Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP006881	3,586,300	C→A	6.4%	G117C (GGC→TGC)	U712_18425 ←	Urease subunit beta

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP006881	3,586,300	0	C	A	6.4%	207.3 / 2.7	62	G117C (GGC→TGC)	U712_18425	Urease subunit beta
Reads supporting (aligned to +/- strand):  ref base C (27/31);  new base A (2/2);  total (29/33)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.35e-01

TATACTGTGAAATCCTTTTCGACTTCGATCCATAAATCCGTGTCGCCCAATCTGATTTTATCGCCCGTTGTCGGGCCAAACAGTTCCGCATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGCTTGTTTTAAGTTGGCCAACGTTTTTTCTTTGCCGCGTTCATCGATAAACGTGTCGGCCATTCCGTTCAGCCCTCTAATTGTCTTGCGTCCTCTGATTTCCACTAGTGAGACCGTTTTCTGCTCTC  >  CP006881/3586165‑3586428                                                                                                                                        |                                                                                                                                 tataCTGTGAAATCCTTTTCGACTTCGATCCATAAATCCGTGTCGCCCAATCTGATTTTATCTCCCGTTGTCGGGCCAAACAGATCCGCATATTACTCCCGTGACCTTTTCATCGGATTACACCCTCCCTCCAGCCggg                                                                                                                               >  6:240006/1‑138 (MQ=255) tataCTGTGAAATCCTTTTCGACTTCGATCCATAAATCCGTGTCGCCCAATCTGATTTTATCGCCCGTTGTCGGGCCAAACAGTTCCGCATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGc                                                                                                                               <  5:58728/139‑1 (MQ=255) tataCTGTGAAATCCTTTTCGACTTCGATCCATAAATCCGTGTCGCCCAATCTGATTTTATCGCCCGTTGTCGGGCCAAACAGTTCCGCATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGc                                                                                                                               <  8:272105/139‑1 (MQ=255) tataCTGTGAAATCCTTTTCGACTTCGATCCATAAATCCGTGTCGCCCAATCTGATTTTATCGCCCGTTGTCGGGCCAAACAGTTCCGCATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGc                                                                                                                               >  7:130171/1‑139 (MQ=255) tataCTGTGAAATCCTTTTCGACTTCGATCCATAAATCCGTGTCGCCCAATCTGATTTTATCGCCCGTTGTCGGGCCAAACAGTTCCGCATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGc                                                                                                                               >  2:227892/1‑139 (MQ=255) tataCTGTGAAATCCTTTTCGACTTCGATCCATAAATCCGTGTCGCCCAATCTGATTTTATCGCCCGTTGTCGGGCCAAACAGTTCCGCATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGc                                                                                                                               >  5:348904/1‑139 (MQ=255) tataCTGTGAAATCCTTTTCGACTTCGATCCATAAATCCGTGTCGCCCAATCTGATTTTATCGCCCGTTGTCGGGCCAAACAGTTCCGCATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGc                                                                                                                               >  6:214444/1‑139 (MQ=255) tataCTGTGAAATCCTTTTCGACTTCGATCCATAAATCCGTGTCGCCCAATCTGATTTTATCGCCCGTTGTCGGGCCAAACAGTTCCGCATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGc                                                                                                                               <  7:178694/139‑1 (MQ=255) actaCTGTGAAATCCTTTTCGACTTCGATCCATAAATCCGGGGCGCCCAATCTGATTTTATCGCCCGTTGTCGGGCCAAACAGGTCCGCATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGc                                                                                                                               <  2:141543/137‑1 (MQ=255)    aCTGTGAAATCCTTTTCGACTTCGATCCATAAATCCGTGTCGCCCAATCTGATTTTATCGCCCGTTGTCGGGCCAAACAGTTCCGCATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGCTTg                                                                                                                            >  4:70339/1‑139 (MQ=255)      tgtgAAATCCTTTTCGACTTCGATCCATAAATCCGTGTCGCCCAATCTGATTTTATCGCCCGTTGTCGGGCCAAACAGTTCCGCATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCCGCGTGtt                                                                                                                          >  5:92375/1‑139 (MQ=255)        tgAAATCCTTTTCGACTTCGATCCATAAATCCGTGTCGCCCAATCTGATTTTATCGCCCGTTGTCGGGCCAAACAGTTCCGCATATTCCTCCCGTGACATTTTCATCTGATTACACCCTCCATCCAGCCGGCTTGttt                                                                                                                         >  7:90603/1‑138 (MQ=255)        tgAAATCCTTTTCGACTTCGATCCATAAATCCGTGTCGCCCAATCTGATTTTATCGCCCGTTGTCGGGCCAAACAGTTCCGCATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGCTTGtttt                                                                                                                        >  4:74040/1‑139 (MQ=255)        tgAAATCCTTTTCGACTTCGATCCATAAATCCGTGTCGCCCAATCTGATTTTATCGCCCGTTGTCGGGCCAAACAGTTCCGCATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGCTTGttt                                                                                                                         >  8:232600/1‑138 (MQ=255)        tgAAATCCTTTTCGACTTCGATCCATAAATCCGTGTCGCCCAATCTGATTTTATCGCCCGTTGTCGGGCCAAACAGTTCCGCATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCAGGCTGGttt                                                                                                                         >  3:147676/1‑138 (MQ=255)        tgAAATCCTTTTCGACTTCGATCCATAAATCCGTGTCGCCCAATCTGATTTTATCGCCCGTTGTCGGGCCAAACAGTTCCGCATATTCCTCACGTGACATTTTCATCGGATTACACCCTCCATCCAGCAGGCTTGttt                                                                                                                         >  3:142248/1‑138 (MQ=255)         gAAATCCTTTTCGACTTCGATCCATAAATCCGTGTCGCCCAATCTGATTTTATCGCCCGTTGTCGGGCCAAACAGTTCCGCATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGc                                                                                                                               >  8:97409/1‑131 (MQ=255)         gAAATCCTTTTCGACTTCGATCCATAAATCCGTGTCGCCCAATCTGATTTTATCGCCCGTTGTCGGGCCAAACAGTTCCGCATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGc                                                                                                                               >  4:272351/1‑131 (MQ=255)         gAAATCCTTTTCGACTTCGATCCATAAATCCGTGTCGCCCAATCTGATTTTATCGCCCGTTGTCGGGCCAAACAGTTCCGCATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGc                                                                                                                               <  3:272351/131‑1 (MQ=255)         gAAATCCTTTTCGACTTCGATCCATAAATCCGTGTCGCCCAATCTGATTTTATCGCCCGTTGTCGGGCCAAACAGTTCCGCATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGc                                                                                                                               <  7:97409/131‑1 (MQ=255)         gAAATCCTTTTCGACTTCGATCCATAAATCCGTGTCGCCCAATCTGATTTTATCGCCCGTTGTCGGGCCAAACAGTTCCGCATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGCTTGtttt                                                                                                                        >  4:265717/1‑138 (MQ=255)                  ttCGACTACGATCCATAAATCCGTGTCGCCCAATCTGATTTTATCGCCCGTTGTCGGGCCAAACAGTTCCGCATATTCCTCCCGTGACATTTTCATCGGATTAACCCCTCCATACAGCCGGCATGTTTTAAGTTGGcc                                                                                                               >  3:75647/1‑138 (MQ=255)                                       cGTGTCGCCCAATCTGATTTTATCGCCCGTTGTCGGGCCAAACAGTTCCGCATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGCTTGTTTTAAGTTGGCCAACGTTTTTTCTTTGCCGCGt                                                                                          <  8:330991/138‑1 (MQ=255)                                        gtgtCGCCCAATCTGATTTTATCGCCCGTTGTCGGGCCAAACAGTTCCGCATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGCTTGTTTTAAGTTGGCCAACGTTTTTTCTTTGCCGCGTTc                                                                                        <  5:58712/139‑1 (MQ=255)                                         tgtCGCCCAATCTGATTTTATCGCCCGTTGTCGGGCCAAACAGTTCCGCATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGCTTGTTTTAAGTTGGCCAACGTTTTTTCTTTGCCGCGTTc                                                                                        <  4:73348/138‑1 (MQ=255)                                         tgtCGCCCAATCTGATTTTATCGCCCGTTGTCGGGCCAAACAGTTCCGCATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGCTTGTTTTAAGTTGGCCAACGTTTTTTCTTTGCCGCGTTc                                                                                        >  3:73348/1‑138 (MQ=255)                                                cAATCTGATTTTATCGCCCGTTGTCGGGCCAAACAGTTCCGCATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGCTTGTTTTAAGTTGGCCAACGTTTTTTCTTTGCCGCGTTCATCGATaa                                                                                <  3:265717/139‑1 (MQ=255)                                                       aTTTTATCGCCCGTTGTCGGGCCAAACAGTTCCGCATATTCCTCCCGTGACATTTTCATCTGATTACACCCTCCATCCAGCCGGCTTGTTTTAAGTTGGCCAACGTTTTTTCTTTGCCGCGTTCATCGATAAACgt                                                                            <  5:190028/136‑1 (MQ=255)                                                       aTTTTATCGCCCGTTGTCGGGCCAAACAGTTCCGCATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGCTTGTTTTAAGTTGGCCAACGTTTTTTCTTTGCCGCGTTCATCGATAAACgt                                                                            <  5:240006/136‑1 (MQ=255)                                                       aTTTTATCGCCCGGTGTCGGGACAAACAGTTCCGCATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGCTTGTTTTAAGTTGGCCAACGTTTTTTCTTTGCCGCGTTCATCGATAAACgt                                                                            <  5:6403/136‑1 (MQ=255)                                                       aTTTTATCGCCCGATGTCGGGCCAAACAGTTCCGCATATTCCTCGCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGCTTGTTTTAAGTTGGCCAACGTTTTTTCTTTGCCGCGTTCATCGATAAACgtgt                                                                          <  2:5976/138‑1 (MQ=255)                                                                 ccGTTGTCGGGCCAAACAGTTCCGCATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGc                                                                                                                               >  6:238002/1‑75 (MQ=255)                                                                 ccGTTGTCGGGCCAAACAGTTCCGCATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGc                                                                                                                               <  5:238002/75‑1 (MQ=255)                                                                   gTTGTCGGGCCAAACAGTTCCGCATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGCTTGTTTTAAGTTGGCCAACGTTTTTTCTTTGCCGCGTTCATCGATAAACGTGTCGGCCATTCCGtt                                                             <  3:74040/139‑1 (MQ=255)                                                                       tCGGGCCAAACAGTTCCGCATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGCTTGTTTTAAGTTGGCCAACGTTTTTTCTTTGCCGCGTTCATCGATAAACGTGTCGGCCATTCCGTTCAg                                                          <  1:227892/138‑1 (MQ=255)                                                                       tCGGGCCAAACAGTTCCGCATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGCTTGTTTTAAGTTGGCCAACGTTTTTTCTTTGCCGCGTTCATCGATAAACGTGTCGGCCATTCCGTTCAg                                                          <  5:214444/138‑1 (MQ=255)                                                                       tCGGGCCAAACAGTTCCGCATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGCTTGTTTTAAGTTGGCCAACGTTTTTTCTTTGCCGCGTTCATCGATAAACGTGTCGGCCATTCCGTTCAg                                                          <  7:232600/138‑1 (MQ=255)                                                                       gcGGGCCAAACAGTTCCGCATATTCCTCCCGTGACAATTTCATCGGATTACACCCTCCATCCAGGCGGCTTGTTTTAAGTTGGCCAACGTTTTTTCTTTGCCGCGTTCATCGATAAACGTGTCGGCCATTCCGTTCAg                                                          <  8:171802/137‑1 (MQ=255)                                                                              aaaCAGTTCCGCATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGCTTGTTTTAAGTTGGCCAACGTTTTTTCTTTGCCGCGTTCATCGATAAACGTGTCGGCCATTCCGTTCAGCCCTCTaa                                                  <  6:185196/139‑1 (MQ=255)                                                                              aaaCAGTTCCGCATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGCTTGTTTTAAGTTGGCCAACGTTTTTTCTTTGCCGCGTTCATCGATAAACGTGTCGGCCATTCCGTTCAGCCCTCTaa                                                  <  8:130171/139‑1 (MQ=255)                                                                              aaaCAGTTCCGCATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGCTTGTTTTAAGTTGGCCAACGTTTTTTCTTTGCCGCGTTCATCGATAAACGTGTCGGCCATTCCGTTCAGCCCTCTaa                                                  <  6:348904/139‑1 (MQ=255)                                                                                    ttCCGCATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGCTTGTTTTAAGTTGGCCAACGTTTTTTCTTTGCCGCGTTCATCGATAAACGTGTCGGCCATTCCGTTCAGCCCTCTAATTGTCt                                            >  7:310969/1‑139 (MQ=255)                                                                                         cATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGc                                                                                                                               >  2:12418/1‑51 (MQ=255)                                                                                         cATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGc                                                                                                                               <  1:12418/51‑1 (MQ=255)                                                                                             ttCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGCTTGTTTTAAGTTGGCCAACGTTTTTTCTTTGCCGCGTTCATCGATAAACGTGTCGGCCATTCCGTTCAGCCCTCTAATTGTCTTGCGTCct                                    <  7:244851/138‑1 (MQ=255)                                                                                             ttCCTCCCGTGACATTTTCATCGGATTACACCCTACCTCCAGCCGGCTTGTTTTAAGTTGGCCAACGGTTTTTCTTTGCCGAGTTCATCGATAAACGTGTCGGCCATTCCGGTCAGCCCTCTAATTGTCTTGCGTCct                                    <  7:244847/138‑1 (MQ=255)                                                                                                 tccCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGCTTGTTTTAAGTTGGCCAACGTTTTTTCTTTGCCGCGTTCATCGTTAAACGTGTGGGCCATTCCGTTCAGCCCTCTAATTGTCTTGCGTCGTCTGAt                               >  4:148768/1‑139 (MQ=255)                                                                                                  cccGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGCTTGTTTTAAGTTGGCCAACGTTTTTTCTTTGCCGCGTTCATCGATAAACGTGTCGGCCATTCCGTTCAGCCCTCTAATTGTCTTGCGTCCTCTGAtt                              >  4:128573/1‑139 (MQ=255)                                                                                                   ccGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGCTTGTTTTAAGTTGGCCAACGTTTTTTCTTTGCCGCGTTCATCGATAAACGTGTCGGCCATTCCGTTCAGCCCTCTAATTGTCTTGCGTCCTCTGAtt                              >  1:74072/1‑138 (MQ=255)                                                                                                   ccGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGCTTGTTTTAAGTTGGCCAACGTTTTTTCTTTGCCGCGTTCATCGATAAACGTGTCGGCCATTCCGTTCAGCCCTCTAATTGTCTTGCGTCCTCTGAt                               <  2:74072/137‑1 (MQ=255)                                                                                                   ccGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGCTTGTTTTAAGTTGGCCAACGTTTTTTCTTTGCCGCGTTCATCGATAAACGTGTCGGCCATTCCGTTCAGCCCTCTAATTGTCTTGCGTCCTCTGAt                               <  3:70339/137‑1 (MQ=255)                                                                                                       gtcATTTTCATCGGATTACACCCTCCATCCAGCAGGCTTGTGTTAAGTTGGCCAACGTTTTTTCTTTGCCGCGTTCATCGATAAACGTGTCGGCCATTCCGTTCAGCCCTCTAATTGTCTTGCGTCCTCTGATTTCCAc                         <  4:147676/137‑1 (MQ=255)                                                                                                        tcATTTTCATCGGATTACACCCTCCATCCAGCAGGCTTGTTTTAAGTTGGCCAACGTTTTTTCTTTGCCGCGTTCATCGATAAACGTGTCGGCCATTCCGTTCAGCCCTCTAATTGTCTTGCGTCCTCTGATTTCCAc                         <  4:142248/137‑1 (MQ=255)                                                                                                             ttCATCGGATTACACCCTCCATCCAGCCGGCTTGTTTTAAGTTGGCCAACGTTTTTTCTTTGCCGCGTTCATCGATAAACGTGTCGGCCATTCCGTTCAGCCCTCTAATTGTCTTGCGTCctct                                  <  2:307413/124‑1 (MQ=255)                                                                                                             ttCATCGGATTACACCCTCCATCCAGCCGGCTTGTTTTAAGTTGGCCAACGTTTTTTCTTTGCCGCGTTCATCGATAAACGTGTCGGCCATTCCGTTCAGCCCTCTAATTGTCTTGCGTCctct                                  >  1:307413/1‑124 (MQ=255)                                                                                                                aTCGGATTACACCCTCCATCCAGCCGGCTTGTTTTAAGTTGGCCAACGTTTTTTCTTTGCCGCGTTCATCGATAAACGTGTCGGCCATTCCGTTCAGCCCTCTAATTGTCTTGCGTCCTCTGATTTCCACTAGTgaga                 <  3:128573/138‑1 (MQ=255)                                                                                                                              tccatccaGCCGGCTTGTTTTAAGTTGGCCCACGTTTTTTCTTTTCCGCGTTCATCGAAAAACGTGTCGGCCATTCCGGTCAGCCCTCTAAATGTGTTGCGTGCTCTGATTTCCACTATTGAGACCGGGTTCTGCtctc  >  8:133615/1‑139 (MQ=255)                                                                                                                              tccatccaGCCGGCTTGTTTTAAGTTGGCCAACGTTTTTTCTTTGCCGCGTTCATCGATAAACGTGTCGGCCATTCCGTTCAg                                                          >  6:66721/1‑83 (MQ=255)                                                                                                                              tccatccaGCCGGCTTGTTTTAAGTTGGCCAACGTTTTTTCTTTGCCGCGTTCATCGATAAACGTGTCGGCCATTCCGTTCAg                                                          <  5:66721/83‑1 (MQ=255)                                                                                                                              tccatccaGCCGGCTTGTTTTAAGTTGGCCAACGTTTTTTCTTTGCCGCGTTCATCGATAAACGTGTCGGCCATTCCGTTCAGCCCTCTAATTGTCTTGCGTCCTCTGATTTCCACTAGTGAGACCGTTTTCTGCtctc  >  6:340597/1‑139 (MQ=255)                                                                                                                              tccatccaGCCGGCTTGTTTTAAGTTGGCCAACGTTTTTTCTTTGCCGCGTTCATCGATAAACGTGTCGGCCATTCCGTTCAGCCCTCTAATTGTCTTGCGTCCTCTGATTTCCACTAGTGAGACCGGTTTCTGCtctc  >  4:207560/1‑139 (MQ=255)                                                                                                                              tccatccaGCCGGCTTGTTTTAAGTTGGCCAACGTTTTTTCTTTGCCGCGTTCATCGATAAACGTGTCGGCCATTCCGTTCAGCCCGCTAATTGTCTTGCGTCCGCTGATTTCCACTAGTGAGACCGTTTTCTGCtctc  >  5:355134/1‑139 (MQ=255)                                                                                                                                        |                                                                                                                                 TATACTGTGAAATCCTTTTCGACTTCGATCCATAAATCCGTGTCGCCCAATCTGATTTTATCGCCCGTTGTCGGGCCAAACAGTTCCGCATATTCCTCCCGTGACATTTTCATCGGATTACACCCTCCATCCAGCCGGCTTGTTTTAAGTTGGCCAACGTTTTTTCTTTGCCGCGTTCATCGATAAACGTGTCGGCCATTCCGTTCAGCCCTCTAATTGTCTTGCGTCCTCTGATTTCCACTAGTGAGACCGTTTTCTGCTCTC  >  CP006881/3586165‑3586428

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑