAAATGATACCAGGAGAAATTATTACAAAAAGt               >  1:227729/1‑141 (MQ=255)                                                                                                                            tCATGGATGGTGTCGAACACATGATTACAGATATCGAAATCGAGGCTACGTTCCCCGATGGTACAAAGATAATCACAGTACATCACCCTATCGTTTAAAGGAGGCAGTCAAATGATACAAGGAGAAATTATTACAAAAAga               >  2:178941/1‑140 (MQ=255)                                                                                                                               tggatggTGTCGAACACATGATTACAGATATCGAAATCGAGGCTACGTTCCCCGATGGTACTAAGTTAATCACAGTACATCACCCTATTGTTTAAAGGAGGCAGTCAAATGATACCAGGAGAAATTATTACAAAAAGTACa            <  2:100871/141‑1 (MQ=255)                                                                                                                               tggatggTGTCGAACACATGATTACAGATATCGAAATCGAGGCTACGTTCCCCGATGGTACTAAGTTAATCACAGTACATCACCCTATTGTTTAAAGGAGGCAGTCAAATGATACCAGGAGAAATTATTACAAAAAGTACa            <  1:455927/141‑1 (MQ=255)                                                                                                                               tggatggTGTCGAACACATGATTACAGATATCGAAATCGAGGCTACGTTCCCCGATGGTACTAAGTTAATCACAGTACATCACCCTATTGTTTAAAGGAGGCAGTCAAATGATACCAGGAGAAATTATTACAAAAAGTACa            <  2:441198/141‑1 (MQ=255)                                                                                                                                     gtgtCGGACACATGATTACAGATATCGAAATCGAGGCTACGTTCCCCGATGGTACTAAGTTAATCACAGTACATCACCCTATTGTTTAAAGGAGGCAGTCAAATGATACCAGGAGAAATTATTACAAAAAGTACAGAGGtt      <  2:326040/141‑1 (MQ=255)                                                                                                                                     gtgtCGAACACATGATTACAGATATCGAAATCGAGGCTACGTTCCCCGATGGTACTAAGTTAATCACAGTACATCACCCTATTGTTTAAAGGAGGCAGTCAAATGATACCAGGAGAAATTATTACAAAAAGTACAGAGGtt      >  1:305389/1‑141 (MQ=255)                                                                                                                                     gtgtCAGACACATGATTACAGATATCGAAATCGGGGCTACGTTCCCCGATGGTACTAAGTTAATCACAGTACATCACCCTATTGTTTAAAGGAGGCAGTCAAATGATACCAGGAGAAATTATTACAAAAAGTACAGAGGtt      <  2:188296/141‑1 (MQ=255)                                                                                                                                         cGAACACATGATTACAGATATCGAAATCGAGGCTACGTTCCCCGATGGTACTAAGTTAATCACAGTACATCACCCTATTGTTTAAAGGAGGCAGTCAAATGATACCAGGAGAAATTATTACACAAAGTACAGAGGTTGaaa  >  1:244637/1‑141 (MQ=255)                                                                                                                                         cGAACACATGATTACAGATATCGAAATCGAGGCTACGTTCCCCGATGGTACTAAGTTAATCACAGTACATCACCCTATTGTTTAAAGGAGGCAGTCAAATGATACCAGGAGAAATTATTACAAAAAGTACAGAGGTTGaaa  >  1:131604/1‑141 (MQ=255)                                                                                                                                           |                                                                                                                                           TGAAACTAAATCATCCTGAGGCATTAGCTTTAATCAGCGATGAATTATTAGAAGGTGCACGCGATGGTAAGACCGTTGCAGAGTTAATGAGTTATGGTAGACAAATTCTAAACAAAGAAGATGTCATGGATGGTGTCGAACACATGATTACAGATATCGAAATCGAGGCTACGTTCCCCGATGGTACTAAGTTAATCACAGTACATCACCCTATTGTTTAAAGGAGGCAGTCAAATGATACCAGGAGAAATTATTACAAAAAGTACAGAGGTTGAAA  >  USA300TCH1516_ALE/2405695‑2405971

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