Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,909,155	G→A	29.5%	intergenic (‑221/‑39)	USA300HOU_1770 ← / → USA300HOU_1771	transaldolase/hypothetical membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,909,155	0	G	A	29.5%	20.0 / 7.5	20	intergenic (‑221/‑39)	USA300HOU_1770/USA300HOU_1771	transaldolase/hypothetical membrane protein
Reads supporting (aligned to +/- strand):  ref base G (7/7);  new base A (3/3);  total (10/10)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.88e-01

TCTTTGTTATATAAAACATTTATATCACGCTTTTATAATATATAGCTAATTTTTTGCCTATATTTTTTAAAAATGACTTTAGCAAACATTGTGTCTACAAGTTAATAAAACTATTGTTTTATGATTGTTTATGATACGATATGTAAATGATAATCATCCAGGAGGTCTAGCATGTCTCGTTCAAAAAAATACTTTTACTTATCTAGCTTAATGATTATTTTAAGCTTTTTCTTTAATACAAATAACGTTTTCCTAAGTGGACT  >  CP000730/1909023‑1909285                                                                                                                                     |                                                                                                                                   tCTTTGTTATATAAAACATTTATATCACGCTTTTATAATATATAGCTAATTTTTTGCCTATATTTTTTAAAAATGACTTTAGCAAACATTGTGTCTACAAGTTAATAAAACTATTGTTTTATGATTGTTTCTGATACGat                                                                                                                             >  2:287122/1‑140 (MQ=255)     ttttATTTTAAACATTTATTTCACGCTTTTATAATATATAGCTAATTTTTTGCCTATATTTTTTAAAAATGACTTTAGCAAACATTGTGTCTACAAGTTAATAAAACTATTGTTTTATGATTGTTTATAATACGATATGt                                                                                                                         <  1:285592/138‑1 (MQ=255)             aaaaCATTTATATCACGCTTTTATAATATATAGCTAATTTTTTGCCTATATTTTTTAAAAATGACTTTAGCAAACATTGTGTCTACAAGTTAATAAAACTATTGTTTTATGATTGTTTATGATACGATATGTAAATGATa                                                                                                                 <  1:152324/140‑1 (MQ=255)                      atatCACGCTTTTATAATATATAGCTAATTTTTTGCCTATATTTTTTAAAAATGACTTTAGCAAACATTGTGTCTACAAGTTAATAAAACTATTGTTTTATGATTGTTTATGATACGTTATTTATATGATATTCATCCag                                                                                                        >  1:144970/1‑140 (MQ=255)                                tttATTATATATAGCTAATTTTTTGCCTATATTTTTTAAAAATGACTTTAGCAAACATTGTGTCTACAAGTTAATAAAACTATTGTTTTATGATTGTTTATGATACGATATGTAAATGATAATCATCCAGGAGGTCTAGc                                                                                              <  1:197010/140‑1 (MQ=255)                                tttATAATATATAGCTAATTTTTTGCCTATATTTTTTAAAAATGACTTTAGAAAACATTGTTTCTACAAGTTAATAAAACTATTGTTTTATGATTGTTTATAATACGATATGTAAATGATAATCATCCATGTTGTCTAGc                                                                                              >  2:91423/1‑140 (MQ=255)                                 ttATAATATATAGCTAATTTTTTGCCTATATTTTTTAAAAATGACTTTAGCAAACATTGTGTCTACAAGTTAATAAAACTATTGTTTTATGATTGTTTATGATACGATATGTAAATGGTAATCATCCAGGAGGTCTAGCa                                                                                             >  2:205058/1‑140 (MQ=255)                                             gCTAATTTTTTGCCTATATTTTTTAAAAATGACTTTAGCAAACATTGTGTCTACAAGTTAATAAAACTATTGTTTTATGATTGTTTATAATACGATATGTAAATGATAATTATTCAGGAGTTCTTTCTTGTTTCGTTcta                                                                                 >  1:172903/1‑138 (MQ=255)                                               tAATTTTTTGCCTATATTTTTTAAAAATGACTTTAGCAAACATTGTGTCTACAAGTTAATAAAACTATTGTTTTATGATTGTTTATGATACGATATGTAAATGATAATCATCCAGGAGGTCTAGCATGTCTCGTTCaaaa                                                                               <  1:4105/140‑1 (MQ=255)                                               tAAGTTTTTGCCGATATTTTTTAAAAATGTTTTTAGCAAACATTGTGTTTACAAGTTAATAAAACTATTGGTTTATTATCGTTTATGATACGATATGTAAATGATAAGCATCCAGGAGGTCTAGCATGTCTCGTTCaaaa                                                                               <  2:50322/140‑1 (MQ=255)                                                 aTTTGTTGCTTATATTTTTTAAAAATGACTTTAGCAAACATTGTGTCTACTAGTTAATAAAACTATTGTTTTATGATTGTTTATAATACGATATGTAAATGATAATCATCCAGGAGGTCTAGCATGTCTCGTTCaaaaaa                                                                             <  1:256680/140‑1 (MQ=255)                                                   tttttGCCTATATTTTTTAAAAATGACTTTAGCAAACATTGTGTCTACAAGTTAATAAAACTATTGTTTTATGATTGTTTATGATACGATATGTAAATGATAATCATCCAGGAGGTCTAGCATGTCTCGTTCAAAAAAAt                                                                           <  1:130121/140‑1 (MQ=255)                                                       tGCCTATATTTTTTAAAAATGACTTTAGCAAACAATGTGTCTACAAGTTAATAAAACTATTGTTTTATGATTGTTTTTGATACGTTATGTAAATGATATTCATCCTGGGGGTCTTGCATGTCTTGTTTAATAAATAACtt                                                                       >  1:38998/1‑140 (MQ=255)                                                         ccTATATTTTTTAAAAATGACTTTAGCAAACATTGTGTCTACAAGTTAATAAAACTATTGTTTTATGATTGTTTATGATACGATATGTAAATGATAATCATCCAGGAGGTCTAGCATGTCTCGTTCAAAAAAATACtttt                                                                     <  2:245918/140‑1 (MQ=255)                                                             tatTTTTGAAAAATGATTTTAGCAAACATTGTGTATACAAGTTAATATAAATATTGTATTATGATTGTTTAAAATACGATTTGTAAATGATAATCATCCAGGAGGTCTAGCATGTCTCGTTCAAAAAAATACTTTTACtt                                                                 <  2:38957/140‑1 (MQ=255)                                                                    tAAAAATGACTTTAGCAAACATTGTGTCTACAAGTTAATAAAACTATTGTTTTATGATTGTTTATGATACGATATGTAAATGATAATCATCCAGGAGGTCTAGCATGTCTCGTTCAAAAAAATACTTTTACTTATCTAGc                                                          <  1:209039/140‑1 (MQ=255)                                                                                       cATTGTGTCTACAAGTTAATAAAACTATTGTTTTATGATTGTTTATAATACGATATGTAAATGATAATCATCCAGTTGGTCTAGCATGTCTCGTTCAAAAAAATACTTTTACTTATCTAGCTTAATGATTATTTTAATCt                                       >  1:185966/1‑140 (MQ=255)                                                                                                           aaaaCTATTGTTTTATGATTGTTTATGATACGATATGTAAATGATAATCATCCAGGAGGTCTAGCATGTCTCGTTCAAAAAAATACTTTTACTTATCTAGCTTAATGATTATTTTAAGCTTTTTCTTTAATACAAATAAc                   >  2:116127/1‑140 (MQ=255)                                                                                                                            aTTGTTTATGATACGATATGTAAATGATAATCATCCAGGAGGTCTAGCATGTCTCGTTCTAAAAAATACTTTTACTTATCTAGCTTAATGATTATTTTAAGCTTTTTATTTAATATAAATAACGTTTTCCTAAGTGGACt  >  2:198905/1‑140 (MQ=255)                                                                                                                            aTTGTTTATGATACGATATGTAAATGATAATCATCCAGGAGGTCTAGCATGTCTCGTTCAAAAAAATACTTTTTCTTATCTAGATTAATGATTATTTTAAGCTTTTTATTTAATACAAATAACGATTTCCTAAGTGCACt  >  2:198930/1‑140 (MQ=255)                                                                                                                                     |                                                                                                                                   TCTTTGTTATATAAAACATTTATATCACGCTTTTATAATATATAGCTAATTTTTTGCCTATATTTTTTAAAAATGACTTTAGCAAACATTGTGTCTACAAGTTAATAAAACTATTGTTTTATGATTGTTTATGATACGATATGTAAATGATAATCATCCAGGAGGTCTAGCATGTCTCGTTCAAAAAAATACTTTTACTTATCTAGCTTAATGATTATTTTAAGCTTTTTCTTTAATACAAATAACGTTTTCCTAAGTGGACT  >  CP000730/1909023‑1909285

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑