Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,929,925	T→A	43.8%	intergenic (‑1008/‑160)	USA300HOU_1794 ← / → USA300HOU_1796	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,929,925	0	T	A	43.8%	0.7 / 22.4	16	intergenic (‑1008/‑160)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (4/5);  new base A (2/5);  total (6/10)
Fisher's exact test for biased strand distribution p-value = 6.33e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.89e-01

CCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAAG‑GTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGT  >  CP000730/1929798‑1930024                                                                                                                                  |                                                                                                    cagatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACT‑TTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGc                                                                                       >  1:84582/3‑141 (MQ=255)   gatggtATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCA‑TTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCtt                                                                                     <  1:17128/141‑2 (MQ=255)       gtataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACT‑TTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTa                                                                                 >  2:83911/2‑141 (MQ=255)       gtataATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACT‑TTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTa                                                                                 <  2:74254/140‑1 (MQ=255)            ataatagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACT‑TTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGc                                                                            <  1:82393/137‑1 (MQ=255)                tagAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACT‑TTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaaca                                                                        <  1:5493/141‑3 (MQ=255)                          tATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACT‑TTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGTATTATACTTATTGGCTTAGTAAACGCaacaaataattaat                                                              <  2:50300/141‑13 (MQ=255)                           aTCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAAG‑GTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGt                                                              >  1:74866/1‑141 (MQ=255)                                tcAGTCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAAG‑GTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACat                                                         >  2:3965/1‑141 (MQ=255)                                                      agagGAGGTGTA‑TAAG‑GTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATcc                                   <  1:76651/141‑1 (MQ=255)                                                      agagGAGGTGTA‑TAAG‑GTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATcc                                   <  2:81692/141‑1 (MQ=255)                                                          gaggTGTA‑TAAG‑GTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTc                               <  1:57808/141‑1 (MQ=255)                                                            ggTGTA‑TAAG‑GTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCAc                             >  1:31499/1‑141 (MQ=255)                                                                              cTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAg             <  2:24082/141‑1 (MQ=255)                                                                               ttATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTTTTTTTTTTTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTCCCGCAAATAGTGAgg            >  2:63601/1‑141 (MQ=255)                                                                                         gcacaTAATAGCACCAGTCAACAGTGGATGTGACATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAACTAGGTGACAGATAGAAGAAAAAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGgtgt  <  2:40690/140‑1 (MQ=255)                                                                                                                                  |                                                                                                    CCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTA‑TAAG‑GTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTATTGGCTAAGTAGACGCAATACAAAATAGGTGACATATAGCCGCACCAATAAAAATCCCCTCACTACCGCAAATAGTGAGGGGATTGGTGT  >  CP000730/1929798‑1930024

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: ‑